Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold194
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: 3945165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1023 characters in sequence are not A, C, G, or T
File 7 of 24
Found at i:1117062 original size:13 final size:13
Alignment explanation
Indices: 1117044--1117075 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1117034 ATAATCCCCC
*
1117044 TGTATCGATACAG
1 TGTATCGATACAA
1117057 TGTATCGATACAA
1 TGTATCGATACAA
1117070 TGTATC
1 TGTATC
1117076 AACAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1123251 original size:13 final size:13
Alignment explanation
Indices: 1123233--1123258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1123223 CAATTTTTTG
1123233 TGTATCGATACAT
1 TGTATCGATACAT
1123246 TGTATCGATACAT
1 TGTATCGATACAT
1123259 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1123273 original size:32 final size:33
Alignment explanation
Indices: 1123213--1123276 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1123203 TACAAGCCAA
** *
1123213 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1123246 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1123277 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1125282 original size:2 final size:2
Alignment explanation
Indices: 1125275--1125309 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1125265 TTTGCAAGGC
1125275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1125310 CTTCTAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1125893 original size:13 final size:13
Alignment explanation
Indices: 1125875--1125901 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1125865 TTTAAGGTTA
1125875 TATCAAATCAATG
1 TATCAAATCAATG
1125888 TATCAAATCAATG
1 TATCAAATCAATG
1125901 T
1 T
1125902 GAAAATAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TATCAAATCAATG
Found at i:1127322 original size:13 final size:13
Alignment explanation
Indices: 1127282--1127334 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1127272 CCGTTACAAG
1127282 CAATGTATCGATA
1 CAATGTATCGATA
1127295 CAA--T-TC-AT-
1 CAATGTATCGATA
1127303 C-ATGTATCGATA
1 CAATGTATCGATA
1127315 CAATGTATCGATA
1 CAATGTATCGATA
*
1127328 TAATGTA
1 CAATGTA
1127335 CCATGTATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 20 0.61
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1127322 original size:33 final size:33
Alignment explanation
Indices: 1127282--1127350 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1127272 CCGTTACAAG
*
1127282 CAATGTATCGATACAAT-TCATCATGTATCGATA
1 CAATGTATCGATACAATGT-ACCATGTATCGATA
*
1127315 CAATGTATCGATATAATGTACCATGTATCGATA
1 CAATGTATCGATACAATGTACCATGTATCGATA
1127348 CAA
1 CAA
1127351 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCGATA
Found at i:1127418 original size:13 final size:13
Alignment explanation
Indices: 1127400--1127426 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1127390 ACAATTGTCC
1127400 ATGTATCGATACA
1 ATGTATCGATACA
1127413 ATGTATCGATACA
1 ATGTATCGATACA
1127426 A
1 A
1127427 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1136341 original size:13 final size:13
Alignment explanation
Indices: 1136323--1136348 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1136313 ATAATCACCC
1136323 TGTATCGATACAA
1 TGTATCGATACAA
1136336 TGTATCGATACAA
1 TGTATCGATACAA
1136349 AGAAAAAATG
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):
TGTATCGATACAA
Found at i:1138447 original size:15 final size:15
Alignment explanation
Indices: 1138427--1138457 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1138417 ATTTCGTTTG
*
1138427 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1138442 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1138457 G
1 G
1138458 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1146061 original size:13 final size:13
Alignment explanation
Indices: 1146043--1146073 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1146033 ACAATTCATC
*
1146043 ATGTATCGATACA
1 ATGTATCAATACA
1146056 ATGTATCAATACA
1 ATGTATCAATACA
1146069 ATGTA
1 ATGTA
1146074 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:1146063 original size:20 final size:20
Alignment explanation
Indices: 1146003--1146057 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
1145993 ATTACAGGCA
1146003 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
1146023 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
1146043 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1146058 GTATCAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:1146068 original size:33 final size:33
Alignment explanation
Indices: 1146023--1146089 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
1146013 ACAATTCATC
* *
1146023 ATGTATCGATACAAT-TCATCATGTATCGATACA
1 ATGTATCAATACAATGT-ACCATGTATCGATACA
1146056 ATGTATCAATACAATGTACCATGTATCGATACA
1 ATGTATCAATACAATGTACCATGTATCGATACA
1146089 A
1 A
1146090 ATAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (33 bp):
ATGTATCAATACAATGTACCATGTATCGATACA
Found at i:1146143 original size:19 final size:20
Alignment explanation
Indices: 1146119--1146170 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1146109 TGCCAGTTTC
*
1146119 ATGTATCGATACAATGAAT-
1 ATGTATCGATACAAAGAATA
*
1146138 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGAATA
1146158 ATGTATCGATACA
1 ATGTATCGATACA
1146171 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACAAAGAATA
Found at i:1148029 original size:20 final size:20
Alignment explanation
Indices: 1148004--1148048 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1147994 TTCAACAATT
*
1148004 TGTATCGATAAATAAGTGAA
1 TGTATCGATAAATAAGTAAA
*
1148024 TGTATCGATACATAAGTAAA
1 TGTATCGATAAATAAGTAAA
1148044 TGTAT
1 TGTAT
1148049 TAATACTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTATCGATAAATAAGTAAA
Found at i:1148054 original size:20 final size:20
Alignment explanation
Indices: 1148004--1148054 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1147994 TTCAACAATT
* * *
1148004 TGTATCGATAAATAAGTGAA
1 TGTATCAATACATAAGTAAA
*
1148024 TGTATCGATACATAAGTAAA
1 TGTATCAATACATAAGTAAA
*
1148044 TGTATTAATAC
1 TGTATCAATAC
1148055 TAGACCATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (20 bp):
TGTATCAATACATAAGTAAA
Found at i:1150676 original size:78 final size:79
Alignment explanation
Indices: 1150522--1150814 Score: 224
Period size: 77 Copynumber: 3.7 Consensus size: 79
1150512 AAATTTTTAA
* * * * *
1150522 ATTTTTAATTCCAAAAGCATCCAATTTTTCACCATCGGGGATACTCCAACCTCATCATCTCTGAG
1 ATTTTTAATTCCAAAATC-TCTAATTTTTCACCATCAGGGATACTCCAACCCCATCATCTCTGAA
*
1150587 TGGATACTCCAACCTC
65 AGGATACTCCAACC-C
* * *
1150603 ATTTTTACTTCCAAAATCTCTAA-TTTTCACCATC-GGGATACTCCAACCCCATTAT-TTTGCAA
1 ATTTTTAATTCCAAAATCTCTAATTTTTCACCATCAGGGATACTCCAACCCCATCATCTCTG-AA
**
1150665 AGGATGGTCCAACCC
65 AGGATACTCCAACCC
* * * * * * * * * **
1150680 TTTTTTATTTCTAAAATAT-TAATTTTTCACCATCAAGGATACTCTAA-CCTATC-TTTCCGAGG
1 ATTTTTAATTCCAAAATCTCTAATTTTTCACCATCAGGGATACTCCAACCCCATCATCTCTGAAA
*
1150742 GGATACTCCAATCTC
66 GGATACTCCAA-CCC
* * * * * *
1150757 ATTTTTAGTTTCAAAATAT-TAAAATTTTCATC-TCAGGGATACTCCAACCCCACCATCT
1 ATTTTTAATTCCAAAATCTCT-AATTTTTCACCATCAGGGATACTCCAACCCCATCATCT
1150815 TCGAGGGGAC
Statistics
Matches: 168, Mismatches: 36, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
76 14 0.08
77 67 0.40
78 54 0.32
79 13 0.08
80 4 0.02
81 16 0.10
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (79 bp):
ATTTTTAATTCCAAAATCTCTAATTTTTCACCATCAGGGATACTCCAACCCCATCATCTCTGAAA
GGATACTCCAACCC
Found at i:1152469 original size:99 final size:97
Alignment explanation
Indices: 1152353--1152582 Score: 221
Period size: 99 Copynumber: 2.4 Consensus size: 97
1152343 CGGGCTAGAC
* * * * * *
1152353 TATCCCCTT-GATGGAATGGGGTTGGAGTATCCTTAACGATGATAATTTAGGCGAAGATAAGATT
1 TATCCCCTTGGA-AGAATGGGGTTGGAGTATCCTTAACGATGACAATTCAAGCAAAAATAAGATT
* * * *
1152417 TAAATCTTGACAAGTTTAAAAAAATGGGGTTGGAA
65 CAAATCTTCACAAG-TT-AAAAAACGAGGTTGGAA
* * * * *
1152452 TATCCCCTTGGAAGAATGGGATTGGATTATCCCTAATGATGACAATTCAAGTAAAAATAAGATTC
1 TATCCCCTTGGAAGAATGGGGTTGGAGTATCCTTAACGATGACAATTCAAGCAAAAATAAGATTC
* * *
1152517 AAATCTTCATAAGTTCAAAAACGAGGTTGGAG
66 AAATCTTCACAAGTTAAAAAACGAGGTTGGAA
* * *
1152549 TAT-CTCTTCGAAAGAATGGGGTTAGAGTATCCTT
1 TATCCCCTT-GGAAGAATGGGGTTGGAGTATCCTT
1152583 GATGAATAAA
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
96 4 0.04
97 36 0.34
98 2 0.02
99 61 0.58
100 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (97 bp):
TATCCCCTTGGAAGAATGGGGTTGGAGTATCCTTAACGATGACAATTCAAGCAAAAATAAGATTC
AAATCTTCACAAGTTAAAAAACGAGGTTGGAA
Found at i:1154170 original size:21 final size:20
Alignment explanation
Indices: 1154140--1154216 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 20
1154130 TTCTACAATT
1154140 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGTAAA
* * *
1154161 TGTATTGATACATAAGTGAA
1 TGTATCGATACAAAAGTAAA
**
1154181 TGTATCGATAC-ATGGCTAAAA
1 TGTATCGATACAAAAG-T-AAA
1154202 TGTATCGATACAAAA
1 TGTATCGATACAAAA
1154217 TCACCCTGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.02
20 16 0.37
21 25 0.58
22 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAAAGTAAA
Found at i:1154184 original size:20 final size:21
Alignment explanation
Indices: 1154140--1154193 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1154130 TTCTACAATT
*
1154140 TGTATCGATACAAACAGTAAA
1 TGTATCGATACATACAGTAAA
* *
1154161 TGTATTGATACATA-AGTGAA
1 TGTATCGATACATACAGTAAA
1154181 TGTATCGATACAT
1 TGTATCGATACAT
1154194 GGCTAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:1156955 original size:78 final size:79
Alignment explanation
Indices: 1156804--1156989 Score: 250
Period size: 78 Copynumber: 2.4 Consensus size: 79
1156794 CCAATCTCAT
* * ** * * *
1156804 TTTTATTTTCAAAATTTTAAATTTTTCATCTTGTAGATACTCCAACCCCATCAATTCCGAGGGGA
1 TTTTATTTTCAAAATATTAAATTTTTCTTCTTCAAGATACTCCAACCCCATCAAGTCCAAGGAGA
1156869 TACTCCAA-CCTTGC
66 TACTCCAACCCTT-C
* **
1156883 TTTTATTTCCAAAATGCTAAATTTTTCTTC-TCAAGATACTCCAACCCCATCAAGTCCAAGGAGA
1 TTTTATTTTCAAAATATTAAATTTTTCTTCTTCAAGATACTCCAACCCCATCAAGTCCAAGGAGA
*
1156947 TACTCCAACCCTTT
66 TACTCCAACCCTTC
1156961 TTTTATTTTCAAAATATTAAATTTTTCTT
1 TTTTATTTTCAAAATATTAAATTTTTCTT
1156990 GAGGGTACTC
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
78 63 0.68
79 30 0.32
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (79 bp):
TTTTATTTTCAAAATATTAAATTTTTCTTCTTCAAGATACTCCAACCCCATCAAGTCCAAGGAGA
TACTCCAACCCTTC
Found at i:1157165 original size:79 final size:79
Alignment explanation
Indices: 1156725--1157166 Score: 332
Period size: 79 Copynumber: 5.6 Consensus size: 79
1156715 CCAACCCCGC
* * * * *
1156725 TTTTATTTCTAAAATATTAAAATTTTCATTTCGGGGATACTCCAACCCCCTTATTTATGAGGGGA
1 TTTTATTTC-AAAATATTAAAATTTTCATCTCGAGGATACTCCAACCCCGTTATTTCTGAGGAGA
*
1156790 TACTCCAA-TCTCAT
65 TACTCCAACCCTCAT
* * * * * * * *
1156804 TTTTATTTTCAAAATTTTAAATTTTTCATCTTGTA-GATACTCCAACCCCATCAATTCCGAGGGG
1 TTTTA-TTTCAAAATATTAAAATTTTCATCTCG-AGGATACTCCAACCCCGTTATTTCTGAGGAG
*
1156868 ATACTCCAACCTTGC--
64 ATACTCCAACCCT-CAT
** * * * * * ** **
1156883 TTTTATTTCCAAAATGCTAAATTTTTCTTCTC-AAGATACTCCAACCCCATCAAGTCCAAGGAGA
1 TTTTATTT-CAAAATATTAAAATTTTCATCTCGAGGATACTCCAACCCCGTTATTTCTGAGGAGA
*
1156947 TACTCCAACCCT-TT
65 TACTCCAACCCTCAT
* * * *
1156961 TTTTATTTTCAAAATATT-AAATTTT--TCTTGAGGGTACTCCAACCTCGTTATTTTTGAGGAGA
1 TTTTA-TTTCAAAATATTAAAATTTTCATCTCGAGGATACTCCAACCCCGTTATTTCTGAGGAGA
* *
1157023 TAATCCAA-GCTCAT
65 TACTCCAACCCTCAT
** * * * * *
1157037 TTTTATTTCCAAAA-ATATCGATTTTTCACCTTGGGGATACTCCAACCCCGTTATTTTTGAGGAG
1 TTTTATTT-CAAAATAT-TAAAATTTTCATCTCGAGGATACTCCAACCCCGTTATTTCTGAGGAG
*
1157101 ATACTCTAACCCT-AT
64 ATACTCCAACCCTCAT
* *
1157116 TTTCAATTCAAAAATATTAAAATTTTCATCTCGAGGATACTCCAACCCCGT
1 TTTTATTTC-AAAATATTAAAATTTTCATCTCGAGGATACTCCAACCCCGT
1157167 AATCCGAAGG
Statistics
Matches: 290, Mismatches: 54, Indels: 38
0.76 0.14 0.10
Matches are distributed among these distances:
75 10 0.03
76 41 0.14
77 12 0.04
78 54 0.19
79 163 0.56
80 9 0.03
81 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (79 bp):
TTTTATTTCAAAATATTAAAATTTTCATCTCGAGGATACTCCAACCCCGTTATTTCTGAGGAGAT
ACTCCAACCCTCAT
Found at i:1157982 original size:19 final size:20
Alignment explanation
Indices: 1157934--1157984 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1157924 CACACCCAAA
1157934 TGTATCGATACATATTGCTT
1 TGTATCGATACATATTGCTT
* * *
1157954 GGTATTGATACATGTT-CTT
1 TGTATCGATACATATTGCTT
1157973 TGTATCGATACA
1 TGTATCGATACA
1157985 CCATAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATATTGCTT
Found at i:1158067 original size:20 final size:20
Alignment explanation
Indices: 1158042--1158080 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1158032 TGTTCATAAT
1158042 TGAATTGTATCGATACATTA
1 TGAATTGTATCGATACATTA
1158062 TGAATTGTATCGATACATT
1 TGAATTGTATCGATACATT
1158081 GAGCCCAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
TGAATTGTATCGATACATTA
Found at i:1158105 original size:52 final size:52
Alignment explanation
Indices: 1158046--1158148 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
1158036 CATAATTGAA
* *
1158046 TTGTATCGATACATTATGAATTGTATCGATACATTGAGCCCAACGGCTATAG
1 TTGTATCGATACATGATGAATTGTATCAATACATTGAGCCCAACGGCTATAG
* *
1158098 TTGTATCGATACATGGTGGATTGTATCAATACATTGAGCCCAACGGCTATA
1 TTGTATCGATACATGATGAATTGTATCAATACATTGAGCCCAACGGCTATA
1158149 ATTTCAAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (52 bp):
TTGTATCGATACATGATGAATTGTATCAATACATTGAGCCCAACGGCTATAG
Found at i:1159763 original size:12 final size:12
Alignment explanation
Indices: 1159746--1159771 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1159736 CGTCCAAGAG
1159746 GATAATGATGAT
1 GATAATGATGAT
1159758 GATAATGATGAT
1 GATAATGATGAT
1159770 GA
1 GA
1159772 AGAGCAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (12 bp):
GATAATGATGAT
Found at i:1160533 original size:73 final size:73
Alignment explanation
Indices: 1160414--1160564 Score: 248
Period size: 73 Copynumber: 2.1 Consensus size: 73
1160404 TAAATCTTAT
* *
1160414 TTTCACTGTTCATCACTATTCATGTATCGATACGTCACTGTTCATCACTATACATTAAGCCCAAC
1 TTTCACTGTCCATCACTATTCATGTATCGATACATCACTGTTCATCACTATACATTAAGCCCAAC
1160479 GGCTATAA
66 GGCTATAA
* * * *
1160487 TTTCACTGTCCATCACTGTTCATGTATCGATATATCACTGTTCATCATTATACATTGAGCCCAAC
1 TTTCACTGTCCATCACTATTCATGTATCGATACATCACTGTTCATCACTATACATTAAGCCCAAC
1160552 GGCTATAA
66 GGCTATAA
1160560 TTTCA
1 TTTCA
1160565 AATGCATGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (73 bp):
TTTCACTGTCCATCACTATTCATGTATCGATACATCACTGTTCATCACTATACATTAAGCCCAAC
GGCTATAA
Found at i:1162179 original size:21 final size:20
Alignment explanation
Indices: 1162154--1162192 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1162144 TTAAGATGAT
* *
1162154 GTTGATGAAGATGATGAAAAG
1 GTTGAGGAA-ATGAAGAAAAG
1162175 GTTGAGGAAATGAAGAAA
1 GTTGAGGAAATGAAGAAA
1162193 TGGCTATACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.21
Consensus pattern (20 bp):
GTTGAGGAAATGAAGAAAAG
Found at i:1162633 original size:21 final size:21
Alignment explanation
Indices: 1162609--1162667 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1162599 TAATATTCTT
* *
1162609 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
1162630 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** *
1162651 GAGGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
1162668 GTTGCAAGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:1164238 original size:32 final size:32
Alignment explanation
Indices: 1164175--1164242 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
1164165 ATTTTTCTAG
*
1164175 ATTGTATCGATATAATTAAATTTATATCGATAC
1 ATTGTATCGATACAATTAAA-TTATATCGATAC
*
1164208 ATTGTATCGATACAATTTTAA-TATATCGATAC
1 ATTGTATCGATACAA-TTAAATTATATCGATAC
1164240 ATT
1 ATT
1164243 ACTCTGGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 14 0.44
33 14 0.44
34 4 0.12
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (32 bp):
ATTGTATCGATACAATTAAATTATATCGATAC
Found at i:1166083 original size:13 final size:13
Alignment explanation
Indices: 1166065--1166089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1166055 GTTTTGCTTA
1166065 GTATCGATACATT
1 GTATCGATACATT
1166078 GTATCGATACAT
1 GTATCGATACAT
1166090 AAACTGGCAG
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):
GTATCGATACATT
Found at i:1166199 original size:71 final size:72
Alignment explanation
Indices: 1166114--1166262 Score: 219
Period size: 71 Copynumber: 2.1 Consensus size: 72
1166104 TAAATCTCAT
* * * * *
1166114 TTTCACTGTTCATCACTATTTATGTATCGATATATCACTGTTCAT-CTATACATTGAGCCCAACG
1 TTTCACTATCCATCACTATTCATGTATCGATACATCACTGTTCATACTATACATTGAGCCCAACA
1166178 GCTATAA
66 GCTATAA
* *
1166185 TTTCACTATCCATCACTGTTCATGTATCGATACATCATTGTTCATCACTATACATTGAGCCCAAC
1 TTTCACTATCCATCACTATTCATGTATCGATACATCACTGTTCAT-ACTATACATTGAGCCCAAC
1166250 AGCTATAA
65 AGCTATAA
1166258 TTTCA
1 TTTCA
1166263 AATGCATATA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 39 0.57
73 30 0.43
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (72 bp):
TTTCACTATCCATCACTATTCATGTATCGATACATCACTGTTCATACTATACATTGAGCCCAACA
GCTATAA
Found at i:1171026 original size:10 final size:10
Alignment explanation
Indices: 1171000--1171029 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1170990 TGTAAATTAG
*
1171000 ATGTTTATGA
1 ATGTTTTTGA
1171010 ATGTTTTTGA
1 ATGTTTTTGA
1171020 ATGTTTTTGA
1 ATGTTTTTGA
1171030 TTGAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (10 bp):
ATGTTTTTGA
Found at i:1173901 original size:52 final size:52
Alignment explanation
Indices: 1173840--1173947 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 52
1173830 TTCATAATTG
* ** *
1173840 AATTGTATCGATAGATTATGAATTGTATCGATACATTGAGCCCAACGGCTAT
1 AATTGTATCGATACAAGATGAATGGTATCGATACATTGAGCCCAACGGCTAT
* *
1173892 AATTGTATCGATACAAGGTGAATGGTATCGATACATTGAGCCTAACGGCTAT
1 AATTGTATCGATACAAGATGAATGGTATCGATACATTGAGCCCAACGGCTAT
1173944 AATT
1 AATT
1173948 TCAAATGCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (52 bp):
AATTGTATCGATACAAGATGAATGGTATCGATACATTGAGCCCAACGGCTAT
Found at i:1174323 original size:52 final size:52
Alignment explanation
Indices: 1174262--1174369 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 52
1174252 TTCATAATTG
* ** *
1174262 AATTGTATCGATAGATTATGAATTGTATCGATACATTGAGCCCAACGGCTAT
1 AATTGTATCGATACAAGATGAATGGTATCGATACATTGAGCCCAACGGCTAT
* *
1174314 AATTGTATCGATACAAGGTGAATGGTATCGATACATTGAGCCTAACGGCTAT
1 AATTGTATCGATACAAGATGAATGGTATCGATACATTGAGCCCAACGGCTAT
1174366 AATT
1 AATT
1174370 TCAAATGCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (52 bp):
AATTGTATCGATACAAGATGAATGGTATCGATACATTGAGCCCAACGGCTAT
Found at i:1174516 original size:422 final size:422
Alignment explanation
Indices: 1173732--1174566 Score: 1661
Period size: 422 Copynumber: 2.0 Consensus size: 422
1173722 CCCTTGAATG
1173732 TATCGATACATATTGCTTGGTATCGATACATGTCCTTTGTATTGATACACCATAAAATGTATTGA
1 TATCGATACATATTGCTTGGTATCGATACATGTCCTTTGTATTGATACACCATAAAATGTATTGA
1173797 TAGATACAACTGGCAGTAGCTACCCCACCACTGTTCATAATTGAATTGTATCGATAGATTATGAA
66 TAGATACAACTGGCAGTAGCTACCCCACCACTGTTCATAATTGAATTGTATCGATAGATTATGAA
1173862 TTGTATCGATACATTGAGCCCAACGGCTATAATTGTATCGATACAAGGTGAATGGTATCGATACA
131 TTGTATCGATACATTGAGCCCAACGGCTATAATTGTATCGATACAAGGTGAATGGTATCGATACA
1173927 TTGAGCCTAACGGCTATAATTTCAAATGCATTGTATCGATACATTATGAATTGTATCAATACATA
196 TTGAGCCTAACGGCTATAATTTCAAATGCATTGTATCGATACATTATGAATTGTATCAATACATA
1173992 GGAGTGTGTATGCACGAAATTAAGCTCCCAACAAGTTAACAACGGCTACAAATACAATCATTCCA
261 GGAGTGTGTATGCACGAAATTAAGCTCCCAACAAGTTAACAACGGCTACAAATACAATCATTCCA
*
1174057 CCTCCAATGGATATGTCAACATTCTAGCTTATAAATATGAGCTTTCATCAGCTGAAGATTAACAA
326 CCTCCAACGGATATGTCAACATTCTAGCTTATAAATATGAGCTTTCATCAGCTGAAGATTAACAA
1174122 CAAATATCAAGAAAGCTAAGAAAGCTTATAAA
391 CAAATATCAAGAAAGCTAAGAAAGCTTATAAA
1174154 TATCGATACATATTGCTTGGTATCGATACATGTCCTTTGTATTGATACACCATAAAATGTATTGA
1 TATCGATACATATTGCTTGGTATCGATACATGTCCTTTGTATTGATACACCATAAAATGTATTGA
1174219 TAGATACAACTGGCAGTAGCTACCCCACCACTGTTCATAATTGAATTGTATCGATAGATTATGAA
66 TAGATACAACTGGCAGTAGCTACCCCACCACTGTTCATAATTGAATTGTATCGATAGATTATGAA
1174284 TTGTATCGATACATTGAGCCCAACGGCTATAATTGTATCGATACAAGGTGAATGGTATCGATACA
131 TTGTATCGATACATTGAGCCCAACGGCTATAATTGTATCGATACAAGGTGAATGGTATCGATACA
1174349 TTGAGCCTAACGGCTATAATTTCAAATGCATTGTATCGATACATTATGAATTGTATCAATACATA
196 TTGAGCCTAACGGCTATAATTTCAAATGCATTGTATCGATACATTATGAATTGTATCAATACATA
1174414 GGAGTGTGTATGCACGAAATTAAGCTCCCAACAAGTTAACAACGGCTACAAATACAATCATTCCA
261 GGAGTGTGTATGCACGAAATTAAGCTCCCAACAAGTTAACAACGGCTACAAATACAATCATTCCA
1174479 CCTCCAACGGATATGTCAACATTCTAGCTTATAAATATGAGCTTTCATCAGCTGAAGATTAACAA
326 CCTCCAACGGATATGTCAACATTCTAGCTTATAAATATGAGCTTTCATCAGCTGAAGATTAACAA
1174544 CAAATATCAAGAAAGCTAAGAAA
391 CAAATATCAAGAAAGCTAAGAAA
1174567 TTCAAGTTCT
Statistics
Matches: 412, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
422 412 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (422 bp):
TATCGATACATATTGCTTGGTATCGATACATGTCCTTTGTATTGATACACCATAAAATGTATTGA
TAGATACAACTGGCAGTAGCTACCCCACCACTGTTCATAATTGAATTGTATCGATAGATTATGAA
TTGTATCGATACATTGAGCCCAACGGCTATAATTGTATCGATACAAGGTGAATGGTATCGATACA
TTGAGCCTAACGGCTATAATTTCAAATGCATTGTATCGATACATTATGAATTGTATCAATACATA
GGAGTGTGTATGCACGAAATTAAGCTCCCAACAAGTTAACAACGGCTACAAATACAATCATTCCA
CCTCCAACGGATATGTCAACATTCTAGCTTATAAATATGAGCTTTCATCAGCTGAAGATTAACAA
CAAATATCAAGAAAGCTAAGAAAGCTTATAAA
Found at i:1180287 original size:30 final size:31
Alignment explanation
Indices: 1180236--1180360 Score: 85
Period size: 30 Copynumber: 4.1 Consensus size: 31
1180226 AGTAAAGTAA
* * *
1180236 CCTT-TTCAAACTCTATGACTCAGTGGCAT-
1 CCTTCTTCAAAGTCCATAACTCAGTGGCATC
* * * *
1180265 CTTTTTTTAAAGTCCATAACTCAGTAGCATC
1 CCTTCTTCAAAGTCCATAACTCAGTGGCATC
* * *
1180296 CCTTCTTCAAAGTCCATGACTTAGTGGCATT
1 CCTTCTTCAAAGTCCATAACTCAGTGGCATC
* * ** * *
1180327 TCTT-TTCAAATTCCACGACTCTGTGGCACC
1 CCTTCTTCAAAGTCCATAACTCAGTGGCATC
1180357 CCTT
1 CCTT
1180361 TTATCCTTTT
Statistics
Matches: 73, Mismatches: 21, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
29 3 0.04
30 43 0.59
31 27 0.37
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (31 bp):
CCTTCTTCAAAGTCCATAACTCAGTGGCATC
Found at i:1180360 original size:61 final size:60
Alignment explanation
Indices: 1180236--1180362 Score: 139
Period size: 61 Copynumber: 2.1 Consensus size: 60
1180226 AGTAAAGTAA
* * * *
1180236 CCTTTTCAAACTCTATGACTCAGTGGCATCTTTTTTTAAAGTCCATAACTCAGTAGCATC
1 CCTTTTCAAACTCCATGACTCAGTGGCATCTTTTTTCAAAGTCCACAACTCAGTAGCACC
* * * * * *
1180296 CCTTCTTCAAAGTCCATGACTTAGTGGCAT-TTCTTTTCAAATTCCACGACTCTGTGGCACC
1 CCTT-TTCAAACTCCATGACTCAGTGGCATCTT-TTTTCAAAGTCCACAACTCAGTAGCACC
1180357 CCTTTT
1 CCTTTT
1180363 ATCCTTTTAG
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
60 8 0.15
61 47 0.85
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.37
Consensus pattern (60 bp):
CCTTTTCAAACTCCATGACTCAGTGGCATCTTTTTTCAAAGTCCACAACTCAGTAGCACC
Found at i:1180554 original size:62 final size:62
Alignment explanation
Indices: 1180393--1181068 Score: 695
Period size: 62 Copynumber: 10.9 Consensus size: 62
1180383 ACAAGACTTC
* ** * * * * *
1180393 TTTT-CTTTCTAAAGCCTACATGAGTTGGTAGCACTTTTTAGTCCTCAAAGAGAAAGATACCTT
1 TTTTCCTTT-TAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC-T
* * *
1180456 TTTTCCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCACGATGCCT
1 TTTTCC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
* *
1180519 TTTTCCTTTTAAAGCCCACACAAGTTGGTGACACCTTTTAGTCTTCAAAGAGCAGGATGCCT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
* ** *
1180581 TTTTCTTTTTAAAGCCCACATGAGTTGGTGGCATCTTTTAGTCCTCAAAGAGCAGGA--CAC-
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGC-CT
* * * * * * * **
1180641 -TTTCCTTTAAAAGCCCACGCAAGCTAGTGGCACCATTTAGTCCTCAAATAGCATGACACCT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
* * * * * *
1180702 TTTTTCTTTTCCAAGCCCACACGAGTTGGTAGCACCCTTTAGTCCTCAAAGAGCAGGATGCCC
1 TTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
* * * * **
1180765 TTTTCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTAGTCTTCAAAAAGCAGGACACC-
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
* * *
1180826 TTTTCCTTTTTAAAGCCCACACAATTTGGTGGCACCTTTTAGTCCTTAAAGAGTAGGA--CCT
1 TTTTCC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
* ** *
1180887 TTTTCTTTTTCTTTCAAAGCCCGTAGAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGC
1 TTTTC-----CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGC
1180952 CT
61 CT
* ** * * *
1180954 TTTTCTTTTTAAAGCCCACATGAGCTAGTGGCACC-TTTAGTCCTCAAAGAGTAGGATGCCT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
* * * *
1181015 TTTTCTTTTTAAATCCCATAAAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCA
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCA
1181069 TGACACTTTT
Statistics
Matches: 510, Mismatches: 85, Indels: 37
0.81 0.13 0.06
Matches are distributed among these distances:
59 45 0.09
60 4 0.01
61 66 0.13
62 235 0.46
63 59 0.12
64 45 0.09
65 47 0.09
66 1 0.00
67 8 0.02
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (62 bp):
TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
Found at i:1180745 original size:246 final size:246
Alignment explanation
Indices: 1180429--1181084 Score: 822
Period size: 246 Copynumber: 2.7 Consensus size: 246
1180419 GGTAGCACTT
* *
1180429 TTTAGTCCTCAAAGAGAAAGATACCTTTTTTCCTTTTTAAAGCCCACACGAGTTGGTGGCACCTT
1 TTTAGTCCTCAAAGAGCAAGATACCTTTTTT-CTTTTTAAAGCCCACACGAGTTGGTGGCACCCT
* * * * *
1180494 TTAGTCCTCAAAAAGCACGATGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGACACCTTTTA
65 TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTA
** * ** *
1180559 GTCTTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCATCTTTTAGTC
130 GTCTTCAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTC
1180624 CTCAAAGAGCAGGACAC-TTTC-CTTTAAAAGCCC-ACGCAAGCTAGTGGCACCA
195 CTCAAAGAGCAGGAC-CTTTTCTCTTTAAAAGCCCGA-G-AAGCTAGTGGCACCA
* * * ** *
1180676 TTTAGTCCTCAAATAGCATGACACCTTTTTTCTTTTCCAAGCCCACACGAGTTGGTAGCACCCTT
1 TTTAGTCCTCAAAGAGCAAGATACCTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTT
*
1180741 TAGTCCTCAAAGAGCAGGATGCCCTTTTCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTAG
66 TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTAG
* *
1180806 TCTTCAAAAAGCAGGACACCTTTTCCTTTTTAAAGCCCACACAATTTGGTGGCACCTTTTAGTCC
131 TCTTCAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCC
* * * * * *
1180871 TTAAAGAGTAGGACCTTTTTCTTTTTCTTTCAAAGCCCGTAGAAGTTGGTGGCACCT
196 TCAAAGAGCAGGACC-TTTTC----TCTTTAAAAGCCCG-AGAAGCTAGTGGCACCA
* * * * *
1180928 TTTAGTCCTCAAAGAGCAGGATGCC-TTTTTCTTTTTAAAGCCCACATGAGCTAGTGGCA-CCTT
1 TTTAGTCCTCAAAGAGCAAGATACCTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTT
* * * *
1180991 TAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTTAAATCCCATAAAAGTTGGTGGCACCTTTTAG
66 TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTAG
* *
1181056 TCCTCAAAGAGCATGACA-CTTTT-CTTTTT
131 TCTTCAAAGAGCAGGACACCTTTTCCTTTTT
1181085 CTTTCTTTAA
Statistics
Matches: 354, Mismatches: 46, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
245 1 0.00
246 158 0.45
247 31 0.09
248 6 0.02
249 5 0.01
250 79 0.22
251 28 0.08
252 44 0.12
253 1 0.00
254 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (246 bp):
TTTAGTCCTCAAAGAGCAAGATACCTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTT
TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTAG
TCTTCAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCC
TCAAAGAGCAGGACCTTTTCTCTTTAAAAGCCCGAGAAGCTAGTGGCACCA
Found at i:1180758 original size:184 final size:184
Alignment explanation
Indices: 1180393--1181078 Score: 779
Period size: 188 Copynumber: 3.7 Consensus size: 184
1180383 ACAAGACTTC
* * * * * *
1180393 TTTTCTTTCTAAAGCCTACATGAGTTGGTAGCACTTTTTAGTCCTCAAAGAGAAAGATACCTTTT
1 TTTTCTTTTTAAAGCCCACATGAGTTGGTGGCAC-TTTTAGTCCTCAAAGAGCAGGACACC--TT
* *
1180458 TTCCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCACGATGCCTTTTT
63 TTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCACGA-CCCTTTTT
* * *
1180523 CCTTTT-AAAGCCCACACAAGTTGGTGACACCTTTTAGTCTTCAAAGAGCAGGATGCCT
127 TCTTTTCAAAGCCCACACGAGTTGGTG-CACCTTTTAGTCCTCAAAGAGCAGGATGCCT
1180581 TTTTCTTTTTAAAGCCCACATGAGTTGGTGGCATCTTTTAGTCCTCAAAGAGCAGGACA-C-TTT
1 TTTTCTTTTTAAAGCCCACATGAGTTGGTGGCA-CTTTTAGTCCTCAAAGAGCAGGACACCTTTT
* * * * * * *
1180644 CC-TTTAAAAGCCCACGCAAGCTAGTGGCACCATTTAGTCCTCAAATAGCATGACACCTTTTTTC
65 CCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCACGAC-CCTTTTTTC
* * *
1180708 TTTTCCAAGCCCACACGAGTTGGTAGCACCCTTTAGTCCTCAAAGAGCAGGATGCCC
129 TTTTCAAAGCCCACACGAGTTGGT-GCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
* ** * *
1180765 TTTTCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTAGTCTTCAAAAAGCAGGACACCTTTT
1 TTTTCTTTTTAAAGCCCACATGAGTTGGTGGCA-CTTTTAGTCCTCAAAGAGCAGGACACCTTTT
* * * * * *
1180830 CCTTTTTAAAGCCCACACAATTTGGTGGCACCTTTTAGTCCTTAAAGAGTAGGACCTTTTTCTTT
65 CCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCACGACC-CTTT-TTT
* **
1180895 TTCTTTCAAAGCCCGTA-GAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
128 CT-TTTCAAAGCCCACACG-AGTTGGT-GCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
* * * * ** *
1180954 TTTTCTTTTTAAAGCCCACATGAGCTAGTGGCACCTTTAGTCCTCAAAGAGTAGGATGCCTTTTT
1 TTTTCTTTTTAAAGCCCACATGAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGGACACCTTTTC
* * * * * *
1181019 CTTTTTAAATCCCATAAAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCATGACACTTTT
66 CTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCACGACCCTTTT
1181079 CTTTTTCTTT
Statistics
Matches: 421, Mismatches: 66, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
183 55 0.13
184 103 0.24
185 2 0.00
186 7 0.02
187 49 0.12
188 128 0.30
189 77 0.18
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (184 bp):
TTTTCTTTTTAAAGCCCACATGAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGGACACCTTTTC
CTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCACGACCCTTTTTTCTT
TTCAAAGCCCACACGAGTTGGTGCACCTTTTAGTCCTCAAAGAGCAGGATGCCT
Found at i:1181846 original size:21 final size:21
Alignment explanation
Indices: 1181817--1181858 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1181807 GTTACATTTT
1181817 TGCCATTGATGTATCGATACA
1 TGCCATTGATGTATCGATACA
*
1181838 TGCCTTTGATGTATCGATACA
1 TGCCATTGATGTATCGATACA
1181859 AGGTCTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (21 bp):
TGCCATTGATGTATCGATACA
Found at i:1184557 original size:78 final size:79
Alignment explanation
Indices: 1184412--1184595 Score: 235
Period size: 78 Copynumber: 2.3 Consensus size: 79
1184402 GAGGGCCCAT
* * * *
1184412 TTTTATTTCTAAAATGTTATATTTTTCATCTTAGGAATACTCCAACCCCATCAATTCCGAGGGGA
1 TTTTATTTCCAAAATGTTAAATTTTTCATCTTAGGAATACTCCAACCCCATCAAGTCCGAAGGGA
1184477 TACTCCAACCTTGC
66 TACTCCAACCTTGC
* * * * * *
1184491 TTTTATTTCCAAAATGCTAAATTTTTCTTC-TCGGGATACTCCAACCCCATTAAGTGCGAAGGGA
1 TTTTATTTCCAAAATGTTAAATTTTTCATCTTAGGAATACTCCAACCCCATCAAGTCCGAAGGGA
* *
1184555 TACTCTAACCTTGT
66 TACTCCAACCTTGC
*
1184569 TTTTATTTTCAAAATGTTAAATGTTTT
1 TTTTATTTCCAAAATGTTAAAT-TTTT
1184596 TTAAGGGTAC
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 60 0.67
79 30 0.33
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.40
Consensus pattern (79 bp):
TTTTATTTCCAAAATGTTAAATTTTTCATCTTAGGAATACTCCAACCCCATCAAGTCCGAAGGGA
TACTCCAACCTTGC
Found at i:1187045 original size:34 final size:34
Alignment explanation
Indices: 1187002--1187068 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1186992 TATTTGGAGT
1187002 TTTAATTCATCACTTAAAGGCATGGGTTGTAATA
1 TTTAATTCATCACTTAAAGGCATGGGTTGTAATA
* * *
1187036 TTTAATTCATCACTTGAGGGCATGGGTTTTAAT
1 TTTAATTCATCACTTAAAGGCATGGGTTGTAAT
1187069 CTAACTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (34 bp):
TTTAATTCATCACTTAAAGGCATGGGTTGTAATA
Found at i:1187966 original size:21 final size:21
Alignment explanation
Indices: 1187933--1187973 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1187923 CTAAGTAAAA
1187933 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1187954 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1187974 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1188038 original size:20 final size:19
Alignment explanation
Indices: 1188013--1188083 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1188003 ACCTTGAAAA
1188013 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1188033 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
1188052 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
1188073 GTATCGATACA
1 GTATCGATACA
1188084 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1188134 original size:53 final size:53
Alignment explanation
Indices: 1188053--1188303 Score: 367
Period size: 53 Copynumber: 4.6 Consensus size: 53
1188043 AGATTGCATA
*
1188053 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACA-AAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
* * *
1188107 GTATCGATACACATAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTC
1 GTATCGATACACAAAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
1188160 GTATCGATACACAAAATATGTATCGATACATTGGTAGTAGCTACTGGCAGTAGCCAAATTT
1 GTATCGATACACAAAATATGTATCGATACA---G--G-A-C-ACTGGCAGTAGCCAAATTT
* *
1188221 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACAAAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
1188274 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACAAAATATGTATCGATACA
1188304 TTGGTAGTAG
Statistics
Matches: 179, Mismatches: 10, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
53 113 0.63
54 14 0.08
56 2 0.01
58 2 0.01
60 1 0.01
61 47 0.26
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACAAAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:1188225 original size:114 final size:114
Alignment explanation
Indices: 1188090--1188316 Score: 436
Period size: 114 Copynumber: 2.0 Consensus size: 114
1188080 TACAGGACAT
*
1188090 TGGCAGTAGCCAAATTTGTATCGATACACATAATATGTATCGATACAGGTCACTGGCAGTAGCCA
1 TGGCAGTAGCCAAATTTGTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCA
1188155 AATTCGTATCGATACACAAAATATGTATCGATACATTGGTAGTAGCTAC
66 AATTCGTATCGATACACAAAATATGTATCGATACATTGGTAGTAGCTAC
1188204 TGGCAGTAGCCAAATTTGTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCA
1 TGGCAGTAGCCAAATTTGTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCA
*
1188269 AATTTGTATCGATACACAAAATATGTATCGATACATTGGTAGTAGCTA
66 AATTCGTATCGATACACAAAATATGTATCGATACATTGGTAGTAGCTA
1188317 AATCTCATTT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (114 bp):
TGGCAGTAGCCAAATTTGTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCA
AATTCGTATCGATACACAAAATATGTATCGATACATTGGTAGTAGCTAC
Found at i:1188369 original size:21 final size:22
Alignment explanation
Indices: 1188335--1188410 Score: 120
Period size: 21 Copynumber: 3.5 Consensus size: 22
1188325 TTTCACTGTT
1188335 CATCACTATTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
1188357 CATCACT-TTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
*
1188378 GATCACT-TTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
*
1188399 CATCACTGTTCA
1 CATCACTATTCA
1188411 CACTGTTCAC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 40 0.78
22 11 0.22
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (22 bp):
CATCACTATTCATGTATCGATA
Found at i:1190138 original size:21 final size:21
Alignment explanation
Indices: 1190112--1190153 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1190102 AATCAATCAT
* *
1190112 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
1190133 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
1190154 AGAAATGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:1192226 original size:13 final size:13
Alignment explanation
Indices: 1192208--1192232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1192198 TTTTCCAGAT
1192208 TGTATCGATACAA
1 TGTATCGATACAA
1192221 TGTATCGATACA
1 TGTATCGATACA
1192233 TTACTTCAGT
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:1193882 original size:21 final size:21
Alignment explanation
Indices: 1193849--1193889 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1193839 CTAAGTAAAA
1193849 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1193870 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1193890 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1193954 original size:20 final size:19
Alignment explanation
Indices: 1193929--1193999 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1193919 ACCTTGAAAA
1193929 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1193949 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
1193968 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
1193989 GTATCGATACA
1 GTATCGATACA
1194000 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1194052 original size:53 final size:53
Alignment explanation
Indices: 1193969--1194105 Score: 211
Period size: 53 Copynumber: 2.6 Consensus size: 53
1193959 AGATTGCATA
* *
1193969 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAATAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAAGACACTGGCAATAGCCAAATTT
* * *
1194023 GTATCGATACACACAATATGTATCGATACAAGTCACTGGTAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAAGACACTGGCAATAGCCAAATTT
*
1194076 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
1194106 TTGGTAGTAG
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 63 0.82
54 14 0.18
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAAGACACTGGCAATAGCCAAATTT
Found at i:1194184 original size:13 final size:13
Alignment explanation
Indices: 1194166--1194190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1194156 TCACTATTCA
1194166 TGTATCGATACAG
1 TGTATCGATACAG
1194179 TGTATCGATACA
1 TGTATCGATACA
1194191 TAATAAATAG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1197054 original size:3 final size:3
Alignment explanation
Indices: 1197046--1197076 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1197036 TCAACCATCA
*
1197046 ATG ATG ATG AAG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1197077 AGTAGTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:1204034 original size:26 final size:23
Alignment explanation
Indices: 1203983--1204026 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1203973 AGATAAGTTT
1203983 AAATATTTTTCAAGCAATAAATC
1 AAATATTTTTCAAGCAATAAATC
*
1204006 AAATGTTTTTCAAGCAA-AAAT
1 AAATATTTTTCAAGCAATAAAT
1204027 AATTCAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (23 bp):
AAATATTTTTCAAGCAATAAATC
Found at i:1209961 original size:20 final size:20
Alignment explanation
Indices: 1209843--1209953 Score: 96
Period size: 20 Copynumber: 5.3 Consensus size: 20
1209833 TTTTAACTAG
*
1209843 ATGTATCGATACATTGAGAA
1 ATGTATCGATACATTGAAAA
* * *
1209863 ATGTATTGATACATAAAAAGACAGA
1 ATGTATCGATACAT----TGA-AAA
* *
1209888 ATGTATCAATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
1209908 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
1209928 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
1209948 ATGTAT
1 ATGTAT
1209954 GAATACATCT
Statistics
Matches: 71, Mismatches: 15, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
20 54 0.76
21 2 0.03
24 2 0.03
25 13 0.18
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:1211182 original size:32 final size:28
Alignment explanation
Indices: 1210866--1211615 Score: 689
Period size: 28 Copynumber: 25.4 Consensus size: 28
1210856 TTTGAAGAAA
* *
1210866 AAAGG-TGCCACTAACATATGTGGCCTTTG
1 AAAGGATGCCACTGAC-T-TGTGGGCTTTG
1210895 AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
**
1210923 AAAGTTTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
1210951 AAAGGATGCCGCTAACTTGTGAGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
1210979 AAAGGATGCCACTAACTTGTGGGTTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
1211007 AAAAGATGCCACTGATTTGTGTAGGCTTTG
1 AAAGGATGCCACTGACTTGTG--GGCTTTG
*
1211037 AGAAGGATGCCACTGACTTATGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
*
1211066 AGAAGGATGTCACTGACTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
1211095 AGAAGGATGCCACTGACTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
1211124 AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1211152 AAATGGGTAGCCACTGACTTGTGTGGGCTTTG
1 AAA-GGAT-GCCACTGAC-T-TGTGGGCTTTG
1211184 AGAAGGATGCCACTGACTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
* *
1211213 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTG
*
1211245 AAATGGGTAGCCACTGACTTGTGTGGGCTTTG
1 AAA-GGAT-GCCACTGAC-T-TGTGGGCTTTG
**
1211277 AAAAGGATGTGACTGACTTGTGGGCTTTG
1 -AAAGGATGCCACTGACTTGTGGGCTTTG
*
1211306 AGAAGGATGCCACTAACTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
* * *
1211335 AAATGGGTTGCCACAGACTTGTGTGGGCTTTCA
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTT-G
*
1211368 AATAGGTTGCCACTGACTTATGTGGGCTTTG
1 AA-AGGATGCCACTGAC-T-TGTGGGCTTTG
* *
1211399 AAATAGGTTGCCA-TCGACTTGTGTGGGCTTTC
1 -AA-AGGATGCCACT-GAC-T-TGTGGGCTTTG
* *
1211431 AAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA-G-GATGCCACTGAC-T-TGTGGGCTTTG
** * **
1211463 AAATAATGCCACTAACTTGTGGGCTTAA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1211491 AAATGGGTGCCACTGACTTGTGGGCTTTG
1 AAA-GGATGCCACTGACTTGTGGGCTTTG
**
1211520 AAA-GAGTGCCACTGACTTGTGGGCTTAA
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
* * * *
1211548 AAAGGATGCTAC-GAAGTTATGGACTTTG
1 AAAGGATGCCACTG-ACTTGTGGGCTTTG
* * * *
1211576 GATGGGTGCCACTGACTTGTGGGCTTTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1211604 AAAAGATGCCAC
1 AAAGGATGCCAC
1211616 GAAGTTGTGG
Statistics
Matches: 609, Mismatches: 80, Indels: 65
0.81 0.11 0.09
Matches are distributed among these distances:
27 2 0.00
28 212 0.35
29 146 0.24
30 57 0.09
31 43 0.07
32 141 0.23
33 7 0.01
34 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (28 bp):
AAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:1211623 original size:28 final size:28
Alignment explanation
Indices: 1211536--1212099 Score: 448
Period size: 28 Copynumber: 20.4 Consensus size: 28
1211526 TGCCACTGAC
* * *
1211536 TTGTGGGCTTAAAAAGGATGCTACGAAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
* ** * * *
1211564 TTATGGACTTTGGATGGGTGCCACTG-AC
1 TTGTGGACTTTAAAAGGATGCCAC-GAAG
* *
1211592 TTGTGGGCTTTAAAAAGATGCCACGAAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
** *
1211620 TTGTGGAC-TTAAAAGGACACCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
1211647 TTGTGGAC-TTAAAA-GAGTGCCACGAAG
1 TTGTGGACTTTAAAAGGA-TGCCACGAAG
* *
1211674 TTGTGGAC-TCAAAAGGGTGCCACGAAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
* *
1211701 TTGTGGACTTTAAAAGAACGCCACGAAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
* * * * *
1211729 TTGTGGACTTGAAACGGACGCCATGGAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
*
1211757 TTGTGGAC-TTAAAAGGGTGCCAC-AGAG
1 TTGTGGACTTTAAAAGGATGCCACGA-AG
*
1211784 TTGTGGAC-TTAGAAGGATGCCAC-AGAG
1 TTGTGGACTTTAAAAGGATGCCACGA-AG
* *
1211811 TTGTGAAC-TTAATAAGG-TACCAC-AGAG
1 TTGTGGACTTTAA-AAGGATGCCACGA-AG
* * * *
1211838 TGGTGGACTTTAAAAGAACGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
* *
1211866 TTGTGGACTTGAAATGGATGCCAC-AGAG
1 TTGTGGACTTTAAAAGGATGCCACGA-AG
* *
1211894 TTGTGGAC-TTAAAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
* *
1211921 TTATGGAC-TTAAAAGGATGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
* *
1211948 TTATGGACTTTAAAAGGGTGCCAC-AGAG
1 TTGTGGACTTTAAAAGGATGCCACGA-AG
*
1211976 TTGTGGACTTTAAAAGGATGCCA-TAGAG
1 TTGTGGACTTTAAAAGGATGCCACGA-AG
* *
1212004 TTATGGAC-TTAAAAGGATGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGAAG
**
1212031 TCATGGACTTTAAAAAGG-TGCCACGAAG
1 TTGTGGACTTT-AAAAGGATGCCACGAAG
* *
1212059 TTATGGACTTTGAAAAGAAATGCCACTGAA-
1 TTGTGGACTTT-AAAAG-GATGCCAC-GAAG
*
1212089 TCGTGGACTTT
1 TTGTGGACTTT
1212100 GAAGAGGTCA
Statistics
Matches: 436, Mismatches: 79, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
26 2 0.00
27 203 0.47
28 206 0.47
29 7 0.02
30 15 0.03
31 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (28 bp):
TTGTGGACTTTAAAAGGATGCCACGAAG
Found at i:1211642 original size:27 final size:27
Alignment explanation
Indices: 1211536--1212068 Score: 438
Period size: 27 Copynumber: 19.4 Consensus size: 27
1211526 TGCCACTGAC
* *
1211536 TTGTGGGCTTAAAAAGGATGCTACGAAG
1 TTGTGGACTT-AAAAGGATGCCACGAAG
* ** * * *
1211564 TTATGGACTTTGGATGGGTGCCACTG-AC
1 TTGTGGAC-TTAAAAGGATGCCAC-GAAG
* *
1211592 TTGTGGGCTTTAAAAAGATGCCACGAAG
1 TTGTGGAC-TTAAAAGGATGCCACGAAG
** *
1211620 TTGTGGACTTAAAAGGACACCACGGAG
1 TTGTGGACTTAAAAGGATGCCACGAAG
1211647 TTGTGGACTTAAAA-GAGTGCCACGAAG
1 TTGTGGACTTAAAAGGA-TGCCACGAAG
* *
1211674 TTGTGGACTCAAAAGGGTGCCACGAAG
1 TTGTGGACTTAAAAGGATGCCACGAAG
* *
1211701 TTGTGGACTTTAAAAGAACGCCACGAAG
1 TTGTGGAC-TTAAAAGGATGCCACGAAG
* * * *
1211729 TTGTGGACTTGAAACGGACGCCATGGAG
1 TTGTGGACTT-AAAAGGATGCCACGAAG
*
1211757 TTGTGGACTTAAAAGGGTGCCAC-AGAG
1 TTGTGGACTTAAAAGGATGCCACGA-AG
*
1211784 TTGTGGACTTAGAAGGATGCCAC-AGAG
1 TTGTGGACTTAAAAGGATGCCACGA-AG
* *
1211811 TTGTGAACTTAATAAGG-TACCAC-AGAG
1 TTGTGGACTTAA-AAGGATGCCACGA-AG
* * * *
1211838 TGGTGGACTTTAAAAGAACGCCACGGAG
1 TTGTGGAC-TTAAAAGGATGCCACGAAG
*
1211866 TTGTGGACTTGAAATGGATGCCAC-AGAG
1 TTGTGGACTT-AAAAGGATGCCACGA-AG
* *
1211894 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCACGAAG
* *
1211921 TTATGGACTTAAAAGGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCACGAAG
* *
1211948 TTATGGACTTTAAAAGGGTGCCAC-AGAG
1 TTGTGGAC-TTAAAAGGATGCCACGA-AG
*
1211976 TTGTGGACTTTAAAAGGATGCCA-TAGAG
1 TTGTGGAC-TTAAAAGGATGCCACGA-AG
* *
1212004 TTATGGACTTAAAAGGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCACGAAG
**
1212031 TCATGGACTTTAAAAAGG-TGCCACGAAG
1 TTGTGGAC-TT-AAAAGGATGCCACGAAG
*
1212059 TTATGGACTT
1 TTGTGGACTT
1212069 TGAAAAGAAA
Statistics
Matches: 414, Mismatches: 70, Indels: 43
0.79 0.13 0.08
Matches are distributed among these distances:
26 2 0.00
27 207 0.50
28 196 0.47
29 9 0.02
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (27 bp):
TTGTGGACTTAAAAGGATGCCACGAAG
Found at i:1211733 original size:137 final size:137
Alignment explanation
Indices: 1211592--1212068 Score: 554
Period size: 137 Copynumber: 3.5 Consensus size: 137
1211582 TGCCACTGAC
* * * ***
1211592 TTGTGGGCTTTAAAAAGATGCCACGAAGTTGTGGACTTAAAAGGACACCACGGAGTTGTGGACTT
1 TTGTGGACTTGAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
*
1211657 AAAA-GAGTGCCACGAAGTTGTGGACTCAAAAGGGTGCCAC-GAAGTTGTGGACTTTAAAAGAAC
66 AAAAGGA-TGCCACGAAGTTGTGGACTTAAAAGGGTGCCACAG-AGTTGTGGACTTTAAAAGAAC
1211720 GCCACGAAG
129 GCCACGAAG
* * * * *
1211729 TTGTGGACTTGAAACGGACGCCATGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTT
1 TTGTGGACTTGAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* * * *
1211794 AGAAGGATGCCAC-AGAGTTGTGAACTTAATAA-GGTACCACAGAGTGGTGGACTTTAAAAGAAC
66 AAAAGGATGCCACGA-AGTTGTGGACTTAA-AAGGGTGCCACAGAGTTGTGGACTTTAAAAGAAC
*
1211857 GCCACGGAG
129 GCCACGAAG
* *
1211866 TTGTGGACTTGAAATGGATGCCAC-AGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACT
1 TTGTGGACTTGAAAAGGATGCCACGA-AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
* * * *
1211930 TAAAAGGATGCCACGGAGTTATGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGAT
65 TAAAAGGATGCCACGAAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGAAC
*
1211995 GCCA-TAGAG
129 GCCACGA-AG
* * ** * * *
1212004 TTATGGACTT-AAAAGGATGCCACGGAGTCATGGACTTTAAAAAGGTGCCACGAAGTTATGGACT
1 TTGTGGACTTGAAAAGGATGCCACGAAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACT
1212068 T
65 T
1212069 TGAAAAGAAA
Statistics
Matches: 289, Mismatches: 40, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
136 1 0.00
137 210 0.73
138 78 0.27
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (137 bp):
TTGTGGACTTGAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
AAAAGGATGCCACGAAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGAACGC
CACGAAG
Found at i:1211791 original size:110 final size:110
Alignment explanation
Indices: 1211579--1212075 Score: 512
Period size: 110 Copynumber: 4.5 Consensus size: 110
1211569 GACTTTGGAT
* * *
1211579 GGGTGCCACTG-ACTTGTGGGCTTTAAAA-AGATGCCACGAAGTTGTGGACTT-AAAAGGACACC
1 GGGTGCCAC-GAAGTTGTGGACTTTAAAAGA-ATGCCACGAAGTTGTGGACTTGAAAAGGACGCC
*
1211641 ACGGAGTTGTGGACTTAAAA-GAGTGCCAC-GAAGTTGTGGACTCAAAA
64 ACGGAGTTGTGGACTTAAAAGGA-TGCCACAG-AGTTGTGGACTTAAAA
* * *
1211688 GGGTGCCACGAAGTTGTGGACTTTAAAAGAACGCCACGAAGTTGTGGACTTGAAACGGACGCCAT
1 GGGTGCCACGAAGTTGTGGACTTTAAAAGAATGCCACGAAGTTGTGGACTTGAAAAGGACGCCAC
* *
1211753 GGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAGAA
66 GGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAA
* * * * * * *
1211798 GGATGCCAC-AGAGTTGTGAAC-TTAATAAG-GTACCAC-AGAGTGGTGGACTTTAAAAGAACGC
1 GGGTGCCACGA-AGTTGTGGACTTTAA-AAGAATGCCACGA-AGTTGTGGACTTGAAAAGGACGC
*
1211859 CACGGAGTTGTGGACTTGAAATGGATGCCACAGAGTTGTGGACTTAAAA
63 CACGGAGTTGTGGACTT-AAAAGGATGCCACAGAGTTGTGGACTTAAAA
* * * * * * **
1211908 GGGTGCCACGGAGTTATGGAC-TTAAAAGGATGCCACGGAGTTATGGACTTTAAAAGGGTGCCAC
1 GGGTGCCACGAAGTTGTGGACTTTAAAAGAATGCCACGAAGTTGTGGACTTGAAAAGGACGCCAC
* * *
1211972 AGAGTTGTGGACTTTAAAAGGATGCCATAGAGTTATGGACTTAAAA
66 GGAGTTGTGGAC-TTAAAAGGATGCCACAGAGTTGTGGACTTAAAA
* * ** * *
1212018 GGATGCCACGGAGTCATGGACTTTAAAA-AGGTGCCACGAAGTTATGGACTTTGAAAAG
1 GGGTGCCACGAAGTTGTGGACTTTAAAAGA-ATGCCACGAAGTTGTGGAC-TTGAAAAG
1212076 AAATGCCACT
Statistics
Matches: 328, Mismatches: 44, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
108 2 0.01
109 91 0.28
110 201 0.61
111 27 0.08
112 7 0.02
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (110 bp):
GGGTGCCACGAAGTTGTGGACTTTAAAAGAATGCCACGAAGTTGTGGACTTGAAAAGGACGCCAC
GGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAA
Found at i:1213013 original size:14 final size:14
Alignment explanation
Indices: 1212994--1213021 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1212984 CTTGAGATCT
1212994 TTCCCGAATAATGA
1 TTCCCGAATAATGA
1213008 TTCCCGAATAATGA
1 TTCCCGAATAATGA
1213022 ACATGATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
TTCCCGAATAATGA
Found at i:1214910 original size:44 final size:43
Alignment explanation
Indices: 1214862--1214985 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 43
1214852 ATTTAATCAT
* *
1214862 GTAGATGCACGTCAAATGATGCAAATACAAGTAT-AAGT-AAAGAG
1 GTAGATGCATGTGAAAT-ATGCAAATACAAGTATCAA-TCAAA-AG
*
1214906 GTAGATGCATGTGAAACTATGCAAATATC-GGTATCAATCAAAAG
1 GTAGATGCATGTGAAA-TATGCAAATA-CAAGTATCAATCAAAAG
* *
1214950 ATAGATGCATGTGAAATAAGGCAAATACAAGTATCA
1 GTAGATGCATGTGAAAT-ATGCAAATACAAGTATCA
1214986 GTTAATAGGC
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
43 2 0.03
44 59 0.87
45 7 0.10
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (43 bp):
GTAGATGCATGTGAAATATGCAAATACAAGTATCAATCAAAAG
Found at i:1215073 original size:89 final size:89
Alignment explanation
Indices: 1214971--1215191 Score: 246
Period size: 89 Copynumber: 2.5 Consensus size: 89
1214961 TGAAATAAGG
* * * * * * *
1214971 CAAATACAAGTATCAGTTAATAGGCAAGTGCACGTGAAGCAATGCAAATGCCAATGTAATCCAAT
1 CAAATGCAAGTATCAGTAAAAAGGCAAATGCACGTGAAACAATGCAAATACCAATGTAATCAAAT
*
1215036 -GATGCAAATGTGCATGAAACAATA
66 AG-TGCAAATGTCCATGAAACAATA
* * * * *
1215060 CAATTGCAAGTATCAATAAAAAGGCAAATGCATGTAAAACAATGTAAATACCAATGTAATCAAAT
1 CAAATGCAAGTATCAGTAAAAAGGCAAATGCACGTGAAACAATGCAAATACCAATGTAATCAAAT
* * ** *
1215125 AGTGTAGATGTCCATGAAATGATG
66 AGTGCAAATGTCCATGAAACAATA
* *
1215149 CAAATGCAAGTATTAGTAAAAAGGCAAATGCACATGAAACAAT
1 CAAATGCAAGTATCAGTAAAAAGGCAAATGCACGTGAAACAAT
1215192 ATGAATTTCA
Statistics
Matches: 107, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
89 106 0.99
90 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (89 bp):
CAAATGCAAGTATCAGTAAAAAGGCAAATGCACGTGAAACAATGCAAATACCAATGTAATCAAAT
AGTGCAAATGTCCATGAAACAATA
Found at i:1215228 original size:14 final size:14
Alignment explanation
Indices: 1215206--1215240 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1215196 ATTTCAATTC
1215206 ATCAAATGATGCAT
1 ATCAAATGATGCAT
*
1215220 ATGAAATGATGCAT
1 ATCAAATGATGCAT
1215234 ATCAAAT
1 ATCAAAT
1215241 TATTTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (14 bp):
ATCAAATGATGCAT
Found at i:1219900 original size:66 final size:68
Alignment explanation
Indices: 1219824--1219968 Score: 152
Period size: 66 Copynumber: 2.2 Consensus size: 68
1219814 TGTAACATAC
* * *
1219824 AAGTTCAACTTCTAACCTATTTAG-AAGAATATAGGCTTAACTCTTTT-T-ACTCATTCAGTAGG
1 AAGTTTAACTTCTAACCTATTTAGAAAG-ACATAGGCATAACTCTTTTATAACTCATTCAGTAGG
*
1219886 ACAT
65 AAAT
* * ** * **
1219890 GAGTTTAACTTTTCGCCTGTTTAGAAAGACATAGGCATAACTCTTTTATAACTTGTTCAGTAGGA
1 AAGTTTAACTTCTAACCTATTTAGAAAGACATAGGCATAACTCTTTTATAACTCATTCAGTAGGA
1219955 AAT
66 AAT
*
1219958 AAGTTTGACTT
1 AAGTTTAACTT
1219969 TTGACTTGTT
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
66 35 0.56
67 4 0.06
68 24 0.38
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (68 bp):
AAGTTTAACTTCTAACCTATTTAGAAAGACATAGGCATAACTCTTTTATAACTCATTCAGTAGGA
AAT
Found at i:1220172 original size:33 final size:34
Alignment explanation
Indices: 1220135--1220217 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 34
1220125 AACTTTACTA
* *
1220135 GTTCAAAAGGACATAAGTTGACT-ATTTGGACTT
1 GTTCAAAAAGACATAAGTTGACTCATTTGAACTT
* * * * *
1220168 GTTCAAAACGAAACAAGTTGACTCTTTTTAACTT
1 GTTCAAAAAGACATAAGTTGACTCATTTGAACTT
1220202 GTTCAAAAAGACATAA
1 GTTCAAAAAGACATAA
1220218 ATTTACTCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 20 0.50
34 20 0.50
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (34 bp):
GTTCAAAAAGACATAAGTTGACTCATTTGAACTT
Found at i:1220226 original size:34 final size:34
Alignment explanation
Indices: 1220164--1220235 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1220154 GACTATTTGG
* *
1220164 ACTTGTTCAAAACGAAACAAGTTGACTCTTTTTA
1 ACTTGTTCAAAAAGAAACAAATTGACTCTTTTTA
* * * *
1220198 ACTTGTTCAAAAAGACATAAATTTACTCTTTTTG
1 ACTTGTTCAAAAAGAAACAAATTGACTCTTTTTA
1220232 ACTT
1 ACTT
1220236 ATTTAGAAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (34 bp):
ACTTGTTCAAAAAGAAACAAATTGACTCTTTTTA
Found at i:1221418 original size:61 final size:61
Alignment explanation
Indices: 1221323--1221445 Score: 194
Period size: 61 Copynumber: 2.0 Consensus size: 61
1221313 GAGTCATCGG
*
1221323 TAGTCACTGGGATGTTTTTATGCCAAAAGGGTGTGTGTAGGAT-AGTTTCACCTTCTTAGGT
1 TAGTCACTGGGATGCTTTTATGCCAAAAGGGTGTGTGTAGGATAAG-TTCACCTTCTTAGGT
** *
1221384 TAGTCACTGGGATGCTTTTATGCCAATGGGGTGTGTGTAGGATAAGTTCACCTTTTTAGGT
1 TAGTCACTGGGATGCTTTTATGCCAAAAGGGTGTGTGTAGGATAAGTTCACCTTCTTAGGT
1221445 T
1 T
1221446 CATTTCAAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
61 55 0.96
62 2 0.04
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.38
Consensus pattern (61 bp):
TAGTCACTGGGATGCTTTTATGCCAAAAGGGTGTGTGTAGGATAAGTTCACCTTCTTAGGT
Found at i:1221783 original size:22 final size:24
Alignment explanation
Indices: 1221753--1221796 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1221743 TCTCTCAATC
*
1221753 TCTTCAAGA-ATTATACCCCAAAT
1 TCTTCAAGAGATTATAACCCAAAT
1221776 TCTT-AAGAGATTATAACCCAA
1 TCTTCAAGAGATTATAACCCAA
1221797 GGTTGAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (24 bp):
TCTTCAAGAGATTATAACCCAAAT
Found at i:1222232 original size:13 final size:13
Alignment explanation
Indices: 1222214--1222239 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1222204 TTTCACTATA
1222214 TATCGATACAATG
1 TATCGATACAATG
1222227 TATCGATACAATG
1 TATCGATACAATG
1222240 CACTATGTAT
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):
TATCGATACAATG
Found at i:1222311 original size:20 final size:18
Alignment explanation
Indices: 1222286--1222357 Score: 65
Period size: 20 Copynumber: 3.8 Consensus size: 18
1222276 TTGTCAATTT
1222286 CATGTATCGATACAATTGA
1 CATGTATCGATACAA-TGA
*
1222305 GCATGTATCGATATAATGA
1 -CATGTATCGATACAATGA
*
1222324 -ATAGTATCGATACAAAGCA
1 CAT-GTATCGATACAATG-A
*
1222343 TAATGTATCGATACA
1 -CATGTATCGATACA
1222358 TCTAGATGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
17 2 0.04
18 12 0.27
19 4 0.09
20 25 0.56
21 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (18 bp):
CATGTATCGATACAATGA
Found at i:1222369 original size:20 final size:20
Alignment explanation
Indices: 1222346--1222396 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1222336 CAAAGCATAA
1222346 TGTATCGATACATCTAGATG
1 TGTATCGATACATCTAGATG
1222366 TGTATCGATACATCTAGATG
1 TGTATCGATACATCTAGATG
1222386 TGTATCGATAC
1 TGTATCGATAC
1222397 TTTCAGGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATCTAGATG
Found at i:1224091 original size:27 final size:25
Alignment explanation
Indices: 1224046--1224100 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
1224036 CTAATACTTC
1224046 TTTTTTTTTTCTCTTTTTTTTTCAT
1 TTTTTTTTTTCTCTTTTTTTTTCAT
* *
1224071 TTTTCTTTCTTTCTTTTTTTTTTTCCT
1 TTTT-TTT-TTTCTCTTTTTTTTTCAT
1224098 TTT
1 TTT
1224101 GAAAGGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 4 0.15
26 3 0.12
27 19 0.73
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTTTTTTTTCTCTTTTTTTTTCAT
Found at i:1231873 original size:19 final size:19
Alignment explanation
Indices: 1231816--1231880 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1231806 TACAAGCCAA
1231816 TGTATCGATACATATTTTT
1 TGTATCGATACATATTTTT
* ***
1231835 TGTGT--AT-CA-ATACAT
1 TGTATCGATACATATTTTT
1231850 TGTATCGATACATATTTTT
1 TGTATCGATACATATTTTT
1231869 TGTATCGATACA
1 TGTATCGATACA
1231881 AGTTTGGCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
15 7 0.21
16 2 0.06
17 4 0.12
18 2 0.06
19 19 0.56
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (19 bp):
TGTATCGATACATATTTTT
Found at i:1238322 original size:21 final size:21
Alignment explanation
Indices: 1238293--1238337 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1238283 AAGTTTTTAT
*
1238293 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1238313 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1238335 TTT
1 TTT
1238338 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1240576 original size:13 final size:13
Alignment explanation
Indices: 1240558--1240583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1240548 ATATTTTTTG
1240558 TGTATCGATACAT
1 TGTATCGATACAT
1240571 TGTATCGATACAT
1 TGTATCGATACAT
1240584 ATTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1240594 original size:32 final size:33
Alignment explanation
Indices: 1240537--1240601 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1240527 TACAAGCCCA
1240537 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
1240571 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
1240602 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:1240595 original size:19 final size:19
Alignment explanation
Indices: 1240537--1240601 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1240527 TACAAGCCCA
1240537 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
1240558 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
1240571 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1240590 TGTATCGATACA
1 TGTATCGATACA
1240602 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1245042 original size:155 final size:155
Alignment explanation
Indices: 1244724--1245492 Score: 789
Period size: 154 Copynumber: 5.0 Consensus size: 155
1244714 CTTTTTAAGA
* * * * *
1244724 TTATCGGGATACTTTTATGTCAAAGGTATACCTT-AGAAGCATTTTTATAA-----CTAGAATCG
1 TTATCGAGATACTTTCATGTCAAA-GTATACCTTAAG-GGCATTTTCATAATTTTTCTAAAATCG
* * * * *
1244783 AGTCCTAAGTTGTCACCGGGATGCTTTTATGTCAAAGGTGTGCATTTGAGG-TAGATTTATCCTA
64 AGTCCTAGGTTGTCACCGAGATGCTTTTATGCCAAAGGTGTGCATTT-AGGATAGATTCATCCCA
*
1244847 TTTATGATTATTTTTAAGTCTTTTAGGG
128 TTTATGATCATTTTTAAGTCTTTTAGGG
* * **
1244875 TTATCGAGATACTTGCATGTCGAAAGTATACCTTAAGGGTATTTTTTTAATTTTTCTAAAATCGA
1 TTATCGAGATACTTTCATGTC-AAAGTATACCTTAAGGGCATTTTCATAATTTTTCTAAAATCGA
* * * * *
1244940 GTCTTAGATTGTCACCGAGATGCTTTTATGCCAAGGGTGTGCATTTAGGATA-ATTTATCCTATT
65 GTCCTAGGTTGTCACCGAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGATTCATCCCATT
* *
1245004 TATGATCATTTTAAAGTCTTTTGGGG
130 TATGATCATTTTTAAGTCTTTTAGGG
* * * * * ** *
1245030 TTATTG-GAATACTTTCATGTTAAAAGTATACATTAGGGGTATTTTTGTAATTTTACT-AAATCG
1 TTATCGAG-ATACTTTCATG-TCAAAGTATACCTTAAGGGCATTTTCATAATTTTTCTAAAATCG
* *
1245093 AGTCCTAGGTTGTCACC-ATGATGCTTTTATGCCGAAGGTGTGCATTTAGCATAGATTCATCCCA
64 AGTCCTAGGTTGTCACCGA-GATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGATTCATCCCA
1245157 TTTATGATCATTTTTAAGTCTTTTAGGG
128 TTTATGATCATTTTTAAGTCTTTTAGGG
* * * ** *
1245185 TTATCAAGATACATTCATGTCAAAGATATACCCTAAAAGCATTTTCATAATTTTTCTAGAATCGA
1 TTATCGAGATACTTTCATGTCAAAG-TATACCTTAAGGGCATTTTCATAATTTTTCTAAAATCGA
* * * * * *
1245250 GTCCTAGGTTGTCA-CTAGAATGC--TTATGCTAAACGTGTGTATTTAGGACAGGTTCATCCCAT
65 GTCCTAGGTTGTCACCGAG-ATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGATTCATCCCAT
* *
1245312 TTATGATCATTTTCAAGTCATTTAGGG
129 TTATGATCATTTTTAAGTCTTTTAGGG
* * *
1245339 TTA-CTGGGATACTTTCATATCAAAGGTATA-CTCTAAGGGCATTTTCATAATTTTCCTAAAATC
1 TTATC-GAGATACTTTCATGTCAAA-GTATACCT-TAAGGGCATTTTCATAATTTTTCTAAAATC
* * ** * *
1245402 AAGTCTTAGGTTGTCA-TTAGTATGCTTTTATGCCAAAGGTGTGCATTTAAGATAGGTTCATCCC
63 GAGTCCTAGGTTGTCACCGAG-ATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGATTCATCCC
* *
1245466 ATTTATAATCATTTTTACGTCTTTTAG
127 ATTTATGATCATTTTTAAGTCTTTTAG
1245493 AATTACTAAG
Statistics
Matches: 519, Mismatches: 77, Indels: 39
0.82 0.12 0.06
Matches are distributed among these distances:
151 37 0.07
152 5 0.01
153 3 0.01
154 184 0.35
155 157 0.30
156 133 0.26
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (155 bp):
TTATCGAGATACTTTCATGTCAAAGTATACCTTAAGGGCATTTTCATAATTTTTCTAAAATCGAG
TCCTAGGTTGTCACCGAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGATTCATCCCATTT
ATGATCATTTTTAAGTCTTTTAGGG
Found at i:1245414 original size:310 final size:308
Alignment explanation
Indices: 1244773--1245517 Score: 849
Period size: 310 Copynumber: 2.4 Consensus size: 308
1244763 CATTTTTATA
* * * * * *
1244773 ACTAGAATCGAGTCCTAAGTTGTCACCGGGATGCTTTTATGTCAAAGGTGTGCATTTGAGGTAGA
1 ACTA-AATCAAGTCCTAGGTTGTCACC-AGATGCTTTTATGCCAAAGGTGTGCATTTAAGATAGA
* * * *
1244838 TTTATCCTATTTATGATTATTTTTAAGTCTTTTAGGGTTATCGAGATACTTGCATGTCGAAAGTA
64 TTCATCCCATTTATGATCATTTTTAAGTCTTTTAGGGTTATCAAGATACTTGCATGTCGAAAGTA
* ** * ** * *
1244903 TACCTTAAGGGTATTTTTTTAATTTTTCTAAAATCGAGTCTTAGATTGTCACCGAGATGCTTTTA
129 TACCCTAAAAGCATTTTCATAATTTTTCTAAAATCGAGTCCTAGATTGTCACAGAGATGC-TTTA
** * * * * *
1244968 TGCCAAGGGTGTGCATTTAGGATAATTTATCCTATTTATGATCATTTTAAAGTCTTTTGGGGTTA
193 TGCCAAACGTGTGCATTTAGGACAATTCATCCCATTTATGATCATTTTAAAGTCATTTAGGGTTA
* * * * * **
1245033 TTGGAATACTTTCATGTTAAAAGTATACATTAGGGGTATTTTTGTAATTTT
258 CTGGAATACTTTCATATCAAAAGTATACATTAAGGGCATTTTCATAATTTT
* *
1245084 ACTAAATCGAGTCCTAGGTTGTCACCATGATGCTTTTATGCCGAAGGTGTGCATTT-AGCATAGA
1 ACTAAATCAAGTCCTAGGTTGTCACCA-GATGCTTTTATGCCAAAGGTGTGCATTTAAG-ATAGA
1245148 TTCATCCCATTTATGATCATTTTTAAGTCTTTTAGGGTTATCAAGATACATT-CATGTC-AAAGA
64 TTCATCCCATTTATGATCATTTTTAAGTCTTTTAGGGTTATCAAGATAC-TTGCATGTCGAAAG-
* *
1245211 TATACCCTAAAAGCATTTTCATAATTTTTCTAGAATCGAGTCCTAGGTTGTCACTAGA-ATGC-T
127 TATACCCTAAAAGCATTTTCATAATTTTTCTAAAATCGAGTCCTAGATTGTCAC-AGAGATGCTT
* * * *
1245274 TATGCTAAACGTGTGTATTTAGGACAGGTTCATCCCATTTATGATCATTTTCAAGTCATTTAGGG
191 TATGCCAAACGTGTGCATTTAGGACA-ATTCATCCCATTTATGATCATTTTAAAGTCATTTAGGG
* *
1245339 TTACTGGGATACTTTCATATCAAAGGTATAC-TCTAAGGGCATTTTCATAATTTT
255 TTACTGGAATACTTTCATATCAAAAGTATACAT-TAAGGGCATTTTCATAATTTT
* * ** *
1245393 CCTAAAATCAAGTCTTAGGTTGTCATTAGTATGCTTTTATGCCAAAGGTGTGCATTTAAGATAGG
1 ACT-AAATCAAGTCCTAGGTTGTCACCAG-ATGCTTTTATGCCAAAGGTGTGCATTTAAGATAGA
* * ** *
1245458 TTCATCCCATTTATAATCATTTTTACGTCTTTTAGAATTA-CTAAGATACTT-TATGTCGAA
64 TTCATCCCATTTATGATCATTTTTAAGTCTTTTAGGGTTATC-AAGATACTTGCATGTCGAA
1245518 GGTTTGTCCT
Statistics
Matches: 371, Mismatches: 51, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
308 23 0.06
309 92 0.25
310 246 0.66
311 10 0.03
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (308 bp):
ACTAAATCAAGTCCTAGGTTGTCACCAGATGCTTTTATGCCAAAGGTGTGCATTTAAGATAGATT
CATCCCATTTATGATCATTTTTAAGTCTTTTAGGGTTATCAAGATACTTGCATGTCGAAAGTATA
CCCTAAAAGCATTTTCATAATTTTTCTAAAATCGAGTCCTAGATTGTCACAGAGATGCTTTATGC
CAAACGTGTGCATTTAGGACAATTCATCCCATTTATGATCATTTTAAAGTCATTTAGGGTTACTG
GAATACTTTCATATCAAAAGTATACATTAAGGGCATTTTCATAATTTT
Found at i:1258726 original size:19 final size:19
Alignment explanation
Indices: 1258680--1258735 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1258670 TTGCCAGTTT
**
1258680 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
1258700 CGTGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1258719 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1258736 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1258738 original size:13 final size:13
Alignment explanation
Indices: 1258720--1258746 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1258710 TACAATGAAC
1258720 ATGTATCGATACA
1 ATGTATCGATACA
1258733 ATGTATCGATACA
1 ATGTATCGATACA
1258746 A
1 A
1258747 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1258757 original size:20 final size:20
Alignment explanation
Indices: 1258732--1258772 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1258722 GTATCGATAC
1258732 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
1258752 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
1258772 A
1 A
1258773 TCGATACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACAAAGCAT
Found at i:1265247 original size:13 final size:13
Alignment explanation
Indices: 1265229--1265258 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1265219 ATTCATCATG
1265229 TATCGATACAATA
1 TATCGATACAATA
*
1265242 TATCGATACAATG
1 TATCGATACAATA
1265255 TATC
1 TATC
1265259 ATGTTTCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:1265251 original size:33 final size:33
Alignment explanation
Indices: 1265204--1265272 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1265194 CCGTTAGAAG
*
1265204 CAATGTATCGATACAAT-TCATCATGTATCGATA
1 CAATATATCGATACAATGT-ATCATGTATCGATA
*
1265237 CAATATATCGATACAATGTATCATGTTTCGATA
1 CAATATATCGATACAATGTATCATGTATCGATA
1265270 CAA
1 CAA
1265273 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (33 bp):
CAATATATCGATACAATGTATCATGTATCGATA
Found at i:1265345 original size:19 final size:19
Alignment explanation
Indices: 1265301--1265356 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1265291 CTACCAGTTT
**
1265301 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1265321 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1265340 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1265357 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1265359 original size:13 final size:13
Alignment explanation
Indices: 1265341--1265367 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1265331 TACAATGAAC
1265341 ATGTATCGATACA
1 ATGTATCGATACA
1265354 ATGTATCGATACA
1 ATGTATCGATACA
1265367 A
1 A
1265368 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1268736 original size:59 final size:59
Alignment explanation
Indices: 1268673--1268791 Score: 202
Period size: 59 Copynumber: 2.0 Consensus size: 59
1268663 ACTCATCAAA
* * *
1268673 TATCATTATTTATTTTATATTAATTCAGTTTTCAAAAATTAATTCATTTTCATGAGTTT
1 TATCATTATTTATTTCATATTAATTCAGTTTTAAAAAATAAATTCATTTTCATGAGTTT
*
1268732 TATCATTATTTATTTCATATTAATTTAGTTTTAAAAAATAAATTCATTTTCATGAGTTT
1 TATCATTATTTATTTCATATTAATTCAGTTTTAAAAAATAAATTCATTTTCATGAGTTT
1268791 T
1 T
1268792 GGATTCTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.54
Consensus pattern (59 bp):
TATCATTATTTATTTCATATTAATTCAGTTTTAAAAAATAAATTCATTTTCATGAGTTT
Found at i:1271404 original size:20 final size:19
Alignment explanation
Indices: 1271333--1271405 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
1271323 TTGCCACTTT
* *
1271333 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-AGAA
* *
1271353 TATGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
** *
1271372 CATGTATTTATACAAAGCAT
1 CATGTATCGATACAAAG-AA
*
1271392 GATGTATCGATACA
1 CATGTATCGATACA
1271406 TCTGGATATG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
19 16 0.38
20 26 0.62
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:1273757 original size:20 final size:21
Alignment explanation
Indices: 1273732--1273779 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1273722 TCTGTTGATG
* *
1273732 ATTTTGATG-AAAAATGGATA
1 ATTTTGATGTAAAAATGAAGA
*
1273752 ATTTTGATGTGAAAATGAAGA
1 ATTTTGATGTAAAAATGAAGA
1273773 ATTTTGA
1 ATTTTGA
1273780 AATGGATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.38
Consensus pattern (21 bp):
ATTTTGATGTAAAAATGAAGA
Found at i:1273917 original size:13 final size:13
Alignment explanation
Indices: 1273898--1273967 Score: 71
Period size: 13 Copynumber: 5.8 Consensus size: 13
1273888 ATAGTAACCC
1273898 ATGTATCGATACA
1 ATGTATCGATACA
*
1273911 TTGTATCGATACA
1 ATGTATCGATACA
1273924 ATGTATCGAT---
1 ATGTATCGATACA
*
1273934 ATG-A-AGA-ACA
1 ATGTATCGATACA
*
1273944 TTGTATCGATACA
1 ATGTATCGATACA
1273957 ATGTATCGATA
1 ATGTATCGATA
1273968 AAATTTCCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
8 2 0.04
9 1 0.02
10 5 0.11
11 1 0.02
12 2 0.04
13 34 0.76
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1278224 original size:20 final size:20
Alignment explanation
Indices: 1278199--1278252 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1278189 CTACCCCTGT
*
1278199 TTGTATCAATACATG-TCACA
1 TTGTATCGATACATGATCA-A
*
1278219 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATCAA
1278239 TTGTATCGATACAT
1 TTGTATCGATACAT
1278253 TACTTCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATCAA
Found at i:1284547 original size:21 final size:22
Alignment explanation
Indices: 1284523--1284573 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
1284513 ATCAAATCTT
* *
1284523 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1284544 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1284566 --TCAAAATA
1 CTTCAAAATA
1284574 ATCAACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 8 0.30
21 11 0.41
22 8 0.30
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:1285466 original size:20 final size:22
Alignment explanation
Indices: 1285425--1285473 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
1285415 TGAAAATAAA
1285425 TTTTTATCAAAGGGGGAGAAATT
1 TTTTTATCAAA-GGGGAGAAATT
1285448 TTTTTATCAAA-GGGA-AAATT
1 TTTTTATCAAAGGGGAGAAATT
1285468 TTTTTA
1 TTTTTA
1285474 ACGAAAGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.42
21 4 0.15
23 11 0.42
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (22 bp):
TTTTTATCAAAGGGGAGAAATT
Found at i:1285480 original size:21 final size:21
Alignment explanation
Indices: 1285438--1285480 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
1285428 TTATCAAAGG
*
1285438 GGGAGAAATTTTTTTATCAAA
1 GGGAGAAATTTTTTTAACAAA
1285459 GGGA-AAATTTTTTTAACGAAA
1 GGGAGAAATTTTTTTAAC-AAA
1285480 G
1 G
1285481 CCTTAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (21 bp):
GGGAGAAATTTTTTTAACAAA
Found at i:1289365 original size:13 final size:13
Alignment explanation
Indices: 1289347--1289373 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1289337 ACAATTGAGT
1289347 ATGTATCGATACA
1 ATGTATCGATACA
1289360 ATGTATCGATACA
1 ATGTATCGATACA
1289373 A
1 A
1289374 AGCTTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1289941 original size:127 final size:127
Alignment explanation
Indices: 1289681--1289947 Score: 367
Period size: 127 Copynumber: 2.1 Consensus size: 127
1289671 GATCCTAACA
* * *
1289681 TATCCATTAAGGTGCAAAATGATTTTTTCCAAACATAAATAAATATTAATTATTTGTAAGTCTTT
1 TATCTATTAAGGTGCAAAATGATTTTTTCCAAACATAAATAAATATTAATCATTTGTAAATCTTT
** ***
1289746 TATATTCCTATGGGTATTTGTAGGGGTATAAAAGATTTCGAAAAATTTTGTATCTTTTCGGG
66 TATATTCCTATGGGTATCCGTAGGGGTATAAAAGATTTCGAAAAATTTTGTATCTTGGAGGG
* *
1289808 TATCTATTAAGGTGCAAAATGATTTTTTTCAAACATAAATAAATATTAATCGTTT-TAAATCTTT
1 TATCTATTAAGGTGCAAAATGATTTTTTCCAAACATAAATAAATATTAATCATTTGTAAATCTTT
* * *
1289872 TATATTCCTATGGGTATCCGTAGGGGTGTTAAAAGATTT-TAAAATTTTTCGTATCTTGGAGGG
66 TATATTCCTATGGGTATCCGTAGGGGT-ATAAAAGATTTCGAAAAATTTT-GTATCTTGGAGGG
* *
1289935 TTTCTATCAAGGT
1 TATCTATTAAGGT
1289948 ACGAAATGGC
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
126 41 0.33
127 82 0.67
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (127 bp):
TATCTATTAAGGTGCAAAATGATTTTTTCCAAACATAAATAAATATTAATCATTTGTAAATCTTT
TATATTCCTATGGGTATCCGTAGGGGTATAAAAGATTTCGAAAAATTTTGTATCTTGGAGGG
Found at i:1296788 original size:50 final size:50
Alignment explanation
Indices: 1296720--1296817 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
1296710 TTTTCGTTGC
* *
1296720 TGTTCGTGCTCGCCTGCTTGTTGGAGCTACTGTTGATGCTGTCGTGCTGT
1 TGTTCATGCTCGCCTGCTTGTTGGAGCTACTGTTGATACTGTCGTGCTGT
* * *
1296770 TGTTCATGCTTGCCTGCTTGTTGGAGCTGCTGTTGCTACTGTCGTGCT
1 TGTTCATGCTCGCCTGCTTGTTGGAGCTACTGTTGATACTGTCGTGCT
1296818 TGTTAGAGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.06, C:0.22, G:0.31, T:0.41
Consensus pattern (50 bp):
TGTTCATGCTCGCCTGCTTGTTGGAGCTACTGTTGATACTGTCGTGCTGT
Found at i:1296820 original size:30 final size:30
Alignment explanation
Indices: 1296784--1296934 Score: 205
Period size: 30 Copynumber: 5.1 Consensus size: 30
1296774 CATGCTTGCC
*
1296784 TGCTTGTTGGAGCTGCTGTTGCTACTGTCG
1 TGCTTGTTGGAGCTGCTGTTGCTGCTGTCG
* * * *
1296814 TGCTTGTTAGAGCTGTTGTTGTTGCTGCCG
1 TGCTTGTTGGAGCTGCTGTTGCTGCTGTCG
* *
1296844 TGCTTGTTGGAGCTGTTGTTGCTGCTATCG
1 TGCTTGTTGGAGCTGCTGTTGCTGCTGTCG
*
1296874 TGCTTGTTGGAGCTGCTGTTGTTGCTG-CG
1 TGCTTGTTGGAGCTGCTGTTGCTGCTGTCG
* *
1296903 TGCTTGTTGGAGCTGCTGTTGTTGCTATCG
1 TGCTTGTTGGAGCTGCTGTTGCTGCTGTCG
1296933 TG
1 TG
1296935 GAAGTTGTTG
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
29 28 0.26
30 79 0.74
ACGTcount: A:0.06, C:0.17, G:0.34, T:0.42
Consensus pattern (30 bp):
TGCTTGTTGGAGCTGCTGTTGCTGCTGTCG
Found at i:1296832 original size:60 final size:59
Alignment explanation
Indices: 1296765--1296934 Score: 232
Period size: 60 Copynumber: 2.8 Consensus size: 59
1296755 ATGCTGTCGT
** *
1296765 GCTGTTGTTCATGCTTGCCTGCTTGTTGGAGCTGCTGTTGCTACTGTCGTGCTTGTTAGA
1 GCTGTTGTTGTTGC-TGCCTGCTTGTTGGAGCTGCTGTTGCTACTATCGTGCTTGTTAGA
* * *
1296825 GCTGTTGTTGTTGCTGCCGTGCTTGTTGGAGCTGTTGTTGCTGCTATCGTGCTTGTTGGA
1 GCTGTTGTTGTTGCTGCC-TGCTTGTTGGAGCTGCTGTTGCTACTATCGTGCTTGTTAGA
* * * *
1296885 GCTGCTGTTGTTGCTGCGTGCTTGTTGGAGCTGCTGTTGTTGCTATCGTG
1 GCTGTTGTTGTTGCTGCCTGCTTGTTGGAGCTGCTGTTGCTACTATCGTG
1296935 GAAGTTGTTG
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
59 34 0.34
60 65 0.66
ACGTcount: A:0.06, C:0.18, G:0.34, T:0.42
Consensus pattern (59 bp):
GCTGTTGTTGTTGCTGCCTGCTTGTTGGAGCTGCTGTTGCTACTATCGTGCTTGTTAGA
Found at i:1296900 original size:12 final size:12
Alignment explanation
Indices: 1296825--1296928 Score: 52
Period size: 12 Copynumber: 8.2 Consensus size: 12
1296815 GCTTGTTAGA
*
1296825 GCTGTTGTTGTT
1 GCTGCTGTTGTT
1296837 GCTGCCGTGCTTGTT
1 GCTG-C-TG-TTGTT
**
1296852 GGAGCTGTTGTT
1 GCTGCTGTTGTT
* *
1296864 GCTGCTATCG-T
1 GCTGCTGTTGTT
**
1296875 GCT--TGTTGGA
1 GCTGCTGTTGTT
1296885 GCTGCTGTTGTT
1 GCTGCTGTTGTT
1296897 GCTGCGTGCTTGTT
1 GCTGC-TG-TTGTT
1296911 GGAGCTGCTGTTGTT
1 ---GCTGCTGTTGTT
1296926 GCT
1 GCT
1296929 ATCGTGGAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
9 3 0.04
10 3 0.04
11 4 0.06
12 28 0.41
13 4 0.06
14 8 0.12
15 12 0.17
16 2 0.03
17 5 0.07
ACGTcount: A:0.04, C:0.17, G:0.36, T:0.43
Consensus pattern (12 bp):
GCTGCTGTTGTT
Found at i:1297279 original size:16 final size:16
Alignment explanation
Indices: 1297254--1297294 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1297244 TGTTTCAGCA
*
1297254 CTTCACGTGCTACATG
1 CTTCATGTGCTACATG
1297270 CTTCATGTGCTACATG
1 CTTCATGTGCTACATG
*
1297286 TTTCATGTG
1 CTTCATGTG
1297295 TTTCTCCACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (16 bp):
CTTCATGTGCTACATG
Found at i:1297848 original size:17 final size:16
Alignment explanation
Indices: 1297812--1297850 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1297802 TAGTTTTTAT
* *
1297812 TTTTATTATTATATTT
1 TTTTATTATTATACTA
1297828 TTTTACTTATTATACTA
1 TTTTA-TTATTATACTA
1297845 TTTTAT
1 TTTTAT
1297851 ATCGAATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTATTATTATACTA
Found at i:1298410 original size:43 final size:43
Alignment explanation
Indices: 1298352--1299428 Score: 459
Period size: 42 Copynumber: 25.4 Consensus size: 43
1298342 CTCTAGGGTT
* * *
1298352 AAAGCCGATAGGCAGACTGAGGGATAGGAAAGTTTTCAAGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * * *
1298395 AAAGCTGACAAGCAGACTGAGGGATAGGAAAGTCTCTAGGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
** * * * * *
1298438 AAAGCCGACAGAAAGACTG-GGAATAGGAAAGTTTCTAGGGTT
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * * * *
1298480 AAAGCCGATAGGCAGAATTTA--GATAAGG-CACTCTCCAAGGTC
1 AAAGCCGACAGGCAG-ACTGAGGGAT-AGGAAAGTCTCCAAGGTC
* * *
1298522 AAAGCCGATAGGCAGACCGAGGGATAGGAAAGTCTCCAGGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * *
1298565 AAAGCCGATAGGCAGACTGAGGGATAAGAAAGCCTCCAAGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * * * * * *
1298608 AAAGCCGACATGTAGACTTTA--GATAAGGCAA-TCTCTAGGGTT
1 AAAGCCGACAGGCAGAC-TGAGGGAT-AGGAAAGTCTCCAAGGTC
* * * * * *
1298650 GAATCCGACAGACATACTTTA--GAT-GGAGTAGTCTCCAAGGTC
1 AAAGCCGACAGGCAGAC-TGAGGGATAGGA-AAGTCTCCAAGGTC
* * *
1298692 AAAGCCGACAGGTAGATTGA-GGATAGGAAAGTCTCCAGGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * * * * *
1298734 AAAGCCAATAGGCAGATTTTA--G-TTGAGACAGTCT-CAAGGGTC
1 AAAGCCGACAGGCAGA-CTGAGGGATAG-GAAAGTCTCCAA-GGTC
** * * * * * *
1298776 AAAGCTAACAGCCAAACTAAGGGACAGAAAAGTCTCCAAGGTG
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * * * *
1298819 AAAGCTGACAGGCAGATTTTA-GAATGAGGCAA-TCTCCAAGGTC
1 AAAGCCGACAGGCAGA-CTGAGGGAT-AGGAAAGTCTCCAAGGTC
* * * * * ** *
1298862 AAAGTCGATAAGCAAACTTTA-AAATGAGG-CAGTCTCCAAGGTC
1 AAAGCCGACAGGCAGAC-TGAGGGAT-AGGAAAGTCTCCAAGGTC
* * * *
1298905 AAAGCCGATAAGCAGACTAAGGG-TA-AAAAGGTCTCCAAGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAA-GTCTCCAAGGTC
* * * *
1298947 AAAGTCAACAGGCAGACTTAGGGATAGGAAAATCTCCAAGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
** * * * * *
1298990 AAAGTTGACACGTAGACTTTA--GATAAGG-CAGTCTCCTAGGGTC
1 AAAGCCGACAGGCAGAC-TGAGGGAT-AGGAAAGTCTCC-AAGGTC
* *
1299033 AAAGCCGACAGGCAGACTAAGGG-TAGGAAAGTCTCCATGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * * * *
1299075 -AAGCCGATAGGCAGGCTTA-GAATGAGG-CAGTCTCCAAGGTC
1 AAAGCCGACAGGCAGACTGAGGGAT-AGGAAAGTCTCCAAGGTC
** * *
1299116 AAAGCTAACAGGCAGACTAAGGG-TAGGAAAGTCTCCAGGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * * ** * * *
1299158 AAAGTCGACAGGTAGACTTA-AAATGAGG-CAGCCTCCAGGGTC
1 AAAGCCGACAGGCAGACTGAGGGAT-AGGAAAGTCTCCAAGGTC
* * * * * * * *
1299200 AAAGTCGACAAGCAGACTAAGGG-CACGAAAATCTCTAGGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * * * * * *
1299242 AAAGTCGACAGGCAAACTTA-GAATAAGG-CAGTCTCTAGGGTC
1 AAAGCCGACAGGCAGACTGAGGGAT-AGGAAAGTCTCCAAGGTC
* ** * * * * *
1299284 AAAGCTGATTGGCAGACTTA-GAATAAGG-CAGTCTTCAGGGTC
1 AAAGCCGACAGGCAGACTGAGGGAT-AGGAAAGTCTCCAAGGTC
* * * *
1299326 AAAGCCGACAGGCTGATTGAAGG-TAGAAAAGTCTCCAAGGTC
1 AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
* * ** *
1299368 AAAGCTGACAGGCAGACTTTA-AAATGAGG-TAGTCTCCAAGGTC
1 AAAGCCGACAGGCAGAC-TGAGGGAT-AGGAAAGTCTCCAAGGTC
*
1299411 AAAGCTGACAGGCAGACT
1 AAAGCCGACAGGCAGACT
1299429 TTAGACAGAG
Statistics
Matches: 786, Mismatches: 198, Indels: 101
0.72 0.18 0.09
Matches are distributed among these distances:
40 3 0.00
41 50 0.06
42 402 0.51
43 310 0.39
44 21 0.03
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (43 bp):
AAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGTC
Found at i:1298475 original size:42 final size:43
Alignment explanation
Indices: 1298343--1298617 Score: 202
Period size: 43 Copynumber: 6.4 Consensus size: 43
1298333 TAAGGTTGTC
* * *
1298343 TCTAGGGTTAAAGCCGATAGGCAGACTGAGGGATAGGAAAGTT
1 TCTAGGGTCAAAGCCGACAGACAGACTGAGGGATAGGAAAGTT
* * *
1298386 T-TCAAGGTCAAAGCTGACA-AGCAGACTGAGGGATAGGAAAGTC
1 TCT-AGGGTCAAAGCCGACAGA-CAGACTGAGGGATAGGAAAGTT
* *
1298429 TCTAGGGTCAAAGCCGACAGAAAGACTG-GGAATAGGAAAGTT
1 TCTAGGGTCAAAGCCGACAGACAGACTGAGGGATAGGAAAGTT
* * * * * * * *
1298471 TCTAGGGTTAAAGCCGATAGGCAGAATTTA--GATAAGG-CACTC
1 TCTAGGGTCAAAGCCGACAGACAG-ACTGAGGGAT-AGGAAAGTT
* * * * * *
1298513 TCCAAGGTCAAAGCCGATAGGCAGACCGAGGGATAGGAAAGTC
1 TCTAGGGTCAAAGCCGACAGACAGACTGAGGGATAGGAAAGTT
* * * * **
1298556 TCCAGGGTCAAAGCCGATAGGCAGACTGAGGGATAAGAAAGCC
1 TCTAGGGTCAAAGCCGACAGACAGACTGAGGGATAGGAAAGTT
* *
1298599 TCCAAGGTCAAAGCCGACA
1 TCTAGGGTCAAAGCCGACA
1298618 TGTAGACTTT
Statistics
Matches: 187, Mismatches: 35, Indels: 20
0.77 0.14 0.08
Matches are distributed among these distances:
41 2 0.01
42 61 0.33
43 122 0.65
44 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (43 bp):
TCTAGGGTCAAAGCCGACAGACAGACTGAGGGATAGGAAAGTT
Found at i:1298610 original size:170 final size:169
Alignment explanation
Indices: 1298299--1299222 Score: 683
Period size: 170 Copynumber: 5.4 Consensus size: 169
1298289 AAGAAAAGAT
* * ** * * *
1298299 TCTCCCGGGTCAAAGCCGACAGGTAGACTTTAGATAAGGTTGTCTCTAGGGTTAAAGCCGATAGG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGCCGATAGG
* * * * * *
1298364 CAGACTGAGGGATAGGAAAGTTTTCAAGGTCAAAGCTGACAAGCAGACTGAGGGATAGGAAAGTC
66 CAGACTGAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTGAGGGATAAGAAAGTC
* * *
1298429 TCTAGGGTCAAAGCCGACAGAAAGACT-GGGAATAGGAAAG
131 TCCAAGGTCAAAGCCAACAG-AAGACTAGGG-ATAGGAAAG
* * * * * *
1298469 TTTCTAGGGTTAAAGCCGATAGGCAGAATTTAGATAAGGCACTCTCCAAGGTCAAAGCCGATAGG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGCCGATAGG
* * *
1298534 CAGACCGAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGATAGGCAGACTGAGGGATAAGAAAGCC
66 CAGACTGAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTGAGGGATAAGAAAGTC
* * *** *
1298599 TCCAAGGTCAAAGCCGACATGTAGACTTTAGATAAGGCAA-
131 TCCAAGGTCAAAGCCAACA-GAAGACTAGGGAT-AGGAAAG
* ** * * * * * *
1298639 TCTCTAGGGTTGAATCCGACAGACATACTTTAGAT-GGAGTAGTCTCCAAGGTCAAAGCCGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATAAG-GCAGTCTCCAAGGTCAAAGCCGATAG
* * * * * * * * *
1298703 GTAGATTGA-GGATAGGAAAGTCTCCAGGGTCAAAGCCAATAGGCAGATTTTA--GTTGAGACAG
65 GCAGACTGAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGA-CTGAGGGATAAGAAAG
* * *
1298765 TCT-CAAGGGTCAAAGCTAACAGCCAA-ACTAAGGGACAGAAAAG
129 TCTCCAA-GGTCAAAGCCAACAG--AAGACT-AGGGATAGGAAAG
* * * * * * * *
1298808 TCTCCAAGGTGAAAGCTGACAGGCAGATTTTAGAATGAGGCAATCTCCAAGGTCAAAGTCGATAA
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAG-ATAAGGCAGTCTCCAAGGTCAAAGCCGATAG
* * ** * * *
1298873 GCAAACTTTA-AAATGAGG-CAGTCTCCAAGGTCAAAGCCGATAAGCAGACTAAGGG-TAA-AAA
65 GCAGAC-TGAGGGAT-AGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTGAGGGATAAGAAA
* * *
1298934 GGTCTCCAAGGTCAAAGTCAACAGGCAGACTTAGGGATAGGAAAA
128 -GTCTCCAAGGTCAAAGCCAACA-GAAGAC-TAGGGATAGGAAAG
* ** * * * *
1298979 TCTCCAAGGTCAAAGTTGACACGTAGACTTTAGATAAGGCAGTCTCCTAGGGTCAAAGCCGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTCC-AAGGTCAAAGCCGATAG
* * * * * * **
1299044 GCAGACTAAGGG-TAGGAAAGTCTCCATGGTC-AAGCCGATAGGCAGGCTTA-GAATGAGGCAGT
65 GCAGACTGAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTGAGGGATAAGAAAGT
* *
1299106 CTCCAAGGTCAAAGCTAACAGGCAGACTAAGGG-TAGGAAAG
130 CTCCAAGGTCAAAGCCAACA-GAAGACT-AGGGATAGGAAAG
* * * * * * * * * *
1299147 TCTCCAGGGTCAAAGTCGACAGGTAGACTTAAAATGAGGCAGCCTCCAGGGTCAAAGTCGACAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGCCGATAGG
*
1299212 CAGACTAAGGG
66 CAGACTGAGGG
1299223 CACGAAAATC
Statistics
Matches: 598, Mismatches: 129, Indels: 57
0.76 0.16 0.07
Matches are distributed among these distances:
167 31 0.05
168 77 0.13
169 117 0.20
170 250 0.42
171 114 0.19
172 9 0.02
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (169 bp):
TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGCCGATAGG
CAGACTGAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTGAGGGATAAGAAAGTC
TCCAAGGTCAAAGCCAACAGAAGACTAGGGATAGGAAAG
Found at i:1298944 original size:128 final size:126
Alignment explanation
Indices: 1298791--1299119 Score: 351
Period size: 128 Copynumber: 2.6 Consensus size: 126
1298781 TAACAGCCAA
* *
1298791 ACTAAGGGACAGAAAAGTCTCCAAGGTGAAAGCTGACAGGCAGATTTTAGAATGAGGCAATCTCC
1 ACTAAGGG-TAGAAAAGTCTCCAAGGT-AAAGCTGACAGGCAGA-CTTAGAATGAGGCAATCTCC
* * *
1298856 AAGGTCAAAGTCGATAAGCAAACTTTAAAATGAGGCAGTCTCC-AAGGTCAAAGCCGATAAGCAG
63 AAGGTCAAAGTCGACAAGCAAACTTT-AAATAAGGCAGTCTCCTAAGGTCAAAGCCGACAAGCAG
* * *
1298920 ACTAAGGGTA-AAAAGGTCTCCAAGGTCAAAG-TCAACAGGCAGACTTAGGGAT-AGGAAAATCT
1 ACTAAGGGTAGAAAA-GTCTCCAAGGT-AAAGCT-GACAGGCAGACTTA-GAATGAGG-CAATCT
* * * * * * *
1298982 CCAAGGTCAAAGTTGACACGTAGACTTTAGATAAGGCAGTCTCCTAGGGTCAAAGCCGACAGGCA
61 CCAAGGTCAAAGTCGACAAGCAAACTTTAAATAAGGCAGTCTCCTAAGGTCAAAGCCGACAAGCA
1299047 G
126 G
* * * * * * *
1299048 ACTAAGGGTAGGAAAGTCTCCATGGTCAAGCCGATAGGCAGGCTTAGAATGAGGCAGTCTCCAAG
1 ACTAAGGGTAGAAAAGTCTCCAAGGTAAAGCTGACAGGCAGACTTAGAATGAGGCAATCTCCAAG
1299113 GTCAAAG
66 GTCAAAG
1299120 CTAACAGGCA
Statistics
Matches: 166, Mismatches: 26, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
126 19 0.11
127 42 0.25
128 94 0.57
129 11 0.07
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (126 bp):
ACTAAGGGTAGAAAAGTCTCCAAGGTAAAGCTGACAGGCAGACTTAGAATGAGGCAATCTCCAAG
GTCAAAGTCGACAAGCAAACTTTAAATAAGGCAGTCTCCTAAGGTCAAAGCCGACAAGCAG
Found at i:1307456 original size:22 final size:20
Alignment explanation
Indices: 1307412--1307456 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
1307402 TAATTGGCTA
* *
1307412 TTTGCTAATTATGTTGACAT
1 TTTGCTAATGATGTTAACAT
1307432 TTTGCTAAATGATGGTTAACAT
1 TTTGCT-AATGAT-GTTAACAT
1307454 TTT
1 TTT
1307457 AAGGGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 5 0.24
22 10 0.48
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.49
Consensus pattern (20 bp):
TTTGCTAATGATGTTAACAT
Found at i:1307881 original size:78 final size:78
Alignment explanation
Indices: 1307794--1307943 Score: 178
Period size: 78 Copynumber: 1.9 Consensus size: 78
1307784 AGAGGCACTC
* * * * *
1307794 CCTACACATTCCTA-ATCATATCCTT-TCTTCCCAAATACCAGATGATGTTGGTGCATCACATGG
1 CCTACACATTCCTAGA-CATATCCTTCT-TTCCCAAACACCAAATGATATTGATGCATCACATGA
1307857 CCAAAAAGGATGTTT
64 CCAAAAAGGATGTTT
* * * *
1307872 CCTATACATTCCTAGACGTATCCTTCTTTCCCAAACACTAAATGGTATTGATGCATCACATGACC
1 CCTACACATTCCTAGACATATCCTTCTTTCCCAAACACCAAATGATATTGATGCATCACATGACC
*
1307937 ATAAAGG
66 AAAAAGG
1307944 GCATATCCCA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
78 58 0.97
79 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (78 bp):
CCTACACATTCCTAGACATATCCTTCTTTCCCAAACACCAAATGATATTGATGCATCACATGACC
AAAAAGGATGTTT
Found at i:1308574 original size:42 final size:42
Alignment explanation
Indices: 1308459--1309006 Score: 356
Period size: 42 Copynumber: 13.1 Consensus size: 42
1308449 GATATGCTTT
* ** *
1308459 ATCAATCGTCTGCCCATCGACTCAGGCTTGAGAGACTTCTTT-
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTT-TTTC
* * * *
1308501 ATCAATCG---ACCCGTTGGCTCAGACCCGGGAGACTTTTTC
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTTTTTC
* **
1308540 ATCAATCGTCTACCCATCAACTCAGGCCCGGGAGA-TTTCTTC
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTTT-TTC
* * * **
1308582 ATCAATCGTCT-CTCCGTCAGCTCAGACCCAAGAGACTTTTTC
1 ATCAATCGTCTGC-CCATCGGCTCAGGCCCGGGAGACTTTTTC
* ** * * ** *
1308624 ATCAATCATCTGCCTGTCAGCTCATGCCTAGGAGACTTCTTC
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTTTTTC
* * ** *
1308666 ATTAATCGTCTACCCATCGGCTCAGGCCTAGGAGACTTCTTC
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTTTTTC
* ** * *
1308708 ATCAATTGTCTGCCCATTAGCTCAGGCTCGGGAGACTTCTTC
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTTTTTC
* * * * * *
1308750 ATCAATTGTTTACCCATCGGCTCAGGCTCGAGAGACTCCTTT-
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACT-TTTTC
* *** * * * ** *
1308792 ATCAATCGTCTACTTGTTGGCTCAGTCTCGGGAGTTTTTTTT
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTTTTTC
* * ** *
1308834 ATCCATTGTCTGCCCATCGGCTCAGGATCGAGAGACTTTTTC
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTTTTTC
* *
1308876 ATCAATCGTCTGCCCGTCGACTCAGGCCCGGGAGACTTCTTT-
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTT-TTTC
* * * *** *
1308918 ATCAATTGTCTGCCGCGTCAGCTCAGGTTTGAGAGACTTCTTTC
1 ATCAATCGTCTGCC-CATCGGCTCAGGCCCGGGAGACTT-TTTC
* * * * *
1308962 AGCAATCATCTGCCCATTGGCTCAGTCTCGGGAGACTTTTTC
1 ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTTTTTC
1309004 ATC
1 ATC
1309007 CTTTGTTTAC
Statistics
Matches: 397, Mismatches: 96, Indels: 26
0.76 0.18 0.05
Matches are distributed among these distances:
38 3 0.01
39 27 0.07
41 7 0.02
42 301 0.76
43 48 0.12
44 11 0.03
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (42 bp):
ATCAATCGTCTGCCCATCGGCTCAGGCCCGGGAGACTTTTTC
Found at i:1309226 original size:168 final size:167
Alignment explanation
Indices: 1308996--1309352 Score: 468
Period size: 168 Copynumber: 2.1 Consensus size: 167
1308986 GTCTCGGGAG
*** * *
1308996 ACTTTTTCATCCTTTGTTTACCCATTGGCTTAGTCCCAAGTAAATCTCTTTTCTTCCGTTGACTT
1 ACTTTTT-ATCCTTTGTTTACCCATCAACCTAGTCCCAAGTAAATCTCTTTTCCTCCGTTGACTT
*
1309061 ATCGGTGTAATCCCGATCAACTTTTTATCCTTCATTCACCTGTCAGCTTCGTCCCAAGCACTTCA
65 ATCAGTGTAATCCCGATCAACTTTTTATCCTTCATTCACCTGTCAGCTTCGTCCCAAGCACTTCA
**
1309126 TTTTATCTTTTGTTGACTTGTC-AGTCCAATCCCGATCA
130 TTTTATCTTTTGTCAACTTGTCGA-TCCAATCCCGATCA
*
1309164 ACTTCTTTATCCTTTGTTTACCCATCAACCTAGTCCCGAGTAAATC-CTTTATCC-CTCGTTGAC
1 ACTT-TTTATCCTTTGTTTACCCATCAACCTAGTCCCAAGTAAATCTCTTT-TCCTC-CGTTGAC
* * * * * * * *
1309227 TTGTCAGTTTAATCTCGGTCAACTTTTTATCCTTCATTCACTTGTCGGCTTGGTCCCAAGTACTT
63 TTATCAGTGTAATCCCGATCAACTTTTTATCCTTCATTCACCTGTCAGCTTCGTCCCAAGCACTT
*
1309292 CCTTTTATCTTTTGTCAACTTGTCGATCCAATCCCGATCA
128 CATTTTATCTTTTGTCAACTTGTCGATCCAATCCCGATCA
*
1309332 ACTTATTTATCCTTTATTTAC
1 ACTT-TTTATCCTTTGTTTAC
1309353 TTGTCGACTT
Statistics
Matches: 165, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
167 5 0.03
168 156 0.95
169 4 0.02
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.42
Consensus pattern (167 bp):
ACTTTTTATCCTTTGTTTACCCATCAACCTAGTCCCAAGTAAATCTCTTTTCCTCCGTTGACTTA
TCAGTGTAATCCCGATCAACTTTTTATCCTTCATTCACCTGTCAGCTTCGTCCCAAGCACTTCAT
TTTATCTTTTGTCAACTTGTCGATCCAATCCCGATCA
Found at i:1309377 original size:168 final size:168
Alignment explanation
Indices: 1309026--1309399 Score: 457
Period size: 168 Copynumber: 2.2 Consensus size: 168
1309016 CCCATTGGCT
* * * *
1309026 TAGTCCCAAGTAAATCTCTTT-T-CTTCCGTTGACTTATCGGTGTAATCCCGATCAACTTTTTAT
1 TAGTCCCGAGTAAATC-CTTTATCCAT-CGTTGACTTGTCAGTGTAATCCCGATCAACTTTTTAT
**
1309089 CCTTCATTCACCTGTCAGCTTCGTCCCAAGCACTTCATTTTATCTTTTGTTGACTTGTCAGTCCA
64 CCTTCATTCACCTGTCAGCTTCGTCCCAAGCACTTCATTTTATCTTTTGTCAACTTGTCAGTCCA
* *
1309154 ATCCCGATCAACTTCTTTATCCTTTGTTTACCCATCAACC
129 ATCCCGATCAACTTATTTATCCTTTATTTACCCATCAACC
* * * *
1309194 TAGTCCCGAGTAAATCCTTTATCCCTCGTTGACTTGTCAGTTTAATCTCGGTCAACTTTTTATCC
1 TAGTCCCGAGTAAATCCTTTATCCATCGTTGACTTGTCAGTGTAATCCCGATCAACTTTTTATCC
* * * * *
1309259 TTCATTCACTTGTCGGCTTGGTCCCAAGTACTTCCTTTTATCTTTTGTCAACTTGTC-GATCCAA
66 TTCATTCACCTGTCAGCTTCGTCCCAAGCACTTCATTTTATCTTTTGTCAACTTGTCAG-TCCAA
*** * *
1309323 TCCCGATCAACTTATTTATCCTTTATTTACTTGTCGACT
130 TCCCGATCAACTTATTTATCCTTTATTTACCCATCAACC
* * * **
1309362 TAGTCTCGGGTAAATCTTTTATCCATTATTGACTTGTC
1 TAGTCCCGAGTAAATCCTTTATCCATCGTTGACTTGTC
1309400 GAATCAGTCT
Statistics
Matches: 176, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
167 5 0.03
168 169 0.96
169 2 0.01
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (168 bp):
TAGTCCCGAGTAAATCCTTTATCCATCGTTGACTTGTCAGTGTAATCCCGATCAACTTTTTATCC
TTCATTCACCTGTCAGCTTCGTCCCAAGCACTTCATTTTATCTTTTGTCAACTTGTCAGTCCAAT
CCCGATCAACTTATTTATCCTTTATTTACCCATCAACC
Found at i:1309381 original size:84 final size:83
Alignment explanation
Indices: 1309024--1309399 Score: 281
Period size: 84 Copynumber: 4.5 Consensus size: 83
1309014 TACCCATTGG
* ** * * **
1309024 CTTAGTCCCAAGTAAATCTCTTT-TCTTCCGTTGACTTATCGGTGTAATCCCGATCAACTTTTTA
1 CTTAGTCCCGAGTAAATCT-TTTATCTTTTGTTGACTTGTCAGTCCAATCCCGATCAACTTTTTA
* * *
1309088 TCCTTCATTCACCTGTC-A
65 TCCTTTATTTACTTGTCGA
* * * **
1309106 GCTTCGTCCCAAGCACTTCATTTTATCTTTTGTTGACTTGTCAGTCCAATCCCGATCAACTTCTT
1 -CTTAGTCCCGAGTAAATC-TTTTATCTTTTGTTGACTTGTCAGTCCAATCCCGATCAACTT-TT
* *** *
1309171 TATCCTTTGTTTACCCATCAA
63 TATCCTTTATTTACTTGTCGA
* * ** * ** * *
1309192 CCTAGTCCCGAGTAAATCCTTTATCCCTCGTTGACTTGTCAGTTTAATCTCGGTCAACTTTTTAT
1 CTTAGTCCCGAGTAAATCTTTTATCTTTTGTTGACTTGTCAGTCCAATCCCGATCAACTTTTTAT
* * *
1309257 CCTTCATTCACTTGTCGG
66 CCTTTATTTACTTGTCGA
* * ** **
1309275 CTTGGTCCCAAGTACTTCCTTTTATCTTTTGTCAACTTGTC-GATCCAATCCCGATCAACTTATT
1 CTTAGTCCCGAGTAAAT-CTTTTATCTTTTGTTGACTTGTCAG-TCCAATCCCGATCAACTT-TT
1309339 TATCCTTTATTTACTTGTCGA
63 TATCCTTTATTTACTTGTCGA
* * ** *
1309360 CTTAGTCTCGGGTAAATCTTTTATCCATTATTGACTTGTC
1 CTTAGTCCCGAGTAAATCTTTTATCTTTTGTTGACTTGTC
1309400 GAATCAGTCT
Statistics
Matches: 220, Mismatches: 66, Indels: 13
0.74 0.22 0.04
Matches are distributed among these distances:
83 45 0.20
84 115 0.52
85 59 0.27
86 1 0.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (83 bp):
CTTAGTCCCGAGTAAATCTTTTATCTTTTGTTGACTTGTCAGTCCAATCCCGATCAACTTTTTAT
CCTTTATTTACTTGTCGA
Found at i:1310178 original size:21 final size:22
Alignment explanation
Indices: 1310138--1310179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1310128 ATGTGTCAAA
* *
1310138 TTTTAGAAATTTATTTATTTTG
1 TTTTAGAAATTCAATTATTTTG
1310160 TTTTAGAAA-TCAATTATTTT
1 TTTTAGAAATTCAATTATTTT
1310180 CCCAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTTAGAAATTCAATTATTTTG
Found at i:1311866 original size:13 final size:13
Alignment explanation
Indices: 1311848--1311884 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1311838 ACAATGTTCT
1311848 TTGTATCGATACA
1 TTGTATCGATACA
1311861 TTGTATCGATACA
1 TTGTATCGATACA
* *
1311874 ATGTGTCGATA
1 TTGTATCGATA
1311885 TATGGGTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1314378 original size:20 final size:19
Alignment explanation
Indices: 1314326--1314382 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1314316 TTGTATCGAT
*
1314326 ACATTGTATTGATACATGT
1 ACATTGTATTGATACATGC
* *
1314345 TCATTGCATTGATACATGC
1 ACATTGTATTGATACATGC
*
1314364 ACAATTGTATCGATACATG
1 AC-ATTGTATTGATACATG
1314383 AAATTGGTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
ACATTGTATTGATACATGC
Found at i:1314450 original size:13 final size:13
Alignment explanation
Indices: 1314432--1314456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1314422 CATGGCAGAT
1314432 TGTATCGATACAA
1 TGTATCGATACAA
1314445 TGTATCGATACA
1 TGTATCGATACA
1314457 TGAAGAATTG
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
Done.