Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold172
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1975206
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.26
Warning! 344189 characters in sequence are not A, C, G, or T
File 8 of 11
Found at i:1057270 original size:107 final size:106
Alignment explanation
Indices: 1057159--1057385 Score: 260
Period size: 107 Copynumber: 2.1 Consensus size: 106
1057149 TTCACCATAA
* *** *
1057159 GGGATACTCTAACCTTATTATTTTTGAGGAGATACT-TCAACCCT-AGTTTTATTTCTAAAACAT
1 GGGATACTCTAACCTTACTATTCCCGAAGAGATACTCT-AACCCTGA-TTTTATTTCTAAAACAT
* * * * *
1057222 CGATTTTCCACCACCGAGGATATTCCAACCCTATTATTTTTGAG
64 CAATTTTCCACCACCG-GGATACTCCAACCCCATTAGTTCTGAG
* * *
1057266 GGGATACTCTAACCTTGCTATTCCCGAAGAGATACTCTAACCCTGATTTTATTTTTAAAGCATCA
1 GGGATACTCTAACCTTACTATTCCCGAAGAGATACTCTAACCCTGATTTTATTTCTAAAACATCA
* * *
1057331 ATTTTCCACCATCGGGATACTCCAACCCCGTTGGTTCTGAG
66 ATTTTCCACCACCGGGATACTCCAACCCCATTAGTTCTGAG
*
1057372 GGGATACTCCAACC
1 GGGATACTCTAACC
1057386 CCGATTTTGT
Statistics
Matches: 101, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
106 34 0.34
107 65 0.64
108 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (106 bp):
GGGATACTCTAACCTTACTATTCCCGAAGAGATACTCTAACCCTGATTTTATTTCTAAAACATCA
ATTTTCCACCACCGGGATACTCCAACCCCATTAGTTCTGAG
Found at i:1060223 original size:24 final size:24
Alignment explanation
Indices: 1060191--1060246 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1060181 CTTATCGAAC
*
1060191 TAAGCATAAAATATTTTACCCAAT
1 TAAGCATAAAATATTTTACCAAAT
*
1060215 TAAGCATAAAATATTTTATCAAAT
1 TAAGCATAAAATATTTTACCAAAT
*
1060239 TAAACATA
1 TAAGCATA
1060247 TGCAATGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAGCATAAAATATTTTACCAAAT
Found at i:1067742 original size:14 final size:13
Alignment explanation
Indices: 1067698--1067747 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
1067688 ACATCCTTTC
*
1067698 TTTTCTTTTTTAT
1 TTTTGTTTTTTAT
**
1067711 TTTTGTTTTTTCCC
1 TTTTGTTTTTT-AT
1067725 TTTTGTTTTTCTAT
1 TTTTGTTTTT-TAT
1067739 TTTTGTTTT
1 TTTTGTTTT
1067748 CTTTTACTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 10 0.33
14 19 0.63
15 1 0.03
ACGTcount: A:0.04, C:0.10, G:0.06, T:0.80
Consensus pattern (13 bp):
TTTTGTTTTTTAT
Found at i:1067766 original size:14 final size:14
Alignment explanation
Indices: 1067698--1067766 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
1067688 ACATCCTTTC
*
1067698 TTTTCTTTTTTA-T
1 TTTTTTTTTTTACT
**
1067711 TTTTGTTTTTTCCCT
1 TTTT-TTTTTTTACT
* * *
1067726 TTTGTTTTTCTATT
1 TTTTTTTTTTTACT
1067740 TTTGTTTTCTTTTACT
1 TTT-TTTT-TTTTACT
1067756 TTTTTTTTTTT
1 TTTTTTTTTTT
1067767 TGAAAGAAGA
Statistics
Matches: 41, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
13 4 0.10
14 18 0.44
15 11 0.27
16 8 0.20
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTTTACT
Found at i:1072523 original size:29 final size:28
Alignment explanation
Indices: 1072481--1072584 Score: 115
Period size: 29 Copynumber: 3.7 Consensus size: 28
1072471 AGTTCTAGTG
*
1072481 TTTTAGTTTACTTTTAATT-CTTTGCAGTA
1 TTTTAGTTGACTTTTAATTCCTTTG--GTA
*
1072510 TTTTAGTTGACTTTTAATTCCCTTTGGTG
1 TTTTAGTTGACTTTTAATT-CCTTTGGTA
* *
1072539 TTTTAATTGCCTTTTAATTCCTTT--TA
1 TTTTAGTTGACTTTTAATTCCTTTGGTA
1072565 CTTTTAGTTGACTTTTAATT
1 -TTTTAGTTGACTTTTAATT
1072585 TCTTAGCTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
26 1 0.02
27 17 0.26
28 5 0.08
29 37 0.57
31 5 0.08
ACGTcount: A:0.18, C:0.12, G:0.11, T:0.59
Consensus pattern (28 bp):
TTTTAGTTGACTTTTAATTCCTTTGGTA
Found at i:1073901 original size:159 final size:158
Alignment explanation
Indices: 1073616--1074293 Score: 451
Period size: 159 Copynumber: 4.3 Consensus size: 158
1073606 TTTGATACAT
* * * * * *
1073616 AGAAAAATGATGGAAAGAAAAGCTTTTTTTGCAAAATCAATGCATC-GATATTGT--ATCCCAAT
1 AGAAAAATGGTGGAAA-AAAAGCTTTTCTTGTAAAACCAAAGCA-CAAATATTGTGAATCCCAAT
* * * * ** * * *
1073678 GCGGAGAACATGTTTTTGTTACCCAATCACGGAAAGA-ATGGAGATTTTAATGAGAATTCATGTT
64 GAGAAGCACATGTTTTTGTTGCCCAATCACAAAAAGAGA-AGAGATTCTAATGAGAATCCATGTT
*
1073742 TGTCTCATTTAGGGGATGAACTTTGATTTTA
128 TGTCTCATTTAAGGGATGAACTTTGATTTTA
* * * * *
1073773 AAAAAAATGGTGGAAAGAAAAGCTTTTCTTGTGAAACCAAAGTACCAATATCT-TGAATCCGAAT
1 AGAAAAATGGTGGAAA-AAAAGCTTTTCTTGTAAAACCAAAGCACAAATAT-TGTGAATCCCAAT
* * * * *
1073837 GAGAAGTATATGTTTTTGTTGCCCATTCACAATAAGAGAAGAGATTCTAACGAGAATCCATGTTT
64 GAGAAGCACATGTTTTTGTTGCCCAATCACAAAAAGAGAAGAGATTCTAATGAGAATCCATGTTT
* * * * * *
1073902 GTTTTATTCATGGAATGAACTTTGATTCTA
129 GTCTCATTTAAGGGATGAACTTTGATTTTA
* ** * * *
1073932 AGGAAAATGGTTAAAACAAAAGCTTTTCTTGTAAAACCAAGGCATAAATATTGTGTATCCCAATG
1 AGAAAAATGGTGGAAA-AAAAGCTTTTCTTGTAAAACCAAAGCACAAATATTGTGAATCCCAATG
* * * *** * *
1073997 GGAAGCACATGTTTTTGTTGGCTAATCACAAAAAGATTGGAGATTCTAATAAGAATCCATGTTTA
65 AGAAGCACATGTTTTTGTTGCCCAATCACAAAAAGAGAAGAGATTCTAATGAGAATCCATGTTTG
* ** *
1074062 TCTCAATTAAGGGATGATTTTTGATACTT-
130 TCTCATTTAAGGGATGAACTTTGAT-TTTA
* * ** * **
1074091 AGAAAAATGGTGGAAAAAAATGCTTTCCTTGCAATGCCAAAACATC-AATATTGTCTAT-CCAAC
1 AGAAAAATGGTGGAAAAAAA-GCTTTTCTTGTAAAACCAAAGCA-CAAATATTGTGAATCCCAA-
* ** * * ** * * *
1074154 TAAGGGGAACATGTTTTTGTTGCCTAATCATGAAAAGA-ATGGAGATTTTAATGAGAA-CCTATA
63 TGAGAAGCACATGTTTTTGTTGCCCAATCACAAAAAGAGA-AGAGATTCTAATGAGAATCC-ATG
* * * *
1074217 TGTGT-TGCATTTTAGGGATGATCTTTCATTTTA
126 TTTGTCT-CATTTAAGGGATGAACTTTGATTTTA
* ** * * * *
1074250 AGGAAAATTATAGAAAGAAAAGCTTTTCTAGTGAAGCCAAAGCA
1 AGAAAAATGGTGGAAA-AAAAGCTTTTCTTGTAAAACCAAAGCA
1074294 TTAAAACATT
Statistics
Matches: 402, Mismatches: 104, Indels: 28
0.75 0.19 0.05
Matches are distributed among these distances:
156 1 0.00
157 41 0.10
158 15 0.04
159 339 0.84
160 6 0.01
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (158 bp):
AGAAAAATGGTGGAAAAAAAGCTTTTCTTGTAAAACCAAAGCACAAATATTGTGAATCCCAATGA
GAAGCACATGTTTTTGTTGCCCAATCACAAAAAGAGAAGAGATTCTAATGAGAATCCATGTTTGT
CTCATTTAAGGGATGAACTTTGATTTTA
Found at i:1077948 original size:42 final size:42
Alignment explanation
Indices: 1077887--1078005 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
1077877 TAGCCCTCAA
* * *
1077887 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGT
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1077929 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1077971 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1078006 GAGAGAAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.43, C:0.02, G:0.45, T:0.10
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1077958 original size:12 final size:12
Alignment explanation
Indices: 1077938--1077972 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1077928 TAGAGATAGT
1077938 AGAGATAGGAGG
1 AGAGATAGGAGG
1077950 -GATGATAGGAGG
1 AGA-GATAGGAGG
1077962 AGAGATAGGAG
1 AGAGATAGGAG
1077973 AGATAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:1077966 original size:24 final size:24
Alignment explanation
Indices: 1077896--1077981 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
1077886 AAGAGAAAGA
*
1077896 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATAGGAGG
* * *
1077920 AGAGACAGTA--GA-GAT---AGT
1 AGAGATAGGAGGGATGATAGGAGG
1077938 AGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATAGGAGG
* *
1077962 AGAGATAGGAGAGATAATAG
1 AGAGATAGGAGGGATGATAG
1077982 AGAGAGGAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
18 10 0.21
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.58
ACGTcount: A:0.42, C:0.01, G:0.44, T:0.13
Consensus pattern (24 bp):
AGAGATAGGAGGGATGATAGGAGG
Found at i:1077981 original size:12 final size:12
Alignment explanation
Indices: 1077941--1077986 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1077931 AGATAGTAGA
*
1077941 GATAGGAGGGAT
1 GATAGGAGAGAT
1077953 GATAGGAGGAGA-
1 GATAGGA-GAGAT
1077965 GATAGGAGAGAT
1 GATAGGAGAGAT
*
1077977 AATA-GAGAGA
1 GATAGGAGAGA
1077987 GGAGGGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 10 0.33
12 17 0.57
13 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:1082397 original size:12 final size:12
Alignment explanation
Indices: 1082380--1082414 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1082370 TTATTTATTT
1082380 CTCCTATCTCTC
1 CTCCTATCTCTC
1082392 CTCCTATCATC-C
1 CTCCTATC-TCTC
1082404 CTCCTATCTCT
1 CTCCTATCTCT
1082415 ACTATCTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:1082439 original size:42 final size:42
Alignment explanation
Indices: 1082346--1082465 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 42
1082336 TTCTTCTCTC
* * * * *
1082346 CTCCTCCTGTCATCCCTCCTCTCTTTATTTATTTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTCTCTCTA-CTATCTCTACTATCT
* *
1082389 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTACTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTACTATCT
* *
1082431 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1082466 TTGAGGGCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 43 0.64
43 24 0.36
ACGTcount: A:0.10, C:0.43, G:0.02, T:0.45
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTACTATCT
Found at i:1087026 original size:11 final size:11
Alignment explanation
Indices: 1087010--1087036 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1087000 CAAAGTACTA
1087010 GCAACATTAGT
1 GCAACATTAGT
1087021 GCAACATTAGT
1 GCAACATTAGT
1087032 GCAAC
1 GCAAC
1087037 TACCACTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (11 bp):
GCAACATTAGT
Found at i:1089923 original size:44 final size:44
Alignment explanation
Indices: 1089860--1089952 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 44
1089850 ACATTAACAC
1089860 AAACCCTAATGGACTTATTGTGCTAACAAACCCAATTCTTAATT
1 AAACCCTAATGGACTTATTGTGCTAACAAACCCAATTCTTAATT
* *
1089904 AAACCCTAATGGACTTATTGTGCTAACAAGCCCAGTTCTTAATT
1 AAACCCTAATGGACTTATTGTGCTAACAAACCCAATTCTTAATT
*
1089948 TAACC
1 AAACC
1089953 AAAATAACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (44 bp):
AAACCCTAATGGACTTATTGTGCTAACAAACCCAATTCTTAATT
Found at i:1092448 original size:15 final size:14
Alignment explanation
Indices: 1092411--1092449 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1092401 AAGAATACAA
1092411 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
1092425 AATACAAAAAGAAAGG
1 AA-AAAAAAAGAAA-G
1092441 AAAAAAAAA
1 AAAAAAAAA
1092450 CCAGTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:1093218 original size:12 final size:11
Alignment explanation
Indices: 1093196--1093271 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1093186 AGAGAAAGAA
*
1093196 GAGAGAGGAGG
1 GAGATAGGAGG
1093207 GATGATAGGAGG
1 GA-GATAGGAGG
*
1093219 AGAGACAGGA--
1 -GAGATAGGAGG
*
1093229 GAGATAGTA--
1 GAGATAGGAGG
1093238 GAGATAGGAGG
1 GAGATAGGAGG
1093249 GATGATAGGAGG
1 GA-GATAGGAGG
*
1093261 AGAGACAGGAG
1 -GAGATAGGAG
1093272 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1093247 original size:42 final size:42
Alignment explanation
Indices: 1093186--1093304 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
1093176 TAGCCCTCAA
* *
1093186 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1093228 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1093270 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1093305 GAGAGAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1093288 original size:18 final size:18
Alignment explanation
Indices: 1093261--1093310 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1093251 TGATAGGAGG
*
1093261 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
1093279 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
1093297 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
1093311 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:1100636 original size:12 final size:12
Alignment explanation
Indices: 1100611--1100644 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1100601 TTAGCTGAAG
1100611 TTCCCTCC-TTC
1 TTCCCTCCTTTC
1100622 TTCCCTCCTTTC
1 TTCCCTCCTTTC
*
1100634 TTCCATCCTTT
1 TTCCCTCCTTT
1100645 AGAGTTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (12 bp):
TTCCCTCCTTTC
Found at i:1101917 original size:23 final size:23
Alignment explanation
Indices: 1101887--1101940 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1101877 CTTTTTTTAA
* *
1101887 TTTTTTTGTATTCTTTCTTCTTT
1 TTTTTTTGTACTCTTTCTTCTTC
1101910 TTTTTTTGTACTCTTTCTTCTTC
1 TTTTTTTGTACTCTTTCTTCTTC
*
1101933 TTCTTTTG
1 TTTTTTTG
1101941 GTGAAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.74
Consensus pattern (23 bp):
TTTTTTTGTACTCTTTCTTCTTC
Found at i:1103261 original size:20 final size:20
Alignment explanation
Indices: 1103219--1103268 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1103209 TTTTACCCAG
* *
1103219 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
*
1103239 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
*
1103259 ATGAATCGAT
1 ATGTATCGAT
1103269 TTGAAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:1103330 original size:20 final size:20
Alignment explanation
Indices: 1103305--1103354 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1103295 TTTTACCCAG
* *
1103305 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
*
1103325 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
1103345 ATGTATCGAT
1 ATGTATCGAT
1103355 TTGAAAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:1103334 original size:86 final size:86
Alignment explanation
Indices: 1103189--1103424 Score: 366
Period size: 86 Copynumber: 2.7 Consensus size: 86
1103179 TGAACAGTAC
1103189 ATGTATCGATACATTCTTTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATG
1 ATGTATCGATACATTCTTTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATG
1103254 TATGAATGAATCGATTTGAAA
66 TATGAATGAATCGATTTGAAA
*
1103275 ATGTATCAATACATTCTTTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATG
1 ATGTATCGATACATTCTTTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATG
*
1103340 TATGAATGTATCGATTTGAAA
66 TATGAATGAATCGATTTGAAA
* * * * ****
1103361 ATGTATCGATACATTATTTTTTTTTACCTA-CTGTATCGATGCATTGAAAAATGTATCGATACAT
1 ATGTATCGATACATT-CTTTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1103425 CTAGTTAGTT
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
86 126 0.91
87 12 0.09
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (86 bp):
ATGTATCGATACATTCTTTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATG
TATGAATGAATCGATTTGAAA
Found at i:1105550 original size:19 final size:19
Alignment explanation
Indices: 1105507--1105575 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
1105497 CACACCTAGA
*
1105507 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
1105527 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
1105546 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
1105566 TGTATCGATA
1 TGTATCGATA
1105576 TAGAAAACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 17 0.39
20 26 0.59
21 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1105633 original size:20 final size:20
Alignment explanation
Indices: 1105608--1105661 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1105598 ATACCACTAT
1105608 TTGTATCGATACATGA-CACA
1 TTGTATCGATACATGATCA-A
* *
1105628 TTGTATCAATACATGATGAA
1 TTGTATCGATACATGATCAA
1105648 TTGTATCGATACAT
1 TTGTATCGATACAT
1105662 TGCTTCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGATCAA
Found at i:1114327 original size:33 final size:32
Alignment explanation
Indices: 1114290--1114358 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
1114280 CTACCACTGT
1114290 TTGTATCGATACATG-GCACATTATATCGATACA
1 TTGTATCGATACATGAG-A-ATTATATCGATACA
*
1114323 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGA-GAATTATATCGATACA
1114356 TTG
1 TTG
1114359 CTTCAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACATGAGAATTATATCGATACA
Found at i:1114329 original size:13 final size:13
Alignment explanation
Indices: 1114307--1114358 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
1114297 GATACATGGC
*
1114307 ACATTATATCGAT
1 ACATTGTATCGAT
1114320 ACATTGTATCGAT
1 ACATTGTATCGAT
1114333 ACA-TG-AT-G--
1 ACATTGTATCGAT
1114341 A-ATTGTATCGAT
1 ACATTGTATCGAT
1114353 ACATTG
1 ACATTG
1114359 CTTCAAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 19 0.59
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:1121130 original size:15 final size:15
Alignment explanation
Indices: 1121110--1121154 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1121100 ATTCCGCCAA
1121110 ATCCACCACAAAATC
1 ATCCACCACAAAATC
** *
1121125 ATCCACCACCTAATT
1 ATCCACCACAAAATC
*
1121140 ACCCACCACAAAATC
1 ATCCACCACAAAATC
1121155 CTCGATACAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (15 bp):
ATCCACCACAAAATC
Found at i:1128424 original size:14 final size:14
Alignment explanation
Indices: 1128339--1128426 Score: 58
Period size: 14 Copynumber: 6.6 Consensus size: 14
1128329 CGATTTGCCA
*
1128339 TTTGTCAAGAAATG
1 TTTGTCAAGAAATT
*
1128353 GTTGTCAAGAAATT
1 TTTGTCAAGAAATT
* * * *
1128367 ATGGTCAAG-GACT
1 TTTGTCAAGAAATT
*
1128380 TTTGTCAAG-AATG
1 TTTGTCAAGAAATT
** *
1128393 TGAG-CAAGAAA-C
1 TTTGTCAAGAAATT
1128405 TTTGTCAAGAAATT
1 TTTGTCAAGAAATT
1128419 TTTGTCAA
1 TTTGTCAA
1128427 TACGACCCCC
Statistics
Matches: 54, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
12 6 0.11
13 21 0.39
14 27 0.50
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (14 bp):
TTTGTCAAGAAATT
Found at i:1128601 original size:57 final size:58
Alignment explanation
Indices: 1128439--1128772 Score: 214
Period size: 57 Copynumber: 5.8 Consensus size: 58
1128429 CGACCCCCTT
* * * * * * * *
1128439 CAAAGCCCACACAAGTTGGTGGCATCCTTTTTACAAAGCCCACGAGCCAGCGGTA-CCCTTT
1 CAAAG-CC-CACAAGTTAGTGGCA-CCCTTTT-CAAAGCCCACAAGTCAACGGCATCTCTTC
* * *** * * * *
1128500 CAAAGGCCACAAGTCAACAGCACCCTTTTCAAAGCCTACTAGTCAATGGC-T-TCATTT
1 CAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAACGGCATCTC-TTC
* * *
1128557 CAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAACCCACGAGTCAGCGGCATCTCTTC
1 CAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAACGGCATCTCTTC
* * * *
1128615 CAAAGCCCACAAGTTAGTGGCACCCTTTT-AAAGCCCACAAGTCAGCGGCACCTTTTT
1 CAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAACGGCATCTCTTC
* * ** * * ** * *
1128672 CAAAGCCCACAAATCAGTGGC-TTCATTTCAAAGCCCACAAGTTAGTGGCA-CCCTTTT
1 CAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAACGGCATCTC-TTC
* * ** *
1128729 CAAAGCCCATAAGTCAGTGGC-TTCATTTCAAAGCCCACAAGTCA
1 CAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCA
1128773 GTGGCACCCT
Statistics
Matches: 225, Mismatches: 42, Indels: 16
0.80 0.15 0.06
Matches are distributed among these distances:
56 6 0.03
57 163 0.72
58 38 0.17
59 12 0.05
60 1 0.00
61 5 0.02
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (58 bp):
CAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAACGGCATCTCTTC
Found at i:1128619 original size:86 final size:87
Alignment explanation
Indices: 1128472--1129056 Score: 428
Period size: 86 Copynumber: 6.8 Consensus size: 87
1128462 ATCCTTTTTA
* * * * * *** * *
1128472 CAAAGCCCACGAGCCAGCGGTACCC-TTTCAAAGGCCACAAGTCAACAGCA-CCCTTTTCAAAGC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCTCATTTCAAAGC
* * *
1128535 CTACTAGTCAATGGCTTCATTT
66 CCACAAGTCAATGGCTCCATTT
* * * * *
1128557 CAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAACCCACGAGTCAGCGGCATCTC-TTCCAAAGC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCTCATTTCAAAGC
* * * *
1128621 CCACAAGTTAGTGGCACCCTTT
66 CCACAAGTCAATGGCTCCATTT
* * * *
1128643 TAAAGCCCACAAGTCAGCGGCACCTTTTTCAAAGCCCACAAATCAGTGGC-T-TCATTTCAAAGC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCTCATTTCAAAGC
* * * *
1128706 CCACAAGTTAGTGGCACCCTTTT
66 CCACAAGTCAATGGC-TCCATTT
* ** * * *
1128729 CAAAGCCCATAAGTCAGTGGC-TTCATTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTTCAAAGC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCTCATTTCAAAGC
* *
1128792 CCATAAGTCAATGGCTTCATTT
66 CCACAAGTCAATGGCTCCATTT
* ** * *
1128814 CGAAGTTCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAATGGC-T-TCATTTCGAAGC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCTCATTTCAAAGC
* * *
1128877 TCACAAGTCAGTGAATGGCACCCTTTT
66 CCACAAGTC----AATGGC-TCCATTT
* ** * * *
1128904 CAAAGCCCACAAGTCAATGGC-TTCATTTCAAA-CTCCACAAGTTAGTGGCA-CCCA-TTCAAAG
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGC-CCACAAGTCAGTGGCATCTCATTTCAAAG
* *
1128965 CCCATAAGTCAATGGCAT-CTTTT
65 CCCACAAGTCAATGGC-TCCATTT
* * * * * * *
1128988 CAAA-CTCCCCGAGTCAGTGGCATCCTTTT-AAAGCCCACAAGTCAGTGGCACCCCTTTTTAAAG
1 CAAAGC-CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCTCATTTCAAAG
1129051 CCCACA
65 CCCACA
1129057 CAAGTCGATG
Statistics
Matches: 394, Mismatches: 85, Indels: 41
0.76 0.16 0.08
Matches are distributed among these distances:
83 1 0.00
84 41 0.10
85 120 0.30
86 165 0.42
87 2 0.01
88 1 0.00
89 41 0.10
90 23 0.06
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (87 bp):
CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCTCATTTCAAAGC
CCACAAGTCAATGGCTCCATTT
Found at i:1128730 original size:143 final size:142
Alignment explanation
Indices: 1128472--1128802 Score: 448
Period size: 143 Copynumber: 2.3 Consensus size: 142
1128462 ATCCTTTTTA
* * * * * * *
1128472 CAAAGCCCACGAGCCAGCGGTACCCTTTCAAAGGCCACAAGTCAACAGCACCCTTTTCAAAGCCT
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAACAGCACCCTTTTCAAAGCCC
* * *
1128537 ACTAGTCAATGGCTTCATTTCAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAACCCACGAGTCA
66 ACAAATCAATGGCTTCATTTCAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAACCCACAAGTCA
1128602 GCGGCATCTC-TTC
131 GCGGC-T-TCATTC
* * * *
1128615 CAAAGCCCACAAGTTAGTGGCACCCTTTTAAAGCCCACAAGTCAGCGGCACCTTTTTCAAAGCCC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAACAGCACCCTTTTCAAAGCCC
* * *
1128680 ACAAATCAGTGGCTTCATTTCAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCATAAGTCA
66 ACAAATCAATGGCTTCATTTCAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAACCCACAAGTCA
* *
1128745 GTGGCTTCATTT
131 GCGGCTTCATTC
*
1128757 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCATAAGTCAA
1 CAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCACAAGTCAA
1128803 TGGCTTCATT
Statistics
Matches: 164, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
141 2 0.01
142 31 0.19
143 131 0.80
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.22
Consensus pattern (142 bp):
CAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAACAGCACCCTTTTCAAAGCCC
ACAAATCAATGGCTTCATTTCAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAACCCACAAGTCA
GCGGCTTCATTC
Found at i:1128776 original size:57 final size:57
Alignment explanation
Indices: 1128554--1129036 Score: 526
Period size: 57 Copynumber: 8.4 Consensus size: 57
1128544 AATGGCTTCA
* ** * * * * *
1128554 TTTCAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAACCCACGAGTCAGCGGCA-TCT
1 TTTCAAAGCCCACAAGTCAGTGGC-TTCATTTCAAAGCCCACAAGTCAGTGGCACCCT
* * ** * * * *
1128611 CTTCCAAAGCCCACAAGTTAGTGGCACCCTTTTAAAGCCCACAAGTCAGCGGCACCTT
1 -TTTCAAAGCCCACAAGTCAGTGGCTTCATTTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1128669 TTTCAAAGCCCACAAATCAGTGGCTTCATTTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCTTCATTTCAAAGCCCACAAGTCAGTGGCACCCT
*
1128726 TTTCAAAGCCCATAAGTCAGTGGCTTCATTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCTTCATTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * **
1128783 TTTCAAAGCCCATAAGTCAATGGCTTCATTTCGAAGTTCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCTTCATTTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1128840 TTTCAAAGCCCACAAGTCAATGGCTTCATTTCGAAGCTCACAAGTCAGTGAATGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCTTCATTTCAAAGCCCACAAGTCA--G--TGGCACCCT
* *
1128901 TTTCAAAGCCCACAAGTCAATGGCTTCATTTCAAA-CTCCACAAGTTAGTGGCACCC-
1 TTTCAAAGCCCACAAGTCAGTGGCTTCATTTCAAAGC-CCACAAGTCAGTGGCACCCT
* * * * * * * *
1128957 ATTCAAAGCCCATAAGTCAATGGCATCTTTTCAAA-CTCCCCGAGTCAGTGGCATCCT
1 TTTCAAAGCCCACAAGTCAGTGGCTTCATTTCAAAGC-CCACAAGTCAGTGGCACCCT
1129014 TTT-AAAGCCCACAAGTCAGTGGC
1 TTTCAAAGCCCACAAGTCAGTGGC
1129037 ACCCCTTTTT
Statistics
Matches: 377, Mismatches: 41, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
56 66 0.18
57 233 0.62
58 24 0.06
59 2 0.01
60 1 0.00
61 51 0.14
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (57 bp):
TTTCAAAGCCCACAAGTCAGTGGCTTCATTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:1129037 original size:28 final size:28
Alignment explanation
Indices: 1128473--1129056 Score: 391
Period size: 28 Copynumber: 20.4 Consensus size: 28
1128463 TCCTTTTTAC
* * * * *
1128473 AAAGCCCACGAGCCAGCGGTACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* ***
1128501 AAAGGCCACAAGTCAACAGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * * ** * *
1128529 CAAAGCCTACTAGTCAATGGCTTCATTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTT
*
1128558 AAAGCCCACAAGTTAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * * * **
1128586 CAAAACCCACGAGTCAGCGGCATCTCTTCC
1 -AAAGCCCACAAGTCAGTGGCA-CCCTTTT
*
1128616 AAAGCCCACAAGTTAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
1128644 AAAGCCCACAAGTCAGCGGCACCTTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* ** * *
1128672 CAAAGCCCACAAATCAGTGGCTTCATTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTT
*
1128701 AAAGCCCACAAGTTAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* ** * *
1128729 CAAAGCCCATAAGTCAGTGGCTTCATTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTT
1128758 AAAGCCCACAAGTCAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * ** * *
1128786 CAAAGCCCATAAGTCAATGGCTTCATTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTT
* **
1128815 GAAGTTCACAAGTCAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* ** * *
1128843 CAAAGCCCACAAGTCAATGGCTTCATTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
1128872 GAAGCTCACAAGTCAGTGAATGGCACCCTTTT
1 AAAGCCCACAAGTCA--G--TGGCACCCTTTT
* ** * *
1128904 CAAAGCCCACAAGTCAATGGCTTCATTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTT
* * *
1128933 AAA-CTCCACAAGTTAGTGGCACCCATTC
1 AAAGC-CCACAAGTCAGTGGCACCCTTTT
* * *
1128961 AAAGCCCATAAGTCAATGGCA-TCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * *
1128988 CAAA-CTCCCCGAGTCAGTGGCATCCTTTT
1 -AAAGC-CCACAAGTCAGTGGCACCCTTTT
1129017 AAAGCCCACAAGTCAGTGGCACCCCTTTTT
1 AAAGCCCACAAGTCAGTGGCA-CCC-TTTT
1129047 AAAGCCCACA
1 AAAGCCCACA
1129057 CAAGTCGATG
Statistics
Matches: 415, Mismatches: 121, Indels: 38
0.72 0.21 0.07
Matches are distributed among these distances:
27 5 0.01
28 215 0.52
29 156 0.38
30 18 0.04
32 8 0.02
33 13 0.03
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTT
Found at i:1129069 original size:32 final size:31
Alignment explanation
Indices: 1129011--1129186 Score: 123
Period size: 31 Copynumber: 5.7 Consensus size: 31
1129001 TCAGTGGCAT
*
1129011 CCTTTTAAAG-CC-CACAAGTC-AGTGGCACC
1 CCTTCTAAAGCCCACACAAGTCGA-TGGCACC
* *
1129040 CCTTTTTAAAGCCCACACAAGTCGATGGCAAC
1 CC-TTCTAAAGCCCACACAAGTCGATGGCACC
* ** *
1129072 CCTTCTAAATCCTGCACAAG-CTGGTGGCAACC
1 CCTTCTAAAGCCCACACAAGTC-GATGGC-ACC
* *
1129104 CC-TCTAAAGCCCACACAAGT-TAGTGGTACC
1 CCTTCTAAAGCCCACACAAGTCGA-TGGCACC
* *
1129134 CCTTCAAAAGCCCACACAAG-CTGGTGGCAACC
1 CCTTCTAAAGCCCACACAAGTC-GATGGC-ACC
**
1129166 TTTTCTAAAGCCCACACAAGT
1 CCTTCTAAAGCCCACACAAGT
1129187 TGGTGACACT
Statistics
Matches: 114, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
29 2 0.02
30 14 0.12
31 57 0.50
32 40 0.35
33 1 0.01
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (31 bp):
CCTTCTAAAGCCCACACAAGTCGATGGCACC
Found at i:1129191 original size:32 final size:32
Alignment explanation
Indices: 1129040--1129260 Score: 184
Period size: 31 Copynumber: 7.0 Consensus size: 32
1129030 CAGTGGCACC
*
1129040 CCTTTT-TAAAGCCCACACAAG-TCGATGGCAA
1 CCTTTTCTAAAGCCCACACAAGCT-GGTGGCAA
* * **
1129071 CC-CTTCTAAATCCTGCACAAGCTGGTGGCAA
1 CCTTTTCTAAAGCCCACACAAGCTGGTGGCAA
** * * *
1129102 CC-CCTCTAAAGCCCACACAAGTTAGTGG-TA
1 CCTTTTCTAAAGCCCACACAAGCTGGTGGCAA
** *
1129132 CCCCTTCAAAAGCCCACACAAGCTGGTGGCAA
1 CCTTTTCTAAAGCCCACACAAGCTGGTGGCAA
* *
1129164 CCTTTTCTAAAGCCCACACAAGTTGGTGAC-A
1 CCTTTTCTAAAGCCCACACAAGCTGGTGGCAA
* * *
1129195 CTTTTCTCTAAATCCCACACAAGCTGGCGGCAA
1 CCTTT-TCTAAAGCCCACACAAGCTGGTGGCAA
**
1129228 CCTCTTCTCTAAAGCATACACAAGCTGGTGGCA
1 CCT-TT-TCTAAAGCCCACACAAGCTGGTGGCA
1129261 TCTCCTCTTA
Statistics
Matches: 151, Mismatches: 32, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
30 5 0.03
31 70 0.46
32 48 0.32
33 3 0.02
34 25 0.17
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (32 bp):
CCTTTTCTAAAGCCCACACAAGCTGGTGGCAA
Found at i:1129227 original size:64 final size:63
Alignment explanation
Indices: 1129040--1129257 Score: 215
Period size: 62 Copynumber: 3.4 Consensus size: 63
1129030 CAGTGGCACC
* * * * **
1129040 CCTTTT-TAAAGCCCACACAAGTCGATGGCAACCCTTCTAAATCCTGCACAAGCTGGTGGCAA
1 CCTTTTCTAAAGCCCACACAAGTTGGTGACACCCCTTCTAAATCCCACACAAGCTGGTGGCAA
** * ** * *
1129102 CC-CCTCTAAAGCCCACACAAGTTAGTGGTACCCCTTCAAAAGCCCACACAAGCTGGTGGCAA
1 CCTTTTCTAAAGCCCACACAAGTTGGTGACACCCCTTCTAAATCCCACACAAGCTGGTGGCAA
*** *
1129164 CCTTTTCTAAAGCCCACACAAGTTGGTGACACTTTTCTCTAAATCCCACACAAGCTGGCGGCAA
1 CCTTTTCTAAAGCCCACACAAGTTGGTGACACCCCT-TCTAAATCCCACACAAGCTGGTGGCAA
** *
1129228 CCTCTTCTCTAAAGCATACACAAGCTGGTG
1 CCT-TT-TCTAAAGCCCACACAAGTTGGTG
1129258 GCATCTCCTC
Statistics
Matches: 126, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
61 1 0.01
62 51 0.40
63 25 0.20
64 27 0.21
65 2 0.02
66 20 0.16
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (63 bp):
CCTTTTCTAAAGCCCACACAAGTTGGTGACACCCCTTCTAAATCCCACACAAGCTGGTGGCAA
Found at i:1130483 original size:20 final size:20
Alignment explanation
Indices: 1130458--1130534 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
1130448 TTTTACCCAA
1130458 ATGTATCGATACATTTTTCG
1 ATGTATCGATACATTTTTCG
* *
1130478 ATGTATCGATACATGTAT-G
1 ATGTATCGATACATTTTTCG
* * *
1130497 AGTATATCGATATATTTTTCC
1 A-TGTATCGATACATTTTTCG
*
1130518 ATGTATCAATACATTTT
1 ATGTATCGATACATTTT
1130535 GTTTTTTTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCG
Found at i:1135999 original size:42 final size:42
Alignment explanation
Indices: 1135944--1136062 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1135934 TTCTTCTCTC
* *
1135944 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1135986 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* * *
1136028 CTCCTCCTATCATCCCTCATCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1136063 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.09, C:0.45, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1136028 original size:18 final size:18
Alignment explanation
Indices: 1135959--1136029 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1135949 CCTGTCATCC
* *
1135959 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1135977 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
1135999 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1136019 CTCCTGTCTCT
1 CTCCTGTCTCT
1136030 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1141243 original size:159 final size:156
Alignment explanation
Indices: 1140685--1141253 Score: 399
Period size: 157 Copynumber: 3.6 Consensus size: 156
1140675 AATGGGAAGA
* * * *
1140685 ACATGTTTTTGTTGCCCAATCATGAATAGAAT-GAAGATTCTAA-GAAGAATCTAAGTTTGTCTC
1 ACATGTTTTTGTTGCCTAATCAT-AAAAGAATAG-AGATTCTAATG-AGAATCCATGTTTGTCTC
* ** * *** * * *
1140748 TTTTGGGGGAT-GAACTTTGATAT-TAAGGAAAATTATGGAAAAAAAATGTTTTTCTTACAAAAC
63 ATTTAAGTGATAG-A-TTTGAT-TCTAAGGAAAACGGT-GAAAAAAAA-GCTTTTCTTGCGAAAC
* * * * * * *
1140811 CAATGCATTAATACCTTCTATCCCAATGAA-AAGC
123 CAAAGAATCAATATCATGTATCCCAAT-AAGAAAC
* *
1140845 ACATGTTTTTGTTGCCTAATCATAAGAAGAGTAGAGATTCTAGCT-A-AAGTCCATGTTTGTCTC
1 ACATGTTTTTGTTGCCTAATCATAA-AAGAATAGAGATTCTA-ATGAGAA-TCCATGTTTGTCTC
* * * * *
1140908 TTTTATG-GATAAATTTTGATTTTAAGGAAAACGGTGAAAAAAAAGCTTTTCTTGCGAAGCCAAA
63 ATTTAAGTGATAGA-TTTGATTCTAAGGAAAACGGTGAAAAAAAAGCTTTTCTTGCGAAACCAAA
* * * *
1140972 GCATCAATATCGTGTATCGCAATGAGAAAC
127 GAATCAATATCATGTATCCCAATAAGAAAC
* * * * *
1141002 ACATGTTTTTCTTACCTAATCATGAAAA-AATAGAGATTCTAATGAGAATCTATGGTTATCTCAT
1 ACATGTTTTTGTTGCCTAATCAT-AAAAGAATAGAGATTCTAATGAGAATCCATGTTTGTCTCAT
* * * *
1141066 TTAAG-GA-ATGTATATTGATTCTAA-GAATAATGGTGGAAAGAAATGCTTTTCTTGCGAAACTA
65 TTAAGTGATA-G-AT-TTGATTCTAAGGAA-AACGGT-GAAAAAAAAGCTTTTCTTGCGAAACCA
* *
1141128 AAGAATGAATATCATTTATCCCAATAAGGAAA-
125 AAGAATCAATATCATGTATCCCAATAA-GAAAC
** * * *
1141160 AGGTTTTTTTGTTGCCCAATCACTAAAAGAATATAGATTCTAATGAGAATCCATGTTTGTCTCAT
1 ACATGTTTTTGTTGCCTAATCA-TAAAAGAATAGAGATTCTAATGAGAATCCATGTTTGTCTCAT
* *
1141225 TTGAGTGATAGACTTTGATTCTACGGAAA
65 TTAAGTGATAGA-TTTGATTCTAAGGAAA
1141254 GTTAATGCTT
Statistics
Matches: 327, Mismatches: 59, Indels: 47
0.76 0.14 0.11
Matches are distributed among these distances:
155 2 0.01
156 36 0.11
157 76 0.23
158 76 0.23
159 76 0.23
160 59 0.18
161 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (156 bp):
ACATGTTTTTGTTGCCTAATCATAAAAGAATAGAGATTCTAATGAGAATCCATGTTTGTCTCATT
TAAGTGATAGATTTGATTCTAAGGAAAACGGTGAAAAAAAAGCTTTTCTTGCGAAACCAAAGAAT
CAATATCATGTATCCCAATAAGAAAC
Found at i:1142238 original size:242 final size:244
Alignment explanation
Indices: 1141783--1142267 Score: 681
Period size: 243 Copynumber: 2.0 Consensus size: 244
1141773 AAACTTTTAT
* * * *
1141783 TCTAAGAAAACTGGTGAAAAAAGCTTCTCTTGTAAAACCAAAGCTTCACTATCATGTATCCCAAA
1 TCTAAGAAAAATGGGGAAAAAAGCTTCTCTTGTAAAACCAAAGCTTCAATATCATGCATCCC---
*
1141848 GAGAAGCACATGTTTTTGTTGCCCAATCATGAAAAGAATGGAGATGCAAACGAGAATCCATGTTA
63 -ACAAGCACATGTTTTTGTTGCCCAATCATGAAAAGAATGGAGATGCAAACGAGAATCCATGTTA
*
1141913 TCTTTTTTGAAGGACAAACTTTGATTCTTAGGAAAATCATGGAAAAAAAAGTTTTTCTTGCAAAT
127 TCTTTTTTGAAGGACAAACTTTGATTCTTAGGAAAATCATGGAAAAAAAAGTTTTCCTTGCAAAT
* * * * *
1141978 CCAAAGAATTAGTATCA-TTCTAACAAATAGGAGAATGTGTTTTTGTTACAAA
192 CCAAAGAATCAATATCATTTCTAACAAAGAGAAGAACGTGTTTTTGTTACAAA
*
1142030 TCTAAGAAAAATGGGGAAAAAAAGCTTCTCTTGTAAAACCAAAGCTTCAATATCATGCGTCCC-C
1 TCTAAGAAAAATGGGG-AAAAAAGCTTCTCTTGTAAAACCAAAGCTTCAATATCATGCATCCCAC
* * *
1142094 AAGCACGTGTTTTTGTTGCCCAATCATGAAAAGATTGGAGATGCAAATGAGAATCCATG-TATCT
65 AAGCACATGTTTTTGTTGCCCAATCATGAAAAGAATGGAGATGCAAACGAGAATCCATGTTATCT
* * * * *
1142158 TTTTTGAAGGATAGACTTTGATTCTTTGGAAAA-CGATGGACAGAAAAGTTTTCCTTGCAAATCC
130 TTTTTGAAGGACAAACTTTGATTCTTAGGAAAATC-ATGGAAAAAAAAGTTTTCCTTGCAAATCC
* * *
1142222 AAGGAATCAATATCATTTCTAGCAAAGAGAATAACGTGTTTTTGTT
194 AAAGAATCAATATCATTTCTAACAAAGAGAAGAACGTGTTTTTGTT
1142268 GCCTGATACT
Statistics
Matches: 212, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
241 1 0.00
242 73 0.34
243 81 0.38
247 14 0.07
248 43 0.20
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (244 bp):
TCTAAGAAAAATGGGGAAAAAAGCTTCTCTTGTAAAACCAAAGCTTCAATATCATGCATCCCACA
AGCACATGTTTTTGTTGCCCAATCATGAAAAGAATGGAGATGCAAACGAGAATCCATGTTATCTT
TTTTGAAGGACAAACTTTGATTCTTAGGAAAATCATGGAAAAAAAAGTTTTCCTTGCAAATCCAA
AGAATCAATATCATTTCTAACAAAGAGAAGAACGTGTTTTTGTTACAAA
Found at i:1142771 original size:160 final size:159
Alignment explanation
Indices: 1142416--1143474 Score: 593
Period size: 159 Copynumber: 6.7 Consensus size: 159
1142406 AATATACACA
* * * * * *
1142416 TGTTTTTGTTGCTCAATCATGAAAACAAAGGAGATTCTAA-ACAGAATCTATGTTTG-TGCTATT
1 TGTTTTTGTTGCCCAATCA-AAAAAGAATGGAGATTCTAATA-AGAATCCATGTTTGTTTC-ATT
* * * * * * * **
1142479 TAAGGG-CTGAGCTTTGATT-GTAAGCAAAAAGATAAAAAG-AAAAGCTTTTCTTGTGAAACCAA
63 TGAGGGAC-AAACTTTGATTCTTAAG-AAAATGGTGAAAAGAAAAAGCTTTTCTTAAGAAACCAA
*
1142541 AGCATCAATATCATGGATCCTACTAA-GGAAAACA--
126 AGCATCAATATCATGTATCCTA--AAGGGAAAA-ATG
* * * * * *
1142575 TGTTTTTATTGCCTAATTAGAAAAAGAATAGAGATTCTACTAAGAATCCATGTTTGTTTCATGTG
1 TGTTTTTGTTGCCCAATCA-AAAAAGAATGGAGATTCTAATAAGAATCCATGTTTGTTTCATTTG
* * *
1142640 AGGGACAAACTTTGATT-TTAAGGGAAATGGTGAAAAGAAAAATCTTTTCTTAAGAAATCAAAGC
65 AGGGACAAACTTTGATTCTTAA-GAAAATGGTGAAAAGAAAAAGCTTTTCTTAAGAAACCAAAGC
* *
1142704 ATTAATATCATGTATCCTAACGGGAAAAATG
129 ATCAATATCATGTATCCTAAAGGGAAAAATG
* * * * *
1142735 TGTTTTTGTTACCCAATTAGGAAAAGAATGGAGATTCTAACAAGAATCCATGTTTGTCTCA-TTG
1 TGTTTTTGTTGCCCAATCA-AAAAAGAATGGAGATTCTAATAAGAATCCATGTTTGTTTCATTTG
* * * * * * * *
1142799 AAGGA-AGAACTTTGATT-GTAAGAAAAATAGTGAAAA-AGAAAAGCCTCTCTTATGGACCCAAA
65 AGGGACA-AACTTTGATTCTTAAG-AAAATGGTGAAAAGA-AAAAGCTTTTCTTAAGAAACCAAA
* * * * * ** **
1142861 GCATCAATATCTTATATCCCAATGAGAAGCACA
127 GCATCAATATCATGTATCCTAAAGGGAAAAATG
* * * * * * * * * *
1142894 TCTTTTTGTTGCCCAATTACAAGAAGAGTTGAGATTTTAATGAGAATCCATGTTTATCTC-GTTG
1 TGTTTTTGTTGCCCAATCA-AAAAAGAATGGAGATTCTAATAAGAATCCATGTTTGTTTCATTTG
* * * * * * * *
1142958 -GTGATATGAACTTTGATT-TTACAGAAAAAGATCAAAAG-AAAAGCTTCTCTTGCA-AAATCAA
65 AGGGACA--AACTTTGATTCTTA-AGAAAATGGTGAAAAGAAAAAGCTTTTCTT-AAGAAACCAA
* * * *
1143019 AGCATCAATATCATGCATCCTAATGAGAAAGCATG
126 AGCATCAATATCATGTATCCTAAAGGGAAA-AATG
* * * *
1143054 TGTTTTTGTTGCCCAACCACAAAAAGAATGGAGATTCAAATAAGAATCTATATTTGTCTT-ATTT
1 TGTTTTTGTTGCCCAATCA-AAAAAGAATGGAGATTCTAATAAGAATCCATGTTTGT-TTCATTT
* * * * * * * *
1143118 GAGGGACAAATTTTGATTCTT-AGAAAATTGGTG-GAAGGAAAAGATTTTTTTTTAG-AACTAGA
64 GAGGGACAAACTTTGATTCTTAAGAAAA-TGGTGAAAAGAAAAAG-CTTTTCTTAAGAAACCAAA
** *
1143180 G-ATCAATATTGTGTATCCTAAAGAGGAGAACA--
127 GCATCAATATCATGTATCCTAAAG-GGA-AAAATG
* * * * * * * *
1143212 TGTTTTTGTTTCCTAATCATGAAAAGAATGAAGATTTTAATGAGAATCCATTTTTG-TTCGTTTG
1 TGTTTTTGTTGCCCAATCA-AAAAAGAATGGAGATTCTAATAAGAATCCATGTTTGTTTCATTTG
* * * * * *
1143276 AGGTACGAACATTGATTCTATTAAG--AGTGGTGGAAAGAAAAA-CTTTTCTTTCA-AAACCAAA
65 AGGGACAAACTTTGATTC--TTAAGAAAATGGTGAAAAGAAAAAGCTTTTC-TTAAGAAACCAAA
*
1143337 GCATCAATATCATGTATCCCAAAGAGG-AAAATG
127 GCATCAATATCATGTATCCTAAAG-GGAAAAATG
* * *
1143370 TGTTATTGTTGCCTAATCACAAAAA-AAGTGGAGATTCTAATGAGAATCCAT-TTT-TTTCATTT
1 TGTTTTTGTTGCCCAATCA-AAAAAGAA-TGGAGATTCTAATAAGAATCCATGTTTGTTTCATTT
* ** * *
1143432 GAGAGATGAACTTTGATTCTTAAAAAAAATGGTGGAAAGAAAA
64 GAGGGACAAACTTTGATTCTT-AAGAAAATGGTGAAAAGAAAA
1143475 GATTTTTTTT
Statistics
Matches: 694, Mismatches: 163, Indels: 87
0.74 0.17 0.09
Matches are distributed among these distances:
155 2 0.00
156 11 0.02
157 58 0.08
158 139 0.20
159 271 0.39
160 194 0.28
161 15 0.02
162 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (159 bp):
TGTTTTTGTTGCCCAATCAAAAAAGAATGGAGATTCTAATAAGAATCCATGTTTGTTTCATTTGA
GGGACAAACTTTGATTCTTAAGAAAATGGTGAAAAGAAAAAGCTTTTCTTAAGAAACCAAAGCAT
CAATATCATGTATCCTAAAGGGAAAAATG
Found at i:1142944 original size:319 final size:316
Alignment explanation
Indices: 1142416--1143112 Score: 715
Period size: 319 Copynumber: 2.2 Consensus size: 316
1142406 AATATACACA
* * * * *
1142416 TGTTTTTGTTGCTCAATCATGAAAACAAAGGAGATTCTAAACAGAATCTATGTTTGTGCTATTTA
1 TGTTTTTGTTGCCCAATCACGAAAAGAATGGAGATTCTAAA-AGAATCTATGTTTGT-CTATTGA
** * * * * *
1142481 AGGGCTGAGCTTTGATTGTAAGCAAAAAGATAAAAAGAAAAGCTTTTCTTGTGAAACCAAAGCAT
64 AGGGAAGAACTTTGATTGTAAGAAAAAAGATAAAAAGAAAAGCCTCTCTTATGAAACCAAAGCAT
* * * * * *
1142546 CAATATCATGGATCCTACTAAGGAAAACATGTTTTTATTGCCTAATTAGAAAAAGAATAGAGATT
129 CAATATCATAGATCCCAATAAGGAAAACATCTTTTTATTGCCCAATTACAAAAAGAATAGAGATT
* * * * * * *
1142611 CTACTAAGAATCCATGTTTGTTTCATGTGAGGGACA-AACTTTGATTTTA-AGGGAAATGGTGAA
194 CTAATAAGAATCCATGTTTATCTCAT-TG-GGGACAGAACTTTGATTTTACA-GAAAAAGATCAA
* * * * *
1142674 AAGAAAAATCTTTTCTT-AAGAAATCAAAGCATTAATATCATGTATCCTAACGGGAAA-AATG
256 AAG-AAAAGCTTCTCTTGAA-AAATCAAAGCATCAATATCATGCATCCTAACGAGAAAGAATG
* * * *
1142735 TGTTTTTGTTACCCAATTAGGAAAAGAATGGAGATTCTAACAAGAATCCATGTTTGTCTCATTGA
1 TGTTTTTGTTGCCCAATCACGAAAAGAATGGAGATTCTAA-AAGAATCTATGTTTGTCT-ATTGA
* *
1142800 A-GGAAGAACTTTGATTGTAAGAAAAATAG-TGAAAAAGAAAAGCCTCTCTTATGGACCCAAAGC
64 AGGGAAGAACTTTGATTGTAAGAAAAA-AGAT-AAAAAGAAAAGCCTCTCTTATGAAACCAAAGC
* * * * * * * *
1142863 ATCAATATCTTATATCCCAATGA-GAAGCACATCTTTTTGTTGCCCAATTACAAGAAGAGTTGAG
127 ATCAATATCATAGATCCCAATAAGGAA-AACATCTTTTTATTGCCCAATTACAAAAAGAATAGAG
* * * * *
1142927 ATTTTAATGAGAATCCATGTTTATCTCGTTGGTGATATGAACTTTGATTTTACAGAAAAAGATCA
191 ATTCTAATAAGAATCCATGTTTATCTCATTGGGGACA-GAACTTTGATTTTACAGAAAAAGATCA
* * *
1142992 AAAGAAAAGCTTCTCTTGCAAAATCAAAGCATCAATATCATGCATCCTAATGAGAAAGCATG
255 AAAGAAAAGCTTCTCTTGAAAAATCAAAGCATCAATATCATGCATCCTAACGAGAAAGAATG
* * * *
1143054 TGTTTTTGTTGCCCAACCACAAAAAGAATGGAGATTCAAATAAGAATCTATATTTGTCT
1 TGTTTTTGTTGCCCAATCACGAAAAGAATGGAGATTCTAA-AAGAATCTATGTTTGTCT
1143113 TATTTGAGGG
Statistics
Matches: 308, Mismatches: 60, Indels: 20
0.79 0.15 0.05
Matches are distributed among these distances:
317 4 0.01
318 73 0.24
319 229 0.74
320 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (316 bp):
TGTTTTTGTTGCCCAATCACGAAAAGAATGGAGATTCTAAAAGAATCTATGTTTGTCTATTGAAG
GGAAGAACTTTGATTGTAAGAAAAAAGATAAAAAGAAAAGCCTCTCTTATGAAACCAAAGCATCA
ATATCATAGATCCCAATAAGGAAAACATCTTTTTATTGCCCAATTACAAAAAGAATAGAGATTCT
AATAAGAATCCATGTTTATCTCATTGGGGACAGAACTTTGATTTTACAGAAAAAGATCAAAAGAA
AAGCTTCTCTTGAAAAATCAAAGCATCAATATCATGCATCCTAACGAGAAAGAATG
Found at i:1143563 original size:157 final size:156
Alignment explanation
Indices: 1143075--1143577 Score: 372
Period size: 157 Copynumber: 3.2 Consensus size: 156
1143065 CCCAACCACA
* * * * * * * * ** *
1143075 AAAAGAATGGAGATTCAAATAAGAATCTATATTTGTCTTATTTGAGGGACAAATTTTGATTCTTA
1 AAAAGAATGAAGATTCTAATGAGAATCCATTTTTGT-TCATTTGAGGTACGAACATTGATTCTAA
* * * * * * * * ** * *
1143140 GAAAATTGGTGGAAGGAAAAGA-TTTTTTTTTAGAACTAGAGATCAATATTGTGTATCCTAAAGA
65 AAAAAATGGTGGAAAGAAAA-ACTTTTCTTTAAAAACCAAAGATCAATATCATATATCCCAAAGA
* * ** * *
1143204 GGAGAA-CATGTTTTTGTTTCCTAATCATG
129 GGAAAATC-TGTTATTACTGCCTAATCA-C
* * **
1143233 AAAAGAATGAAGATTTTAATGAGAATCCATTTTTGTTCGTTTGAGGTACGAACATTGATTCTATT
1 AAAAGAATGAAGATTCTAATGAGAATCCATTTTTGTTCATTTGAGGTACGAACATTGATTCTAAA
* * * *
1143298 AAGAGTGGTGGAAAGAAAAACTTTTCTTTCAAAACCAAAGCATCAATATCATGTATCCCAAAGAG
66 AAAAATGGTGGAAAGAAAAACTTTTCTTTAAAAACCAAAG-ATCAATATCATATATCCCAAAGAG
* **
1143363 GAAAATGTGTTATTGTTGCCTAATCAC
130 GAAAATCTGTTATTACTGCCTAATCAC
* * * *
1143390 AAAAAAAGTGGAGATTCTAATGAGAATCCATTTTT-TTCATTTGAGAG-ATGAACTTTGATTCTT
1 AAAAGAA-TGAAGATTCTAATGAGAATCCATTTTTGTTCATTTGAG-GTACGAACATTGATTC-T
* * * *
1143453 AAAAAAAATGGTGGAAAGAAAAGA-TTTTTTTTGAAAAACCAAAG-T-AGTGATCCTATATCTCA
63 AAAAAAAATGGTGGAAAGAAAA-ACTTTTCTTT-AAAAACCAAAGATCAAT-ATCATATATCCCA
* * * *
1143515 AGGAGGAGAATCTGTTTTTACTGCCTGATCAC
125 AAGAGGAAAATCTGTTATTACTGCCTAATCAC
*
1143547 AATAAGAATAAAGATTCTAATGAGAATCCAT
1 AA-AAGAATGAAGATTCTAATGAGAATCCAT
1143578 GTGTTGCCTT
Statistics
Matches: 278, Mismatches: 57, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
156 3 0.01
157 136 0.49
158 128 0.46
159 11 0.04
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (156 bp):
AAAAGAATGAAGATTCTAATGAGAATCCATTTTTGTTCATTTGAGGTACGAACATTGATTCTAAA
AAAAATGGTGGAAAGAAAAACTTTTCTTTAAAAACCAAAGATCAATATCATATATCCCAAAGAGG
AAAATCTGTTATTACTGCCTAATCAC
Found at i:1143570 original size:315 final size:316
Alignment explanation
Indices: 1142992--1143577 Score: 688
Period size: 315 Copynumber: 1.9 Consensus size: 316
1142982 AAAAAGATCA
* * * *
1142992 AAAGAAAAGCTTCTCTTGCAAAATCAAAGCATCAATATCATGCATCCTAATGAGAAAGCATGTGT
1 AAAGAAAAACTTCTCTTGCAAAACCAAAGCATCAATATCATGCATCCCAAAGAGAAA-CATGTGT
* * *
1143057 TTTTGTTGCCCAACCACAAAAAGAATGGAGATTCAAATAAGAATCTATATTTGTCTTATTTGAGG
65 TATTGTTGCCCAACCACAAAAAGAATGGAGATTCAAATAAGAATCCATATTTGTCTTATTTGAGA
* * * * * * * *
1143122 GACAAATTTTGATTCTTAGAAAATTGGTGGAAGGAAAAGATTTTTTTTTAGAACTAGAGATCAAT
130 GACAAACTTTGATTCTTAAAAAAATGGTGGAAAGAAAAGATTTTTTTTAAAAACCAAAGATCAAT
** * ** * * * *
1143187 ATTGTGTATCCTAAAGAGGAGAACATGTTTTTGTTTCCTAATCATGAAAAGAATGAAGATTTTAA
195 ATCCTATATCCTAAAGAGGAGAACATGTTTTTACTGCCTAATCATCAAAAGAATAAAGATTCTAA
1143252 TGAGAATCCATTTTTGTTCGTTTGAGGTACGAACATTGATTCTATTAAGAGTGGTGG
260 TGAGAATCCATTTTTGTTCGTTTGAGGTACGAACATTGATTCTATTAAGAGTGGTGG
* * *
1143309 AAAGAAAAACTTTTCTTTCAAAACCAAAGCATCAATATCATGTATCCCAAAGAGGAAA-ATGTGT
1 AAAGAAAAACTTCTCTTGCAAAACCAAAGCATCAATATCATGCATCCCAAAGA-GAAACATGTGT
* * * *
1143373 TATTGTTGCCTAATCACAAAAA-AAGTGGAGATTCTAATGAGAATCCAT-TTT-T-TTCATTTGA
65 TATTGTTGCCCAACCACAAAAAGAA-TGGAGATTCAAATAAGAATCCATATTTGTCTT-ATTTGA
**
1143434 GAGATGAACTTTGATTCTTAAAAAAAATGGTGGAAAGAAAAGATTTTTTTTGAAAAACCAAAG-T
128 GAGACAAACTTTGATTCTT-AAAAAAATGGTGGAAAGAAAAGATTTTTTTT-AAAAACCAAAGAT
* * *
1143498 -AGTGATCCTATAT-CTCAAGGAGGAGAATC-TGTTTTTACTGCCTGATCA-CAATAAGAATAAA
191 CAAT-ATCCTATATCCT-AAAGAGGAGAA-CATGTTTTTACTGCCTAATCATCAA-AAGAATAAA
1143559 GATTCTAATGAGAATCCAT
252 GATTCTAATGAGAATCCAT
1143578 GTGTTGCCTT
Statistics
Matches: 224, Mismatches: 36, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
313 2 0.01
314 28 0.12
315 91 0.41
316 53 0.24
317 46 0.21
318 4 0.02
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (316 bp):
AAAGAAAAACTTCTCTTGCAAAACCAAAGCATCAATATCATGCATCCCAAAGAGAAACATGTGTT
ATTGTTGCCCAACCACAAAAAGAATGGAGATTCAAATAAGAATCCATATTTGTCTTATTTGAGAG
ACAAACTTTGATTCTTAAAAAAATGGTGGAAAGAAAAGATTTTTTTTAAAAACCAAAGATCAATA
TCCTATATCCTAAAGAGGAGAACATGTTTTTACTGCCTAATCATCAAAAGAATAAAGATTCTAAT
GAGAATCCATTTTTGTTCGTTTGAGGTACGAACATTGATTCTATTAAGAGTGGTGG
Found at i:1144477 original size:157 final size:161
Alignment explanation
Indices: 1144275--1144563 Score: 390
Period size: 157 Copynumber: 1.8 Consensus size: 161
1144265 TTTGTTCCCT
* * *
1144275 ATCATGAAAAGTATGAAGATTCTAATGAGAATCCATTTTTATCTCATTTGACGGATGAATTTTGA
1 ATCATGAAAAGAATGAAGATTCTAATGAGAATCCATGTTTATCTCATTTAACGGATGAATTTTGA
* * * *
1144340 TTCT-TAGAAAACTAATG-GAAAGAAAAGCTTTTC-TTCAAAACCAAAGCATCAATATTATGT-T
66 TTATAAAGAAAA-TAATGAAAAAAAAAAGCTTTTCTTTCAAAACCAAAGCATCAATATTATGTAT
1144401 TCCCAACGGGGAGAACGTGCTTTCATTGCTTA
130 TCCCAACGGGGAGAACGTGCTTTCATTGCTTA
* * * *
1144433 ATCATGAAAA-AATGGAGTTTCTAATGAGAATCCATGTTTGTCTCATTTAACGTATGAATTTTGA
1 ATCATGAAAAGAATGAAGATTCTAATGAGAATCCATGTTTATCTCATTTAACGGATGAATTTTGA
* ** * *
1144497 TTATAAAGAAAATGATGAAAAAAAAAAGCTTTTCTTTCTTAACCAAAGCATTAATATTGTGTATT
66 TTATAAAGAAAATAATGAAAAAAAAAAGCTTTTCTTTCAAAACCAAAGCATCAATATTATGTATT
1144562 CC
131 CC
1144564 AAAGAGGAAA
Statistics
Matches: 111, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
157 54 0.49
158 30 0.27
159 23 0.21
160 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (161 bp):
ATCATGAAAAGAATGAAGATTCTAATGAGAATCCATGTTTATCTCATTTAACGGATGAATTTTGA
TTATAAAGAAAATAATGAAAAAAAAAAGCTTTTCTTTCAAAACCAAAGCATCAATATTATGTATT
CCCAACGGGGAGAACGTGCTTTCATTGCTTA
Found at i:1150593 original size:12 final size:11
Alignment explanation
Indices: 1150571--1150646 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
1150561 AGAGAAAGAA
*
1150571 GAGAGAGGAGG
1 GAGATAGGAGG
1150582 GATGATAGGAGG
1 GA-GATAGGAGG
*
1150594 AGAGACAGGA--
1 -GAGATAGGAGG
*
1150604 GAGATAGTA--
1 GAGATAGGAGG
1150613 GAGATAGGAGG
1 GAGATAGGAGG
1150624 GATGATAGGAGG
1 GA-GATAGGAGG
1150636 AGAGATAGGAG
1 -GAGATAGGAG
1150647 AGATAATAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.07
12 31 0.57
13 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.49, T:0.11
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1150603 original size:24 final size:24
Alignment explanation
Indices: 1150570--1150655 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1150560 AAGAGAAAGA
*
1150570 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATAGGAGG
* *
1150594 AGAGACAGGA--GA-GAT---AGT
1 AGAGATAGGAGGGATGATAGGAGG
1150612 AGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATAGGAGG
* *
1150636 AGAGATAGGAGAGATAATAG
1 AGAGATAGGAGGGATGATAG
1150656 AGAGAGGAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 29 0.58
ACGTcount: A:0.42, C:0.01, G:0.45, T:0.12
Consensus pattern (24 bp):
AGAGATAGGAGGGATGATAGGAGG
Found at i:1150605 original size:9 final size:9
Alignment explanation
Indices: 1150591--1150651 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
1150581 GGATGATAGG
*
1150591 AGGAGAGAC
1 AGGAGAGAT
1150600 AGGAGAGAT
1 AGGAGAGAT
*
1150609 AGTAGAGAT
1 AGGAGAGAT
*
1150618 AGGAGGGAT
1 AGGAGAGAT
* *
1150627 --GATAG-G
1 AGGAGAGAT
1150633 AGGAGAGAT
1 AGGAGAGAT
1150642 AGGAGAGAT
1 AGGAGAGAT
1150651 A
1 A
1150652 ATAGAGAGAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.43, C:0.02, G:0.44, T:0.11
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1150622 original size:42 final size:42
Alignment explanation
Indices: 1150561--1150679 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1150551 TAGCCCTCAA
* *
1150561 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1150603 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1150645 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1150680 GAGAGAAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1150655 original size:12 final size:12
Alignment explanation
Indices: 1150615--1150660 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1150605 AGATAGTAGA
*
1150615 GATAGGAGGGAT
1 GATAGGAGAGAT
1150627 GATAGGAGGAGA-
1 GATAGGA-GAGAT
1150639 GATAGGAGAGAT
1 GATAGGAGAGAT
*
1150651 AATA-GAGAGA
1 GATAGGAGAGA
1150661 GGAGGGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 10 0.33
12 17 0.57
13 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:1156429 original size:35 final size:35
Alignment explanation
Indices: 1156383--1156451 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
1156373 TGGGCTTGTT
* *
1156383 AGCACAATAAGCTCCTTAGGGTTTGTGTTAACTAA
1 AGCACAATAAGCCCCTTAAGGTTTGTGTTAACTAA
1156418 AGCACAATAAGCCCCTTAAGGTTTGTGTTAACTA
1 AGCACAATAAGCCCCTTAAGGTTTGTGTTAACTA
1156452 TGGCTTATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (35 bp):
AGCACAATAAGCCCCTTAAGGTTTGTGTTAACTAA
Found at i:1157701 original size:12 final size:12
Alignment explanation
Indices: 1157684--1157748 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 12
1157674 AAAAGAAAGA
1157684 AGAGATAGGAGG
1 AGAGATAGGAGG
1157696 AGAGATAGGAAAGACAG
1 AGAGATAGG--AG---G
1157713 TAGAGATAGGAGG
1 -AGAGATAGGAGG
*
1157726 -GATGATAGAAGG
1 AGA-GATAGGAGG
1157738 AGAGATAGGAG
1 AGAGATAGGAG
1157749 AGATAATAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 2 0.05
12 24 0.56
13 3 0.07
14 2 0.05
16 2 0.05
17 1 0.02
18 9 0.21
ACGTcount: A:0.45, C:0.02, G:0.43, T:0.11
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:1157709 original size:30 final size:30
Alignment explanation
Indices: 1157675--1157733 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1157665 TAGCCCTCAA
1157675 AAAGAAAGAAGAGATAGGAGGAGA-GATAGG
1 AAAGAAAGAAGAGATAGGAGG-GATGATAGG
* *
1157705 AAAGACAGTAGAGATAGGAGGGATGATAG
1 AAAGAAAGAAGAGATAGGAGGGATGATAG
1157734 AAGGAGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.49, C:0.02, G:0.39, T:0.10
Consensus pattern (30 bp):
AAAGAAAGAAGAGATAGGAGGGATGATAGG
Found at i:1157733 original size:42 final size:42
Alignment explanation
Indices: 1157687--1157785 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
1157677 AGAAAGAAGA
* *
1157687 GATAGGAGGAGAGATAGGAAAGACAGTAGAGATAGGAGGGAT
1 GATAGGAGGAGAGATAGGAAAGACAATAGAGAGAGGAGGGAT
* * * *
1157729 GATAGAAGGAGAGATAGGAGAGATAATAGAGAGAGGTGGGAT
1 GATAGGAGGAGAGATAGGAAAGACAATAGAGAGAGGAGGGAT
**
1157771 GGCAGGAGGAAGAGA
1 GATAGGAGG-AGAGA
1157786 GAAGAAGATG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 42 0.89
43 5 0.11
ACGTcount: A:0.42, C:0.02, G:0.44, T:0.11
Consensus pattern (42 bp):
GATAGGAGGAGAGATAGGAAAGACAATAGAGAGAGGAGGGAT
Found at i:1157749 original size:9 final size:9
Alignment explanation
Indices: 1157693--1157753 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
1157683 AAGAGATAGG
1157693 AGGAGAGAT
1 AGGAGAGAT
* *
1157702 AGGAAAGAC
1 AGGAGAGAT
*
1157711 AGTAGAGAT
1 AGGAGAGAT
*
1157720 AGGAGGGAT
1 AGGAGAGAT
*
1157729 --GATAGA-
1 AGGAGAGAT
1157735 AGGAGAGAT
1 AGGAGAGAT
1157744 AGGAGAGAT
1 AGGAGAGAT
1157753 A
1 A
1157754 ATAGAGAGAG
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
7 4 0.10
8 5 0.13
9 30 0.77
ACGTcount: A:0.46, C:0.02, G:0.41, T:0.11
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1506117 original size:51 final size:50
Alignment explanation
Indices: 1506047--1506316 Score: 283
Period size: 51 Copynumber: 5.3 Consensus size: 50
1506037 TTAATCATCG
* * *
1506047 GGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTTCATAATC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAATACTAATTTTTCATAATC
* * *
1506097 AGGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTTCATAATC
1 -GGGATACTCCAACCCCGATTTTATTTTCAAAATACTAATTTTTCATAATC
* * **
1506148 AGGGATACTCCAACCCCGATTTTA-TTGCTAAAACACTAATTTTTCCGCAATC
1 -GGGATACTCCAACCCCGATTTTATTTTC-AAAATACTAATTTTT-CATAATC
* * * * *
1506200 GGGGATACTCCAACCCCGGTTTTATTTTC-AAACACCAATTTTCCTTTAATC
1 -GGGATACTCCAACCCCGATTTTATTTTCAAAATACTAATTTTTC-ATAATC
* * * *
1506251 GAGGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAATC
1 G-GGATACTCCAACCCCGATTTTATTTTCAAAATACTAATTTTTCATAATC
1506302 GAGGATACTCCAACC
1 G-GGATACTCCAACC
1506317 TCGTTATTTC
Statistics
Matches: 191, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
50 5 0.03
51 143 0.75
52 40 0.21
53 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAATACTAATTTTTCATAATC
Found at i:1506257 original size:103 final size:101
Alignment explanation
Indices: 1506043--1506316 Score: 291
Period size: 103 Copynumber: 2.7 Consensus size: 101
1506033 CCCGTTAATC
* * * * * * *
1506043 ATCGGGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTTCATAATCAGGGATACTCC
1 ATCGAGGATACTCCAACCCCGATTTTATTCT-AAAATACTAATTTTTCACAATCGGGGATACTCC
* *** *
1506108 AACCCCGACTTTATTTTCAAAATATTGATTTTTCATA
65 AACCCCGACTTTATTTTCAAAACACCAATTTTCCATA
* *
1506145 ATC-AGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCGCAATCGGGGATACT
1 ATCGA-GGATACTCCAACCCCGATTTTATT-CTAAAATACTAATTTTT-CACAATCGGGGATACT
** *
1506209 CCAACCCCGGTTTTATTTTC-AAACACCAATTTTCCTTTA
63 CCAACCCCGACTTTATTTTCAAAACACCAATTTTCC-ATA
* * * *
1506248 ATCGAGGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAATCGAGGATACTCC
1 ATCGAGGATACTCCAACCCCGATTTTA-TTCTAAAATACTAATTTTTCACAATCGGGGATACTCC
1506313 AACC
65 AACC
1506317 TCGTTATTTC
Statistics
Matches: 143, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
102 68 0.48
103 72 0.50
104 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (101 bp):
ATCGAGGATACTCCAACCCCGATTTTATTCTAAAATACTAATTTTTCACAATCGGGGATACTCCA
ACCCCGACTTTATTTTCAAAACACCAATTTTCCATA
Found at i:1506335 original size:28 final size:28
Alignment explanation
Indices: 1506299--1506375 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1506289 ATTTTTCACA
* * *
1506299 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
1506327 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
1506355 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1506376 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:1506389 original size:107 final size:108
Alignment explanation
Indices: 1506253--1506454 Score: 255
Period size: 107 Copynumber: 1.9 Consensus size: 108
1506243 CTTTAATCGA
* * * * *
1506253 GGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAATCGAGGATACTCCAACCT
1 GGATACTCCAACCCCGACTTTATTCCCAAAATACCAATTTCTCACAATCGAGGATACTCCAACCC
*
1506318 CGTTATTTCAT-CGGGGATACTCCAA-CCCCGTTACTTCCGAGG
66 CGTTATTT-ATGAGGGGATACTCCAATCCCCGTTACTTCCGAGG
* *** * * *
1506360 GGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCC
1 GGATACTCCAACCCCGACTTTATTCCCAAAATACCAATTTCTCACAATCGAGGATACTCCAACCC
*
1506425 CGTTATTTTTGAGGGGATACTCCAATCCCC
66 CGTTATTTATGAGGGGATACTCCAATCCCC
1506455 ATTTTTTTTC
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
106 1 0.01
107 74 0.94
108 4 0.05
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (108 bp):
GGATACTCCAACCCCGACTTTATTCCCAAAATACCAATTTCTCACAATCGAGGATACTCCAACCC
CGTTATTTATGAGGGGATACTCCAATCCCCGTTACTTCCGAGG
Found at i:1506449 original size:28 final size:29
Alignment explanation
Indices: 1506409--1506463 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
1506399 TCTCATAATT
*
1506409 GGGGATACTCCAA-CCCCGTTATTTTTGA
1 GGGGATACTCCAATCCCCATTATTTTTGA
*
1506437 GGGGATACTCCAATCCCCATTTTTTTT
1 GGGGATACTCCAATCCCCATTATTTTT
1506464 CTAATCATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (29 bp):
GGGGATACTCCAATCCCCATTATTTTTGA
Found at i:1508597 original size:4 final size:4
Alignment explanation
Indices: 1508590--1508614 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1508580 TCTTGAGGTG
1508590 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1508615 ATATCTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1512793 original size:21 final size:21
Alignment explanation
Indices: 1512769--1512809 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1512759 AACATGTCAT
1512769 AAATGCATGAAGCATAGCTTA
1 AAATGCATGAAGCATAGCTTA
* *
1512790 AAATGCATGAATCATGGCTT
1 AAATGCATGAAGCATAGCTT
1512810 GTTAACATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (21 bp):
AAATGCATGAAGCATAGCTTA
Found at i:1513749 original size:52 final size:51
Alignment explanation
Indices: 1513664--1513787 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
1513654 ATATGAAAAG
* *
1513664 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
1513715 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
1513767 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1513788 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:1513800 original size:51 final size:51
Alignment explanation
Indices: 1513664--1513807 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
1513654 ATATGAAAAG
*
1513664 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1513716 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1513767 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1513808 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1513814 original size:13 final size:13
Alignment explanation
Indices: 1513796--1513820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1513786 CAAAGATCAG
1513796 TGTATCGATACAA
1 TGTATCGATACAA
1513809 TGTATCGATACA
1 TGTATCGATACA
1513821 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1513901 original size:13 final size:13
Alignment explanation
Indices: 1513883--1513907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1513873 CAAAAAAATA
1513883 TGTATCGATACAT
1 TGTATCGATACAT
1513896 TGTATCGATACA
1 TGTATCGATACA
1513908 ACATTTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1513922 original size:33 final size:33
Alignment explanation
Indices: 1513861--1513927 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1513851 AGTAGCTTAA
*
1513861 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATATATCGATAC
* ***
1513894 ATTGTATCGATACAACATTTTATATATCGATAC
1 ATTGTATCGATACAAAAAAATATATATCGATAC
1513927 A
1 A
1513928 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATATATCGATAC
Found at i:1514962 original size:91 final size:93
Alignment explanation
Indices: 1514790--1514969 Score: 285
Period size: 91 Copynumber: 1.9 Consensus size: 93
1514780 AAAAGGATGT
1514790 CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGG-AAAGGTGCCAATATGCTGATT
*
1514855 CAAGGCCAGCTATATTGGACTTAAGGTGC
65 CAAGGCCAGCGATATTGGACTTAAGGTGC
* *
1514884 CAATGTGCTGATTCAAGGTC-AGCTACATTGGACTTAAATAT-G-AAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGG-CGAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATT
*
1514946 TAAGGCCAGCGATATTGGACTTAA
65 CAAGGCCAGCGATATTGGACTTAA
1514970 AGGCAAGGTG
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
91 42 0.52
93 1 0.01
94 37 0.46
95 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (93 bp):
CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTTAAGGTGC
Found at i:1514963 original size:49 final size:49
Alignment explanation
Indices: 1514877--1515021 Score: 195
Period size: 49 Copynumber: 3.0 Consensus size: 49
1514867 TATTGGACTT
* * * *
1514877 AAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATG-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-AGGC
* *
1514926 AAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AAAGGC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGC
* *
1514974 AAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGGCTTAAAAGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGG
1515022 AGACGCCACC
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
47 2 0.02
48 40 0.48
49 42 0.50
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (49 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGC
Found at i:1514999 original size:48 final size:46
Alignment explanation
Indices: 1514790--1515018 Score: 232
Period size: 48 Copynumber: 4.8 Consensus size: 46
1514780 AAAAGGATGT
* * * *
1514790 CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G--AAGGTGC
1514842 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGC
* * *
1514884 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-GAAGGTGC
* *
1514933 CAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGGCAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-G-AAGGTGC
* *
1514981 CAATATGCTAATTCAAGGCCAGCTATATTGGGCTTAAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1515019 AGGAGACGCC
Statistics
Matches: 152, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
42 39 0.26
47 2 0.01
48 43 0.28
49 37 0.24
52 31 0.20
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (46 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGC
Found at i:1515121 original size:30 final size:30
Alignment explanation
Indices: 1515062--1515166 Score: 169
Period size: 30 Copynumber: 3.6 Consensus size: 30
1515052 AGGTTTGCAT
* *
1515062 CACTGACTTGTGGGCTTTT--AAAGGTTGC
1 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1515090 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
*
1515120 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1515150 CACTAACTTGTGGGCTT
1 CACTAACTTGTGGGCTT
1515167 AAAAAGAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 18 0.25
30 53 0.75
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (30 bp):
CACTAACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:1515275 original size:27 final size:28
Alignment explanation
Indices: 1515237--1515298 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
1515227 CTTCGAAAAA
* *
1515237 AAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAGGGTGCCACTGACTTGTGGACTTTTG
*
1515264 AAGGTTGCCACTGACTTGTGGACTTTTG
1 AAGGGTGCCACTGACTTGTGGACTTTTG
1515292 AAGGGTG
1 AAGGGTG
1515299 ATAAATGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.18, C:0.15, G:0.35, T:0.32
Consensus pattern (28 bp):
AAGGGTGCCACTGACTTGTGGACTTTTG
Found at i:1516734 original size:1 final size:1
Alignment explanation
Indices: 1516728--1516827 Score: 83
Period size: 1 Copynumber: 100.0 Consensus size: 1
1516718 CATCCAGACC
* * * * * * ** * *
1516728 TTTTTTTTTTTGTTTTTTTTTTGTTTTTTTCTTTGTATTTTTGTTTTTGCTTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
1516793 TTTTTTTTTTGTTTTGTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1516828 GTGGAGGACG
Statistics
Matches: 74, Mismatches: 25, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.01, C:0.02, G:0.10, T:0.87
Consensus pattern (1 bp):
T
Found at i:1516745 original size:11 final size:11
Alignment explanation
Indices: 1516729--1516827 Score: 112
Period size: 11 Copynumber: 8.7 Consensus size: 11
1516719 ATCCAGACCT
1516729 TTTTTTTTTTG
1 TTTTTTTTTTG
1516740 TTTTTTTTTTG
1 TTTTTTTTTTG
1516751 TTTTTTTCTTTG
1 TTTTTTT-TTTG
1516763 TATTTTTGTTTTTG
1 --TTTTT-TTTTTG
*
1516777 CTTTTTTTTTG
1 TTTTTTTTTTG
*
1516788 TTTTGTTTTT-
1 TTTTTTTTTTG
*
1516798 TTTTTGTTTTG
1 TTTTTTTTTTG
1516809 TTTTGTTTTTT-
1 TTTT-TTTTTTG
1516820 TTTTTTTT
1 TTTTTTTT
1516828 GTGGAGGACG
Statistics
Matches: 76, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
10 12 0.16
11 40 0.53
12 13 0.17
14 9 0.12
15 2 0.03
ACGTcount: A:0.01, C:0.02, G:0.10, T:0.87
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:1516769 original size:37 final size:35
Alignment explanation
Indices: 1516732--1516829 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 35
1516722 CAGACCTTTT
1516732 TTTTTTTGTTTTTTTTTTGTTTT-TTTCTTTGTATTTT
1 TTTTTTTGTTTTTTTTTTGTTTTGTTT-TTT-T-TTTT
* *
1516769 TGTTTTTGCTTTTTTTTTGTTTTGTTTTTTTTTTGT
1 TTTTTTTGTTTTTTTTTTGTTTTGTTTTTTTTTT-T
1516805 TTTGTTTTGTTTTTTTTTT-TTTTGT
1 TTT-TTTTGTTTTTTTTTTGTTTTGT
1516830 GGAGGACGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
35 3 0.06
36 10 0.19
37 38 0.70
38 3 0.06
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.86
Consensus pattern (35 bp):
TTTTTTTGTTTTTTTTTTGTTTTGTTTTTTTTTTT
Found at i:1526476 original size:10 final size:11
Alignment explanation
Indices: 1526448--1526475 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1526438 ATGTATCAAG
1526448 CAAAAAACAAA
1 CAAAAAACAAA
1526459 CAAAAAACAAA
1 CAAAAAACAAA
1526470 CAAAAA
1 CAAAAA
1526476 CTTAGTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAACAAA
Found at i:1529748 original size:21 final size:21
Alignment explanation
Indices: 1529724--1529764 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1529714 AACATGTCAT
1529724 AAATGCATGAAGCATAGCTTA
1 AAATGCATGAAGCATAGCTTA
* *
1529745 AAATGCATGAATCATGGCTT
1 AAATGCATGAAGCATAGCTT
1529765 GTTAACATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (21 bp):
AAATGCATGAAGCATAGCTTA
Found at i:1530705 original size:52 final size:51
Alignment explanation
Indices: 1530620--1530743 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
1530610 ATATGAAAAG
* *
1530620 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
1530671 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
1530723 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1530744 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:1530756 original size:51 final size:51
Alignment explanation
Indices: 1530620--1530763 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
1530610 ATATGAAAAG
*
1530620 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1530672 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1530723 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1530764 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1530770 original size:13 final size:13
Alignment explanation
Indices: 1530752--1530776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1530742 CAAAGATCAG
1530752 TGTATCGATACAA
1 TGTATCGATACAA
1530765 TGTATCGATACA
1 TGTATCGATACA
1530777 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1530854 original size:33 final size:33
Alignment explanation
Indices: 1530817--1530883 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1530807 AGTAGCTTAA
1530817 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1530850 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1530883 A
1 A
1530884 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1530857 original size:13 final size:13
Alignment explanation
Indices: 1530839--1530863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1530829 CAAAAAAATA
1530839 TGTATCGATACAT
1 TGTATCGATACAT
1530852 TGTATCGATACA
1 TGTATCGATACA
1530864 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1539353 original size:18 final size:17
Alignment explanation
Indices: 1539330--1539382 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
1539320 ACATTCTCTT
*
1539330 AAAAAAAAGC-AAAAAA
1 AAAAAAAAACAAAAAAA
1539346 AAAAAAAAACAAAACAAA
1 AAAAAAAAACAAAA-AAA
*
1539364 AAAACAAAACAAAGAAAA
1 AAAAAAAAACAAA-AAAA
1539382 A
1 A
1539383 GAGAGAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 9 0.28
17 3 0.09
18 19 0.59
19 1 0.03
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAA
Found at i:1539359 original size:13 final size:13
Alignment explanation
Indices: 1539330--1539382 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
1539320 ACATTCTCTT
*
1539330 AAAAAAAAGCAAA-
1 AAAAAAAA-AAAAC
1539343 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
*
1539356 AAAACAAAAAAAC
1 AAAAAAAAAAAAC
1539369 AAAACAAAGAAAAA
1 AAAA-AAA-AAAAA
1539383 GAGAGAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 3 0.09
13 24 0.71
14 2 0.06
15 5 0.15
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:1540579 original size:59 final size:59
Alignment explanation
Indices: 1540369--1541734 Score: 1961
Period size: 59 Copynumber: 23.3 Consensus size: 59
1540359 ACTTTTTAGC
* * * **
1540369 CCTCAAAGAGCAGGATGCCTTTTCCTTTAAAAAGCCCCCACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACGCCTTTT-CTTT-TAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
**
1540431 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
*
1540491 CCTCAAAGAGCAGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
*
1540550 CCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1540609 CCTCAAAGAGC-GTGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAG-GACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
*
1540668 CCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1540727 CCTCAAAGAGC-GTGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAG-GACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
*
1540786 CCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* * *
1540845 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTCAGT
* * ** *
1540906 CCCCAAAGAGCAGGACTCC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCCAAT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
* * **
1540961 CCTCAAAGAGCAGGAC-AC----CTTTTAAAGCACACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
**
1541016 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
*
1541076 CCTCAAAGAGCAGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
*
1541135 CCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1541194 CCTCAAAGAGC-GTGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAG-GACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
*
1541253 CCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* * *
1541312 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTCAGT
* * ** *
1541373 CCCCAAAGAGCAGGACTCC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCCAAT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
* * **
1541428 CCTCAAAGAGCAGGAC-AC----CTTTTAAAGCACACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
* *
1541483 CCTCAAAGAGCAGGACACCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* *
1541542 CCTTAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* * *
1541601 CCTTAAAGAACGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* *
1541660 CCTCAAAGAGC-GAGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGT
1 CCTCAAAGAGCAG-GACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGT
1541720 CCTCAAAGAGCAGGA
1 CCTCAAAGAGCAGGA
1541735 TACACTTTAT
Statistics
Matches: 1210, Mismatches: 61, Indels: 68
0.90 0.05 0.05
Matches are distributed among these distances:
51 2 0.00
54 6 0.00
55 172 0.14
56 2 0.00
58 4 0.00
59 679 0.56
60 276 0.23
61 47 0.04
62 22 0.02
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (59 bp):
CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
Found at i:1541478 original size:467 final size:465
Alignment explanation
Indices: 1540369--1541730 Score: 2341
Period size: 467 Copynumber: 2.9 Consensus size: 465
1540359 ACTTTTTAGC
* ** * * *
1540369 CCTCAAAGAGCAGGATGCCTTTTCCTTTAAAAAGCCCCCACAAGTTGGTGGCA-TTTTCCAGTCC
1 CCTCAAAGAGCAGGATG-CTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTT-CAGTCC
* * *
1540433 TCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
64 CCAAAGAGCAGGACTCC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAA
* ** *
1540498 GAGCAGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCG
124 GAGCAGGACA-C----CTTTTAAAGCACACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCA
1540562 GGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGTGACGC
184 GGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCG-GACGC
1540627 CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTC
248 CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTC
1540692 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGTGACGCCTTTTCTTTTAA
313 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGTGACGCCTTTTCTTTTAA
1540757 AGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCA
378 AGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCA
1540822 CACAAGTTGGTGGCACCTTCAGT
443 CACAAGTTGGTGGCACCTTCAGT
1540845 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCCC
1 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCCC
1540910 AAAGAGCAGGACTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGG
66 AAAGAGCAGGACTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGG
1540975 ACACCTTTTAAAGCACACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTC
131 ACACCTTTTAAAGCACACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTC
** *
1541040 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTTCTTTTA
196 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGC-GGACGCCTTTTCTTTTA
1541105 AAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCC
259 AAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCC
1541170 ACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGTGACGCCTTTTCTTTTAAAGCCCACACAA
324 ACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGTGACGCCTTTTCTTTTAAAGCCCACACAA
1541235 GTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGT
389 GTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGT
1541300 GGCACCTTCAGT
454 GGCACCTTCAGT
1541312 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCCC
1 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCCC
1541377 AAAGAGCAGGACTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGG
66 AAAGAGCAGGACTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGG
*
1541442 ACACCTTTTAAAGCACACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTTC
131 ACACCTTTTAAAGCACACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTC
* *
1541507 TTTTAAAGCCTACACAAGTTGGTGGCACCTTCAGTCCTTAAAGAGCGGGACGCCTTTTCTTTTAA
196 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC-GGACGCCTTTTCTTTTAA
* *
1541572 AGCCCACACAAGTTGGTGGCACCTTCAGTCCTTAAAGAACGGGACGCCTTTTCTTTTAAAGCCCA
260 AGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCA
*
1541637 CACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGAGACGCCTTTTCTTTTAAAGCCCACACAAG
325 CACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGTGACGCCTTTTCTTTTAAAGCCCACACAAG
* *
1541702 TTGGTGGCACTTTTTAGTCCTCAAAGAGC
390 TTGGTGGCAC-CTTCAGTCCTCAAAGAGC
1541731 AGGATACACT
Statistics
Matches: 853, Mismatches: 28, Indels: 19
0.95 0.03 0.02
Matches are distributed among these distances:
465 29 0.03
466 224 0.26
467 475 0.56
468 1 0.00
469 1 0.00
470 48 0.06
474 4 0.00
475 51 0.06
476 20 0.02
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (465 bp):
CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCCC
AAAGAGCAGGACTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGG
ACACCTTTTAAAGCACACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTC
TTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGACGCCTTTTCTTTTAAA
GCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCAC
ACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGTGACGCCTTTTCTTTTAAAGCCCACACAAGT
TGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGG
CACCTTCAGT
Found at i:1542575 original size:19 final size:19
Alignment explanation
Indices: 1542551--1542604 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
1542541 TTTCAGTGAT
1542551 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
1542570 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
1542589 TTGTATCGATACATAA
1 TTGTATCGATACATAA
1542605 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:1545149 original size:54 final size:52
Alignment explanation
Indices: 1545027--1545150 Score: 155
Period size: 51 Copynumber: 2.4 Consensus size: 52
1545017 CAATTCTCCA
* * *
1545027 CAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTAT
*
1545079 -AATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACCACCAA-TTTCT-T
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAA-CACCAATTTTCTAT
1545130 CGCAATCGGGGATACTCCAAC
1 --CAATCGGGGATACTCCAAC
1545151 CCCGTTAATC
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
51 31 0.49
52 9 0.14
53 5 0.08
54 18 0.29
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTAT
Found at i:1545239 original size:51 final size:51
Alignment explanation
Indices: 1545164--1545385 Score: 255
Period size: 52 Copynumber: 4.3 Consensus size: 51
1545154 GTTAATCATT
* * * * *
1545164 GGGGATACTTCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCATAATC
* * *
1545215 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTT-CATAATC
* * * *
1545267 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTC-ATAATC
* * * * *
1545319 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTTACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAACACTAATTTTTCATAATC
*
1545371 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1545386 TCGTTATTTC
Statistics
Matches: 144, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
51 37 0.26
52 95 0.66
53 12 0.08
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCATAATC
Found at i:1545404 original size:28 final size:30
Alignment explanation
Indices: 1545368--1545442 Score: 104
Period size: 28 Copynumber: 2.6 Consensus size: 30
1545358 ATTTTTTACA
* *
1545368 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
1545396 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
1545426 A--GGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
1545443 TGGCTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 38 0.88
29 4 0.09
30 1 0.02
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:1551655 original size:20 final size:20
Alignment explanation
Indices: 1551613--1551666 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1551603 TTCTACGATT
* *
1551613 TGTATCGATACAATTAGTGAA
1 TGTATCGATAC-ATAAATGAA
1551634 TGTATCGATACATAAATGAA
1 TGTATCGATACATAAATGAA
*
1551654 TGCATCGATACAT
1 TGTATCGATACAT
1551667 GTCTCAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAATGAA
Found at i:1554195 original size:24 final size:26
Alignment explanation
Indices: 1554167--1554219 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
1554157 ACCAAAATTT
*
1554167 TATTCATT-AGGG-TTACTCCAACCC
1 TATTCATTCAGGGAATACTCCAACCC
*
1554191 TATTCTTTCGAGGGAATACTCCAACCC
1 TATTCATTC-AGGGAATACTCCAACCC
1554218 TA
1 TA
1554220 GTTTTAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
26 4 0.17
27 13 0.54
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.32
Consensus pattern (26 bp):
TATTCATTCAGGGAATACTCCAACCC
Found at i:1555140 original size:59 final size:59
Alignment explanation
Indices: 1555048--1555169 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
1555038 GACTCCAAAA
1555048 CTTCTATTACTTCGTGGTGACTGTTGAGGATCGATTAGATGGGTGATTCATCTACTGAT
1 CTTCTATTACTTCGTGGTGACTGTTGAGGATCGATTAGATGGGTGATTCATCTACTGAT
1555107 CTTCTATTACTTCGTGGTGACTGTTGAGGATCGATTAGATGGGTGATTCATCTACTGAT
1 CTTCTATTACTTCGTGGTGACTGTTGAGGATCGATTAGATGGGTGATTCATCTACTGAT
1555166 CTTC
1 CTTC
1555170 CCCACTTTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (59 bp):
CTTCTATTACTTCGTGGTGACTGTTGAGGATCGATTAGATGGGTGATTCATCTACTGAT
Found at i:1556641 original size:80 final size:81
Alignment explanation
Indices: 1556495--1556649 Score: 186
Period size: 80 Copynumber: 1.9 Consensus size: 81
1556485 TGGTATCATT
* * * * * **
1556495 TCATAGGCATTTGCCTTTTTATTGATGCTTGCATTCGCATCATTTCATGCACATTTGTACTGTTA
1 TCATAGGCATTTGCCTATTTATTGAGGCTTGCATTCACATCATTTCATGCACATCTGCACCATTA
1556560 GATAACATTCATTATC
66 GATAACATTCATTATC
* * * * *
1556576 TCATATGCATTTGCC-ATTTATTGAGGCTTGCGTTTACATCATTTGATGTACATCTGCACCATTA
1 TCATAGGCATTTGCCTATTTATTGAGGCTTGCATTCACATCATTTCATGCACATCTGCACCATTA
*
1556640 GATGACATTC
66 GATAACATTC
1556650 GCATTTGCCT
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
80 47 0.77
81 14 0.23
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (81 bp):
TCATAGGCATTTGCCTATTTATTGAGGCTTGCATTCACATCATTTCATGCACATCTGCACCATTA
GATAACATTCATTATC
Found at i:1557409 original size:88 final size:89
Alignment explanation
Indices: 1557260--1557685 Score: 457
Period size: 88 Copynumber: 4.8 Consensus size: 89
1557250 TGACCACAAA
* * * * *
1557260 AAGGTGTAACCCACACACTCCAAATCATATCCCCTTCATCCAACCACTAGATGGCATTGATGCTT
1 AAGGTGTAACCCACACATTCCCAATCATATCCCCTTTATCCAACCACTAGATGGTATTGATGCAT
1557325 CACAAAGCCTAATTTCCTT-GGGC
66 CACAAAGCCTAATTTCCTTAGGGC
* *
1557348 AAGGTGCAACCCACACATTCCCAATCATATCCCCTTTATCCAACCACTAGATGGTATTGATGTAT
1 AAGGTGTAACCCACACATTCCCAATCATATCCCCTTTATCCAACCACTAGATGGTATTGATGCAT
* *
1557413 CATAAAGTCTAATTTCCTTAGGGC
66 CACAAAGCCTAATTTCCTTAGGGC
* * * * * * * *
1557437 AGGGTGTAGCCCACACATTGCCAATGATATCTCTTTTATCCAACCATTGGATGGTATT-ATGCAT
1 AAGGTGTAACCCACACATTCCCAATCATATCCCCTTTATCCAACCACTAGATGGTATTGATGCAT
*
1557501 CACAAAGCCTAATTTCCTTGGGGC
66 CACAAAGCCTAATTTCCTTAGGGC
* * * *
1557525 AAGGTGTAGCCCACACATTCCTAATCATATCTCTTTTA-CTCAACCACTAGATGGTATTGATGCA
1 AAGGTGTAACCCACACATTCCCAATCATATCCCCTTTATC-CAACCACTAGATGGTATTGATGCA
** * *
1557589 TCACAAAGCCTGGTTTCCCTGGGGC
65 TCACAAAGCCTAATTTCCTTAGGGC
* ** ** * * *
1557614 AA-GTATATCACGACCACTTATTCCCAATCATAT-CCCAATCTCTTAGCCACTAGATGGTATTGA
1 AAGGTGTA--AC--CCACACATTCCCAATCATATCCCCTTTATC-CAACCACTAGATGGTATTGA
1557677 TGCATCACA
61 TGCATCACA
1557686 TGACCTGGTC
Statistics
Matches: 287, Mismatches: 43, Indels: 12
0.84 0.13 0.04
Matches are distributed among these distances:
87 1 0.00
88 155 0.54
89 82 0.29
90 1 0.00
91 2 0.01
92 46 0.16
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (89 bp):
AAGGTGTAACCCACACATTCCCAATCATATCCCCTTTATCCAACCACTAGATGGTATTGATGCAT
CACAAAGCCTAATTTCCTTAGGGC
Found at i:1557571 original size:177 final size:177
Alignment explanation
Indices: 1557262--1557596 Score: 469
Period size: 177 Copynumber: 1.9 Consensus size: 177
1557252 ACCACAAAAA
*
1557262 GGTGTAACCCACACACTCCAAATCATATCCCCTTCATCCAACCACTAGATGGCATTGATGCTTCA
1 GGTGTAACCCACACACTCCAAATCATATCCCCTTCATCCAACCACTAGATGGCATTGATGCATCA
1557327 CAAAGCCTAATTTCCTTGGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTTATCCAAC
66 CAAAGCCTAATTTCCTTGGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTTATCCAAC
* *
1557392 CACTAGATGGTATTGATGTATCATAAAGTCTAATTTCCTTAGGGCAG
131 CACTAGATGGTATTGATGCATCACAAAGTCTAATTTCCTTAGGGCAG
* * * * * * * * *
1557439 GGTGTAGCCCACACATTGCC-AATGATATCTCTTTTATCCAACCATTGGATGGTATT-ATGCATC
1 GGTGTAACCCACACACT-CCAAATCATATCCCCTTCATCCAACCACTAGATGGCATTGATGCATC
* * * * *
1557502 ACAAAGCCTAATTTCCTTGGGGCAAGGTGTAGCCCACACATTCCTAATCATATCTCTTTTA-CTC
65 ACAAAGCCTAATTTCCTT-GGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTTATC-C
1557566 AACCACTAGATGGTATTGATGCATCACAAAG
128 AACCACTAGATGGTATTGATGCATCACAAAG
1557597 CCTGGTTTCC
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
176 25 0.18
177 111 0.80
178 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (177 bp):
GGTGTAACCCACACACTCCAAATCATATCCCCTTCATCCAACCACTAGATGGCATTGATGCATCA
CAAAGCCTAATTTCCTTGGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTTATCCAAC
CACTAGATGGTATTGATGCATCACAAAGTCTAATTTCCTTAGGGCAG
Found at i:1558082 original size:41 final size:41
Alignment explanation
Indices: 1558016--1558247 Score: 229
Period size: 41 Copynumber: 5.7 Consensus size: 41
1558006 AATTGGTTCA
* *
1558016 CTTTAT-AGGTTTTGCCCTAGTCAACCTTTCTAACCCGTTGG
1 CTTTATCA-GTTTTGCCCTGGCCAACCTTTCTAACCCGTTGG
* * * *
1558057 CTTTAT-AGGTTTTGCCTTGGCCAACCCTTCTAACCTGTTAG
1 CTTTATCA-GTTTTGCCCTGGCCAACCTTTCTAACCCGTTGG
* ** *
1558098 CTTTATCAGTTTTGCCCTGGCCAATCTTT-TAATTCGTTGA
1 CTTTATCAGTTTTGCCCTGGCCAACCTTTCTAACCCGTTGG
* ** *
1558138 CTTTATCAATTTTGCCCTGGTTAACCCTTCTAACCCGTTGG
1 CTTTATCAGTTTTGCCCTGGCCAACCTTTCTAACCCGTTGG
* ** *
1558179 CTTTATCAGTTTTGCCCTAGCCAACCTTT-TAACTGGTTGA
1 CTTTATCAGTTTTGCCCTGGCCAACCTTTCTAACCCGTTGG
** *
1558219 CTTTATCAGTTTCACCTTGGCCAACCTTT
1 CTTTATCAGTTTTGCCCTGGCCAACCTTT
1558248 TAATTGATTG
Statistics
Matches: 155, Mismatches: 34, Indels: 5
0.80 0.18 0.03
Matches are distributed among these distances:
40 63 0.41
41 91 0.59
42 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.41
Consensus pattern (41 bp):
CTTTATCAGTTTTGCCCTGGCCAACCTTTCTAACCCGTTGG
Found at i:1558152 original size:81 final size:81
Alignment explanation
Indices: 1558016--1558244 Score: 273
Period size: 81 Copynumber: 2.8 Consensus size: 81
1558006 AATTGGTTCA
* * * *
1558016 CTTTAT-AGGTTTTGCCCTAGTCAACCTTTCTAACCCGTTGGCTTTAT-AGGTTTTGCCTTGGCC
1 CTTTATCA-GTTTTGCCCTAGCCAACCTTT-TAACTCGTTGACTTTATCA-ATTTTGCCTTGGCC
*
1558079 AACCCTTCTAACCTGTTAG
63 AACCCTTCTAACCCGTTAG
* * * * **
1558098 CTTTATCAGTTTTGCCCTGGCCAATCTTTTAATTCGTTGACTTTATCAATTTTGCCCTGGTTAAC
1 CTTTATCAGTTTTGCCCTAGCCAACCTTTTAACTCGTTGACTTTATCAATTTTGCCTTGGCCAAC
*
1558163 CCTTCTAACCCGTTGG
66 CCTTCTAACCCGTTAG
* * **
1558179 CTTTATCAGTTTTGCCCTAGCCAACCTTTTAACTGGTTGACTTTATCAGTTTCACCTTGGCCAAC
1 CTTTATCAGTTTTGCCCTAGCCAACCTTTTAACTCGTTGACTTTATCAATTTTGCCTTGGCCAAC
1558244 C
66 C
1558245 TTTTAATTGA
Statistics
Matches: 123, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
81 97 0.79
82 25 0.20
83 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (81 bp):
CTTTATCAGTTTTGCCCTAGCCAACCTTTTAACTCGTTGACTTTATCAATTTTGCCTTGGCCAAC
CCTTCTAACCCGTTAG
Found at i:1558153 original size:40 final size:40
Alignment explanation
Indices: 1558015--1558270 Score: 216
Period size: 40 Copynumber: 6.3 Consensus size: 40
1558005 TAATTGGTTC
* * *
1558015 ACTTTAT-AGGTTTTGCCCTAGTCAACCTTTCTAACCCGTTG
1 ACTTTATCA-GTTTTGCCCTGGCCAACCTTT-TAACTCGTTG
* * *
1558056 GCTTTAT-AGGTTTTGCCTTGGCCAACCCTTCTAAC-CTGTT-
1 ACTTTATCA-GTTTTGCCCTGGCCAA-CCTTTTAACTC-GTTG
* *
1558096 AGCTTTATCAGTTTTGCCCTGGCCAATCTTTTAATTCGTTG
1 A-CTTTATCAGTTTTGCCCTGGCCAACCTTTTAACTCGTTG
* ** * *
1558137 ACTTTATCAATTTTGCCCTGGTTAACCCTTCTAACCCGTTG
1 ACTTTATCAGTTTTGCCCTGGCCAA-CCTTTTAACTCGTTG
* * *
1558178 GCTTTATCAGTTTTGCCCTAGCCAACCTTTTAACTGGTTG
1 ACTTTATCAGTTTTGCCCTGGCCAACCTTTTAACTCGTTG
** * *
1558218 ACTTTATCAGTTTCACCTTGGCCAACCTTTTAA-TTGATTG
1 ACTTTATCAGTTTTGCCCTGGCCAACCTTTTAACTCG-TTG
*
1558258 ACTTTATCGGTTT
1 ACTTTATCAGTTT
1558271 CACCTTATTC
Statistics
Matches: 175, Mismatches: 32, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
39 2 0.01
40 86 0.49
41 82 0.47
42 5 0.03
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.41
Consensus pattern (40 bp):
ACTTTATCAGTTTTGCCCTGGCCAACCTTTTAACTCGTTG
Found at i:1558292 original size:28 final size:28
Alignment explanation
Indices: 1558260--1558313 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1558250 ATTGATTGAC
*
1558260 TTTATCGGTTTCACCTTATTCAACCCAT
1 TTTATCAGTTTCACCTTATTCAACCCAT
*
1558288 TTTATCAGTTTCATCTTATTCAACCC
1 TTTATCAGTTTCACCTTATTCAACCC
1558314 TTCGAACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.06, T:0.44
Consensus pattern (28 bp):
TTTATCAGTTTCACCTTATTCAACCCAT
Found at i:1558444 original size:46 final size:46
Alignment explanation
Indices: 1558385--1558534 Score: 201
Period size: 46 Copynumber: 3.3 Consensus size: 46
1558375 CTTACCACCC
* *
1558385 TCAAACCCTTTTCATTCTTATTTGACTATATTAGTTACCACCTTGG
1 TCAAACCCTTTTCATTCTTATTTGACTGTATCAGTTACCACCTTGG
* * *
1558431 TCAAACCCTTTTCATTCTTATTTGATTGTATCAGTTACCACCCTAG
1 TCAAACCCTTTTCATTCTTATTTGACTGTATCAGTTACCACCTTGG
* * * *
1558477 TCAAACACTTTTCATTCTTATTTTACTGTATCGGTTAACACCTTGG
1 TCAAACCCTTTTCATTCTTATTTGACTGTATCAGTTACCACCTTGG
* *
1558523 TCGAACTCTTTT
1 TCAAACCCTTTT
1558535 AATCCTCGTT
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 90 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.43
Consensus pattern (46 bp):
TCAAACCCTTTTCATTCTTATTTGACTGTATCAGTTACCACCTTGG
Found at i:1558831 original size:85 final size:85
Alignment explanation
Indices: 1558628--1558954 Score: 326
Period size: 85 Copynumber: 3.8 Consensus size: 85
1558618 GGTTCAATTT
* * * *
1558628 CGATCGACTTTTTTATCCTTTGCTTTACCTGTTGGCTTAGT-CTCAAGTAAATCCTTTTTATCCT
1 CGATCAAC-TTTTTATCTTTTG-TTTACCTGTCGGCTTAGTCCT-GAGTAAATCCTTTTTATCCT
* * * *
1558692 TTGTTGGCTTATCGGTTTAACCC
63 TTGTTGACTTGTCAGTTCAACCC
* * *
1558715 CGGTCAACTTTTGTACCCTTTGTTTACCTGTCGGCTTAGTCCTGAGTAAATCC-TTTTATCCTTT
1 CGATCAACTTTT-TATCTTTTGTTTACCTGTCGGCTTAGTCCTGAGTAAATCCTTTTTATCCTTT
*
1558779 GTTGACTTGTCAGTTCAAGCC
65 GTTGACTTGTCAGTTCAACCC
* * * *
1558800 TGATCAACCTTTTTATCTTTTATTTACCTGTCGGCTTAGTCC-CAGGTAAAT-TTTTTTATCCTT
1 CGATCAA-CTTTTTATCTTTTGTTTACCTGTCGGCTTAGTCCTGA-GTAAATCCTTTTTATCCTT
* *
1558863 TGTTGACTTGTCAATTCAATCC
64 TGTTGACTTGTCAGTTCAACCC
* ** *
1558885 CGATCAAC-TTTTATCTCCTTTGTTTACTTGTCAACTTAGTCCCGAGT-AA-CCTTTTTTATCCT
1 CGATCAACTTTTTATCT--TTTGTTTACCTGTCGGCTTAGTCCTGAGTAAATCC-TTTTTATCCT
1558947 TTGTTGAC
63 TTGTTGAC
1558955 CTGATTGCTA
Statistics
Matches: 204, Mismatches: 26, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
83 8 0.04
84 4 0.02
85 140 0.69
86 36 0.18
87 16 0.08
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.45
Consensus pattern (85 bp):
CGATCAACTTTTTATCTTTTGTTTACCTGTCGGCTTAGTCCTGAGTAAATCCTTTTTATCCTTTG
TTGACTTGTCAGTTCAACCC
Found at i:1558894 original size:170 final size:171
Alignment explanation
Indices: 1558637--1558954 Score: 410
Period size: 170 Copynumber: 1.9 Consensus size: 171
1558627 TCGATCGACT
* * * *
1558637 TTTTTATCCTTTGCTTTACCTGTTGGCTTAGTCTCAAGTAAATCCTTTTTATCCTTTGTTGGCTT
1 TTTTTATCCTTTGATTTACCTGTCGGCTTAGTCCCAAGTAAATCCTTTTTATCCTTTGTTGACTT
** * * * ** *
1558702 ATCGGTTTAACCCCGGTCAACTTTTGTAC-CCTTTGTTTACCTGTCGGCTTAGTCCTGAGTAAAT
66 ATCAATTCAACCCCGATCAACTTTTAT-CTCCTTTGTTTACCTGTCAACTTAGTCCCGAGT-AA-
1558766 CC-TTTTATCCTTTGTTGACTTGTCAGTTCAAGCCTGATCAACC
128 CCTTTTTATCCTTTGTTGACTTGTCAGTTCAAGCCTGATCAACC
* * *
1558809 TTTTTAT-CTTTTATTTACCTGTCGGCTTAGTCCCAGGTAAAT-TTTTTTATCCTTTGTTGACTT
1 TTTTTATCCTTTGATTTACCTGTCGGCTTAGTCCCAAGTAAATCCTTTTTATCCTTTGTTGACTT
* * *
1558872 GTCAATTCAATCCCGATCAACTTTTATCTCCTTTGTTTACTTGTCAACTTAGTCCCGAGTAACCT
66 ATCAATTCAACCCCGATCAACTTTTATCTCCTTTGTTTACCTGTCAACTTAGTCCCGAGTAACC-
1558937 TTTTTATCCTTTGTTGAC
130 TTTTTATCCTTTGTTGAC
1558955 CTGATTGCTA
Statistics
Matches: 125, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
168 2 0.02
169 3 0.02
170 83 0.66
171 30 0.24
172 7 0.06
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.46
Consensus pattern (171 bp):
TTTTTATCCTTTGATTTACCTGTCGGCTTAGTCCCAAGTAAATCCTTTTTATCCTTTGTTGACTT
ATCAATTCAACCCCGATCAACTTTTATCTCCTTTGTTTACCTGTCAACTTAGTCCCGAGTAACCT
TTTTATCCTTTGTTGACTTGTCAGTTCAAGCCTGATCAACC
Found at i:1558928 original size:42 final size:43
Alignment explanation
Indices: 1558851--1558954 Score: 124
Period size: 42 Copynumber: 2.4 Consensus size: 43
1558841 CCAGGTAAAT
*
1558851 TTTTTTATCCTTTGTTGACTTGTCAATTCAATCCCGA-TCAA-C
1 TTTTATATCCTTTGTTGACTTGTCAATTCAATCCCGAGT-AACC
* * *
1558893 TTTTATCTCCTTTGTTTACTTGTCAACTT-AGTCCCGAGTAACC
1 TTTTATATCCTTTGTTGACTTGTCAA-TTCAATCCCGAGTAACC
*
1558936 TTTTTTATCCTTTGTTGAC
1 TTTTATATCCTTTGTTGAC
1558955 CTGATTGCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 32 0.62
43 20 0.38
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (43 bp):
TTTTATATCCTTTGTTGACTTGTCAATTCAATCCCGAGTAACC
Found at i:1570720 original size:20 final size:20
Alignment explanation
Indices: 1570695--1570741 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1570685 TGTGCAAATG
**
1570695 TATCGATACATGAGTTTATC
1 TATCGATACATGAACTTATC
*
1570715 TATCGATACATGAACTTATG
1 TATCGATACATGAACTTATC
1570735 TATCGAT
1 TATCGAT
1570742 GCTAGACCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TATCGATACATGAACTTATC
Found at i:1584155 original size:22 final size:22
Alignment explanation
Indices: 1584113--1584156 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1584103 CTCATTTAAG
* *
1584113 AATTTTAGGAATTGGATTCCCA
1 AATTTTAGGAATTGCACTCCCA
*
1584135 AATTTTAGGAATTTCACTCCCA
1 AATTTTAGGAATTGCACTCCCA
1584157 CTAGGAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
AATTTTAGGAATTGCACTCCCA
Found at i:1590037 original size:24 final size:24
Alignment explanation
Indices: 1590005--1590050 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1589995 AGAAATATTG
1590005 CTATGGAAATTTTAGCATTCTTGT
1 CTATGGAAATTTTAGCATTCTTGT
1590029 CTATGGAAATTTTAGCATTCTT
1 CTATGGAAATTTTAGCATTCTT
1590051 TTGTCATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (24 bp):
CTATGGAAATTTTAGCATTCTTGT
Found at i:1593272 original size:158 final size:159
Alignment explanation
Indices: 1592961--1593302 Score: 372
Period size: 158 Copynumber: 2.2 Consensus size: 159
1592951 GAAAAACACA
* * * * *
1592961 TTCTACTCATTGAGACACATGATATTGACACTTCGATTTTGAAAGAAAAGCTTTTGTCTCCACCA
1 TTCTCCTCATTGGGAAACATGATATTGACACTTCGATTTCGAAAGAAAAGCTTTTCTCTCCACCA
* * *
1593026 TTTTCCTTAGAATCAAAGTTTATCCCTTAAATAAGGAAAACTTAGATTCTAGTAATAATCCTTAT
66 TTTTCCTTAGAATCAAAGTTCATCCCTCAAATAAGGAAAACTTAGATTATAGTAATAATCCTTAT
* * *
1593091 TTTTTTCATGATTGGGGACCATAAACATG
131 TTTTATCATGATTAGGAACCATAAACATG
* * ** * *
1593120 TTTTCTTCATTGGGAAACATGATATTGATGCTTTGGTTTCGAAAGAAAAGCTTTTCTCT-CACCA
1 TTCTCCTCATTGGGAAACATGATATTGACACTTCGATTTCGAAAGAAAAGCTTTTCTCTCCACCA
* * *
1593184 TTTTCCTTAGAATCAGAGTTCATCCCTCAAGTGA-GACAAACATTA-ATTATCA-TAATAAT-CT
66 TTTTCCTTAGAATCAAAGTTCATCCCTCAAATAAGGA-AAAC-TTAGATTAT-AGTAATAATCCT
* * *
1593245 TCATTGTTTAT-GTGGTTAGGAATCATAAACATG
128 T-ATT-TTTATCATGATTAGGAACCATAAACATG
* *
1593278 TTCTCCTCATTTGGATACATGATAT
1 TTCTCCTCATTGGGAAACATGATAT
1593303 CAAAACTTTG
Statistics
Matches: 151, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
157 5 0.03
158 90 0.60
159 56 0.37
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (159 bp):
TTCTCCTCATTGGGAAACATGATATTGACACTTCGATTTCGAAAGAAAAGCTTTTCTCTCCACCA
TTTTCCTTAGAATCAAAGTTCATCCCTCAAATAAGGAAAACTTAGATTATAGTAATAATCCTTAT
TTTTATCATGATTAGGAACCATAAACATG
Found at i:1593312 original size:158 final size:158
Alignment explanation
Indices: 1593001--1593366 Score: 359
Period size: 158 Copynumber: 2.3 Consensus size: 158
1592991 CTTCGATTTT
* * * *
1593001 GAAAGAAAAGCTTTTGTCTCCACCATTTTCCTTAGAATCAAAGTTTATCCCTTAAATAAGGAAAA
1 GAAAGAAAAGCTTTTCTCT-CACCATTTTCCTTAGAATCAGAGTTCATCCCTCAAATAAGGAAAA
* * * * * *
1593066 CTTAGATTCTAGTAATAATCCTTATTTTTTTCATGATTGGGGACCATAAACATGTTTTCTTCATT
65 CTTAGATTATAGTAATAATCCTTATTTTTATCATGATTAGGAACCATAAACATGTTCTCCTCATT
** ** *
1593131 GGGAAACATGATATTGATGCTTTGGTTTC
130 GGGAAACATGATATCAAAACTTTGCTTTC
* *
1593160 GAAAGAAAAGCTTTTCTCTCACCATTTTCCTTAGAATCAGAGTTCATCCCTCAAGTGA-GACAAA
1 GAAAGAAAAGCTTTTCTCTCACCATTTTCCTTAGAATCAGAGTTCATCCCTCAAATAAGGA-AAA
* * *
1593224 CATTA-ATTATCA-TAATAAT-CTTCATTGTTTAT-GTGGTTAGGAATCATAAACATGTTCTCCT
65 C-TTAGATTAT-AGTAATAATCCTT-ATT-TTTATCATGATTAGGAACCATAAACATGTTCTCCT
* *
1593285 CATTTGGATACATGATATCAAAACTTTGCTTTC
126 CATTGGGAAACATGATATCAAAACTTTGCTTTC
** * * *
1593318 CTAAGAAAAGCTTATCT-TC-CCGTAATTTTCTTTAAAATCAGAGTTCATC
1 GAAAGAAAAGCTTTTCTCTCACC---ATTTTCCTTAGAATCAGAGTTCATC
1593367 TGTGAAATGA
Statistics
Matches: 172, Mismatches: 27, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
156 2 0.01
157 7 0.04
158 114 0.66
159 49 0.28
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (158 bp):
GAAAGAAAAGCTTTTCTCTCACCATTTTCCTTAGAATCAGAGTTCATCCCTCAAATAAGGAAAAC
TTAGATTATAGTAATAATCCTTATTTTTATCATGATTAGGAACCATAAACATGTTCTCCTCATTG
GGAAACATGATATCAAAACTTTGCTTTC
Found at i:1599270 original size:28 final size:28
Alignment explanation
Indices: 1599230--1599302 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
1599220 TAAAGCCGGA
* * *
1599230 GTTGGAGTATCCCC-TTGGAAGTAACGGG
1 GTTGGAGTATCCCCGAT-GAAATAACGAG
1599258 GTTGGAGTATCCCCGATGAAATAACGAG
1 GTTGGAGTATCCCCGATGAAATAACGAG
*
1599286 GTTGGAGTATCCTCGAT
1 GTTGGAGTATCCCCGAT
1599303 TATGAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GTTGGAGTATCCCCGATGAAATAACGAG
Found at i:1599349 original size:52 final size:52
Alignment explanation
Indices: 1599286--1599455 Score: 177
Period size: 52 Copynumber: 3.3 Consensus size: 52
1599276 AAATAACGAG
* *
1599286 GTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAACCGGA
* * ** *
1599338 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTTGGAAATAAAACC-GGA
* * * *
1599391 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAAATTGGTATTTTTG-GAAATAAAACCGGA
1599442 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1599456 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
51 3 0.03
52 77 0.79
53 17 0.18
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAACCGGA
Found at i:1599501 original size:27 final size:28
Alignment explanation
Indices: 1599438--1599513 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
1599428 GCGATAAAAC
*
1599438 CGGAGTTGGAGTATCCCCTCA-GAAATAA
1 CGGAGTTGGAGTATCCCC-GATGAAATAA
* *
1599466 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGAGTTGGAGTATCCCCGATGAAATAA
1599493 CGGAGTTGGAGTATCCCCGAT
1 CGGAGTTGGAGTATCCCCGAT
1599514 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (28 bp):
CGGAGTTGGAGTATCCCCGATGAAATAA
Found at i:1599525 original size:107 final size:104
Alignment explanation
Indices: 1599172--1599525 Score: 276
Period size: 107 Copynumber: 3.3 Consensus size: 104
1599162 CCCTCGAAAA
* * * * * *
1599172 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGAGTTGGAG
1 TAACGGAGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTT-GGAATAAAACCGGAGTTGGAG
* * *
1599237 TATCCCCTTGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
65 TATCCCC-TCGAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * *
1599279 TAAC-GAGGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGG
1 TAACGGA-GTTGGAGTATCCCCGATTATGAAAAATTAGTA-TTTTGG-AATAAAACCGGAGTTGG
* * ** * ** **
1599343 AGTAT-CCC-CG-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
63 AGTATCCCCTCGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * *
1599381 AAAACCAGGA-TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGT
1 -TAA-C-GGAGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTT-G-GAATAAAACCGGAGT
1599444 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAT
60 TGGAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATGAT
*
1599490 TAACGGAGTTGGAGTATCCCCGATTGTGAAGAAATT
1 TAACGGAGTTGGAGTATCCCCGATTATGAA-AAATT
1599526 GGTGTTTTTT
Statistics
Matches: 190, Mismatches: 36, Indels: 42
0.71 0.13 0.16
Matches are distributed among these distances:
102 1 0.01
103 4 0.02
104 48 0.25
105 16 0.08
106 23 0.12
107 62 0.33
108 32 0.17
109 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (104 bp):
TAACGGAGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAATAAAACCGGAGTTGGAGT
ATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:1599552 original size:55 final size:51
Alignment explanation
Indices: 1599493--1599628 Score: 148
Period size: 51 Copynumber: 2.6 Consensus size: 51
1599483 CGATGATTAA
* * *
1599493 CGGAGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATGAAAT
1 CGGAGTTGGAGTATCCCCGATTGTG-AGAAATTAGTG---TTTTGAAAATAAAAT
* *
1599548 CGGAGTTAGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAAT
1 CGGAGTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAAT
* *
1599599 CGGAGTTGGAATATCCTCGATTGTGGAGAA
1 CGGAGTTGGAGTATCCCCGATTGT-GAGAA
1599629 TTGATAAACT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
51 33 0.48
52 2 0.03
53 4 0.06
54 8 0.12
55 22 0.32
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (51 bp):
CGGAGTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAAT
Found at i:1599614 original size:51 final size:53
Alignment explanation
Indices: 1599286--1599620 Score: 176
Period size: 52 Copynumber: 6.3 Consensus size: 53
1599276 AAATAACGAG
* * * *
1599286 GTTGGAGTATCCTCGATTATGAA-AAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
* * *
1599338 GTTGGAGTATCCCCGATTA--AAGGAAAATTGGCG-TTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATTATGAA-G-AAATTAGTGTTTTTGAAAATAAAATC-GGA
* * ** *
1599391 -TTGGAGTATCCCCGATTGTGGAA-AAATTAGTGTTTTAG-CGATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
* *** * **** ** *
1599442 GTTGGAGTATCCCCTCAGA-AAT-AACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGA
1 GTTGGAGTAT-CCC-C-GATTATGAA-GAAATT--AGTGTTTTTGAAAATAAAATCGGA
* * * *
1599497 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATGAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTG--TTTTTGAAAATAAAATCGGA
*
1599552 GTTAGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGA
* *
1599603 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
1599621 GTGGAGAATT
Statistics
Matches: 213, Mismatches: 46, Indels: 49
0.69 0.15 0.16
Matches are distributed among these distances:
50 2 0.01
51 37 0.17
52 77 0.36
53 28 0.13
54 19 0.09
55 40 0.19
56 7 0.03
57 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:1602000 original size:13 final size:13
Alignment explanation
Indices: 1601982--1602007 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1601972 ACAAAGATCC
1601982 ATGTATCGATACA
1 ATGTATCGATACA
1601995 ATGTATCGATACA
1 ATGTATCGATACA
1602008 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1602003 original size:33 final size:33
Alignment explanation
Indices: 1601961--1602027 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1601951 AAAATTTCTA
***
1601961 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1601994 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1602027 A
1 A
1602028 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1602071 original size:19 final size:18
Alignment explanation
Indices: 1602047--1602114 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1602037 CAGTAGCTAA
1602047 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1602066 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1602081 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1602098 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1602115 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Done.