Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009584.1 Hibiscus syriacus cultivar Beakdansim tig00116961_pilon, whole genome shotgun sequence
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: 2003061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1594480 original size:138 final size:138
Alignment explanation
Indices: 1594132--1594543 Score: 425
Period size: 138 Copynumber: 3.0 Consensus size: 138
1594122 TTATGTATAC
* * * * * * * * **
1594132 TGGAGATAATATGCTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGAAACTGCTCCTACG
1 TGGAGATAACACGGTTCCTACGTGATAAAGAAGTCTGGTTATATAAGGGTGACACAACTCCTACG
** * ** * * * * *
1594197 TGATGAGGAAATCTGGTCAGTAGATTACACAGTTCCTACGTGATGAGGATGGTTGGCCATCTTTA
66 TGACAAGGACATCCAGTCAGTGGATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTA
1594262 GGGAT-AA
131 GGGATAAA
* * * *
1594269 TGGAGATAACACGGTTTCTACGTGATAAGGAAGTCTGGTTATATAAGGGTGACACGACTTCTACG
1 TGGAGATAACACGGTTCCTACGTGATAAAGAAGTCTGGTTATATAAGGGTGACACAACTCCTACG
* * * *
1594334 TGACAAGGAGATCCAGTCAGTGGATGACGCGGTTCCTACGTGATGTGGACGTG-TGGCCATCTTC
66 TGACAAGGACATCCAGTCAGTGGATGACACGGTTCCTACGTGATGAGGACG-GCTGGCCATCTTT
1594398 AGGGATAAA
130 AGGGATAAA
* * * * * *
1594407 TGGTGATAACATGGTTCCTACGTGATAAAGATAGT-TGGTTATCTAAGGTTGACTCAACTCCTAT
1 TGGAGATAACACGGTTCCTACGTGATAAAGA-AGTCTGGTTATATAAGGGTGACACAACTCCTAC
* ** * *
1594471 GTGATAAGGACATCTGGTCAGTGGATGACATGATTCCTACGTGATGAGGACGGCTGGCCATCTTT
65 GTGACAAGGACATCCAGTCAGTGGATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTT
*
1594536 AGAGATAA
130 AGGGATAA
1594544 TTATTTCAAG
Statistics
Matches: 228, Mismatches: 43, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
137 111 0.49
138 114 0.50
139 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (138 bp):
TGGAGATAACACGGTTCCTACGTGATAAAGAAGTCTGGTTATATAAGGGTGACACAACTCCTACG
TGACAAGGACATCCAGTCAGTGGATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTA
GGGATAAA
Found at i:1594660 original size:66 final size:67
Alignment explanation
Indices: 1594544--1594717 Score: 271
Period size: 67 Copynumber: 2.6 Consensus size: 67
1594534 TTAGAGATAA
* * * *
1594544 TTATTTCAAGAGAAACGGTCTCAAGCGAGACAAAATTTGTTTCAATGG-AAAGAGACTCAAAGAT
1 TTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTATCAATGGAAAACAGACTCAAAGAT
1594608 TT
66 TT
*
1594610 TTATTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTATCAA-GGAAAACAGACTCAAAGA
1 TTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTATCAATGGAAAACAGACTCAAAGA
1594674 TTT
65 TTT
*
1594677 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTA
1 TTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTA
1594718 ATATTAACAG
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
66 40 0.40
67 59 0.60
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (67 bp):
TTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTATCAATGGAAAACAGACTCAAAGAT
TT
Found at i:1594927 original size:36 final size:36
Alignment explanation
Indices: 1594877--1595009 Score: 151
Period size: 39 Copynumber: 3.6 Consensus size: 36
1594867 CATCTCAAAG
1594877 GAAAAA-TGTCTCAAGCGAGACAAAATTTGTTTTGA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
* * *
1594912 GAAAATTTGTCTCAAGTGAGACAAAATTTATTTTTAGA
1 GAAAAATTGTCTCAAGCGAGACAAAATTT-GTTTT-GA
* * * *
1594950 GAAAAGACTATCTCAAGCAAGACAAAATTTGTTTTTAA
1 GAAAA-ATTGTCTCAAGCGAGACAAAATTTG-TTTTGA
*
1594988 GAAAAATTGTCTCTAGCGAGAC
1 GAAAAATTGTCTCAAGCGAGAC
1595010 GACACTTTGT
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
35 5 0.06
36 21 0.27
37 17 0.22
38 13 0.16
39 23 0.29
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (36 bp):
GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
Found at i:1594938 original size:21 final size:21
Alignment explanation
Indices: 1594883--1594940 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
1594873 AAAGGAAAAA
*
1594883 TGTCTCAAGCGAGACAAAATT
1 TGTCTCAAGTGAGACAAAATT
*
1594904 TGT-T---TTGAG--AAAATT
1 TGTCTCAAGTGAGACAAAATT
1594919 TGTCTCAAGTGAGACAAAATT
1 TGTCTCAAGTGAGACAAAATT
1594940 T
1 T
1594941 ATTTTTAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 12
0.65 0.07 0.28
Matches are distributed among these distances:
15 9 0.32
16 1 0.04
17 3 0.11
19 4 0.14
20 1 0.04
21 10 0.36
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTCTCAAGTGAGACAAAATT
Found at i:1596566 original size:25 final size:23
Alignment explanation
Indices: 1596536--1596604 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 23
1596526 TTTTATTTTC
*
1596536 AAAATTTTGAAAAATATTAATTA
1 AAAATTTTGAAAAATATTAATCA
*
1596559 AAGGAATTTTGAAAAATGTTTAATCA
1 AA--AATTTTGAAAAAT-ATTAATCA
1596585 AAAATTTTGAAAACATATTA
1 AAAATTTTGAAAA-ATATTA
1596605 CCCCTTTCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 2 0.05
24 14 0.36
25 15 0.38
26 8 0.21
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (23 bp):
AAAATTTTGAAAAATATTAATCA
Found at i:1597488 original size:12 final size:11
Alignment explanation
Indices: 1597473--1597565 Score: 64
Period size: 12 Copynumber: 8.0 Consensus size: 11
1597463 TCTTGTCTTC
1597473 TTTCTTTATTTT
1 TTTCTTT-TTTT
*
1597485 TTTCTTTGGTTT
1 TTTCTTT-TTTT
1597497 TTTCTTTGTTTT
1 TTTCTTT-TTTT
*
1597509 TTT-TTTCTTTG
1 TTTCTTT-TTTT
*
1597520 CTTCTTTTTTCT
1 TTTCTTTTTT-T
*
1597532 TTGC-TTTTTT
1 TTTCTTTTTTT
*
1597542 CTTCTTTGTTTT
1 TTTCTTT-TTTT
1597554 TTCTCTTTTTTT
1 TT-TCTTTTTTT
1597566 GGTTTGATCT
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
10 3 0.05
11 18 0.28
12 38 0.59
13 5 0.08
ACGTcount: A:0.01, C:0.13, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:1597512 original size:15 final size:15
Alignment explanation
Indices: 1597494--1597555 Score: 90
Period size: 15 Copynumber: 4.2 Consensus size: 15
1597484 TTTTCTTTGG
*
1597494 TTTTTTCTTTGTTTT
1 TTTTTTCTTTGCTTT
*
1597509 TTTTTTCTTTGCTTC
1 TTTTTTCTTTGCTTT
1597524 TTTTTTCTTTGCTTT
1 TTTTTTCTTTGCTTT
*
1597539 TTTCTTCTTTG-TTT
1 TTTTTTCTTTGCTTT
1597553 TTT
1 TTT
1597556 CTCTTTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
14 6 0.14
15 37 0.86
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTTCTTTGCTTT
Found at i:1598442 original size:12 final size:11
Alignment explanation
Indices: 1598414--1598452 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1598404 TCAATCATTA
*
1598414 AAATATTTAAA
1 AAATATTTAAG
1598425 AAATATTTAAG
1 AAATATTTAAG
*
1598436 CAAATATTAAAG
1 -AAATATTTAAG
1598448 AAATA
1 AAATA
1598453 ACAAAAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (11 bp):
AAATATTTAAG
Found at i:1601228 original size:2 final size:2
Alignment explanation
Indices: 1601221--1601295 Score: 66
Period size: 2 Copynumber: 38.5 Consensus size: 2
1601211 AATATGAATA
* * ** * *
1601221 AT AT AT AT AT AT AT AT AT AT AT GAG AT A- AT TT AT GC AT AC AC
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
1601263 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1601296 AGAAATCTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
1 3 0.05
2 55 0.93
3 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1603440 original size:12 final size:12
Alignment explanation
Indices: 1603425--1603459 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1603415 AAAATAGTGT
1603425 TAATATTAATAA
1 TAATATTAATAA
*
1603437 TAATATTAGTAA
1 TAATATTAATAA
*
1603449 TAATATCAATA
1 TAATATTAATA
1603460 TTATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:1606490 original size:29 final size:30
Alignment explanation
Indices: 1606433--1606490 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1606423 ATACAATTTC
**
1606433 TAAATTTGACACCCAAAAATATTTTTTCTT
1 TAAATTTGACACCCAAAAATAAATTTTCTT
*
1606463 TAAATTTGACACTC-AAAATAAATTTTCT
1 TAAATTTGACACCCAAAAATAAATTTTCT
1606491 AGTGCCGCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.41
Consensus pattern (30 bp):
TAAATTTGACACCCAAAAATAAATTTTCTT
Found at i:1607289 original size:27 final size:27
Alignment explanation
Indices: 1607254--1607324 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
1607244 AATGTAATTT
* *
1607254 ATTTTATTTTATTCTATACAAATTAAA
1 ATTTCATTTGATTCTATACAAATTAAA
1607281 ATTTCATTTGATTCTATACAAATTAAA
1 ATTTCATTTGATTCTATACAAATTAAA
1607308 ATTTCATTTGATTCTAT
1 ATTTCATTTGATTCTAT
1607325 TTTCAGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.51
Consensus pattern (27 bp):
ATTTCATTTGATTCTATACAAATTAAA
Found at i:1608146 original size:2 final size:2
Alignment explanation
Indices: 1608139--1608169 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1608129 ATTTAAGGTT
1608139 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 T
1608170 TGTTGTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1608968 original size:23 final size:23
Alignment explanation
Indices: 1608921--1608989 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
1608911 TAATATTTGA
* *
1608921 GAACATGTTCATTTATATGTTCAC
1 GAACGTGTTCATTTA-GTGTTCAC
1608945 GAACGTGTTCATTTAGTGTTCAC
1 GAACGTGTTCATTTAGTGTTCAC
1608968 GAACGTGTTCATTTAGTGTTCA
1 GAACGTGTTCATTTAGTGTTCA
1608990 AGAATATGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
23 29 0.67
24 14 0.33
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (23 bp):
GAACGTGTTCATTTAGTGTTCAC
Found at i:1609005 original size:23 final size:23
Alignment explanation
Indices: 1608920--1609012 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 23
1608910 TTAATATTTG
* *
1608920 AGAACATGTTCATTTATATGTTCA
1 AGAACATGCTCATTTA-GTGTTCA
* * *
1608944 CGAACGTGTTCATTTAGTGTTCA
1 AGAACATGCTCATTTAGTGTTCA
* * *
1608967 CGAACGTGTTCATTTAGTGTTCA
1 AGAACATGCTCATTTAGTGTTCA
* * *
1608990 AGAATATGCTCGTTTAGTATTCA
1 AGAACATGCTCATTTAGTGTTCA
1609013 TTTAGTTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
23 46 0.77
24 14 0.23
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (23 bp):
AGAACATGCTCATTTAGTGTTCA
Found at i:1610152 original size:36 final size:31
Alignment explanation
Indices: 1610075--1610147 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
1610065 TTTTATTGTT
*
1610075 TCGGGTCGGGTTTCTAATTTATATATTCGGG
1 TCGGGTCGGGTTTCTAATTCATATATTCGGG
1610106 TCGGGTCGGGTTTCTAATTCATATATTCGGG
1 TCGGGTCGGGTTTCTAATTCATATATTCGGG
*
1610137 TTGGGTCGGGT
1 TCGGGTCGGGT
1610148 CGGGTGAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.14, C:0.14, G:0.33, T:0.40
Consensus pattern (31 bp):
TCGGGTCGGGTTTCTAATTCATATATTCGGG
Found at i:1610551 original size:258 final size:263
Alignment explanation
Indices: 1610106--1610705 Score: 838
Period size: 259 Copynumber: 2.3 Consensus size: 263
1610096 TATATTCGGG
1610106 TCGGGTCGGGTTTCTAATTCATATATTCGGGTTGGGTCGGGTCGGGTGAAACTTTATTTTGGTCG
1 TCGGGTCGGGTTTCTAATTCATATATTCGGGTT-GGT----TCGGGTGAAACTTTATTTTGGTCG
* * *
1610171 CGTCGGGTCGATTTTTTTAAGTGCGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAT
61 GGTCAGGTCGATTTTTTTAAGTGCGATATTCGGGTCGGG-CGAGTTCGGATTTAGGGTGAAAAAT
* *
1610236 GCCCGACCCGACCCGACCAGAAAATATATATAATTTTACATTATATATTTAGGAATAATTACAAT
125 ACCCGACCCAACCCGACCAGAAAATATATATAATTTTACATTATATATTTAGGAATAATTACAAT
*
1610301 AATACCCCTCTATATATAT-TTTTTTTCAATTAAGTCATTATTTTTATTGAATAAAAATAATTTT
190 AATACCCCTCTATATATATATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTT
1610365 TTTATTATT
255 TTTATTATT
* * * * * *
1610374 TCGGGTAGGGTTTCTAATTCGTATATTCGGGTTGGTTTGAGTGAAACTTTATTTTGGACGGGTTA
1 TCGGGTCGGGTTTCTAATTCATATATTCGGGTTGGTTCGGGTGAAACTTTATTTTGGTCGGGTCA
* * *
1610439 GTTCCGGTTTTTTTAAGTGTGATATTCGGGTC-GG-G-G-TCGGATTTAGGGTGAAAAATACCCG
66 GGT-CGATTTTTTTAAGTGCGATATTCGGGTCGGGCGAGTTCGGATTTAGGGTGAAAAATACCCG
*
1610500 ACCCAACCCGACCCA-AAAA-ATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATA
130 ACCCAACCCGA-CCAGAAAATATATATAATTTTACATTATATATTTAGGAATAATTACAATAATA
* * *
1610563 CCCCTCTCTATATATATTTTTTTCAATTAAGTCACTGTTTTTATTGCATAAAAATAATTTTTTTA
194 CCCCTCTATATATATATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTTTTTA
1610628 TTATT
259 TTATT
*
1610633 TCGGGTCGGTCGGGTTTCTAATTCATATATTCGGGTCAGG-TCGGGTGAAACTTTATTTTGGTCG
1 TC--G--GGTCGGGTTTCTAATTCATATATTCGGGT-TGGTTCGGGTGAAACTTTATTTTGGTCG
*
1610697 GGTCTGGTC
61 GGTCAGGTC
1610706 TCAGATGGAG
Statistics
Matches: 296, Mismatches: 28, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
258 57 0.19
259 90 0.30
260 4 0.01
261 2 0.01
262 1 0.00
263 80 0.27
264 28 0.09
267 3 0.01
268 31 0.10
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (263 bp):
TCGGGTCGGGTTTCTAATTCATATATTCGGGTTGGTTCGGGTGAAACTTTATTTTGGTCGGGTCA
GGTCGATTTTTTTAAGTGCGATATTCGGGTCGGGCGAGTTCGGATTTAGGGTGAAAAATACCCGA
CCCAACCCGACCAGAAAATATATATAATTTTACATTATATATTTAGGAATAATTACAATAATACC
CCTCTATATATATATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTTTTTATT
ATT
Found at i:1611052 original size:18 final size:18
Alignment explanation
Indices: 1611029--1611063 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1611019 AATTTATGGT
1611029 AGATTCCAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
1611047 AGATTCCAATTCCTTCA
1 AGATTCCAATTCCTTCA
1611064 TAAACATTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:1614180 original size:41 final size:41
Alignment explanation
Indices: 1614017--1614448 Score: 439
Period size: 41 Copynumber: 10.5 Consensus size: 41
1614007 GGTTTATAGC
* * * *
1614017 GGCGTTTTTAGAACAAACGCGGCTAAAGACTCATACTTTAGC
1 GGCGTTTTTA-TACAAACGCCGCTATAGACTCATACTTTAGT
* * * *
1614059 GGTGTTTCTATA-AAACGCCGCTAAATACT-ATACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGT
* * **
1614098 GGCGTTTCTATA-AAAGCGCCGCTAAAGA-TTGTACTTTAGT
1 GGCGTTTTTATACAAA-CGCCGCTATAGACTCATACTTTAGT
* * *
1614138 GGCATTTTTATACAAACGCCGCTATAGAATCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGT
* * *
1614179 GGCATTTTTATATAAACGCCGCTATAGACT-ACTACCTATAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCA-TA-CTTTAGT
1614221 GGC-TTTTTATACAAACGCCGCTATAGACTCATGA-TTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCAT-ACTTTAGT
* * *
1614261 GGCGTTTGTGTTTACAAACGCCGCTATAGATTCATACCTTAGT
1 GGCGTTT-T-TATACAAACGCCGCTATAGACTCATACTTTAGT
* * *
1614304 GG-GTTTTTATATAAACGCCGCTAAAGACTCAAACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGT
* * *
1614344 GGCGTTTGTATTCAAACGCCGCTAGAGACTCATACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGT
* * * **
1614385 GGCGTTTTTATGCAAACGCCACTATAGACTCGTGTTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGT
*
1614426 GGCGTTTGTTTTACAAACGCCGC
1 GGCGTTT-TTATACAAACGCCGC
1614449 AAGTTTACAA
Statistics
Matches: 333, Mismatches: 43, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
39 24 0.07
40 93 0.28
41 149 0.45
42 37 0.11
43 30 0.09
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGT
Found at i:1614342 original size:165 final size:164
Alignment explanation
Indices: 1614030--1614448 Score: 460
Period size: 165 Copynumber: 2.6 Consensus size: 164
1614020 GTTTTTAGAA
* * * * * * * * *
1614030 CAAACGCGGCTAAAGACTCATACTTTAGCGGTGTTTCTATA-AAACGCCGCTAAATACT-AT-AC
1 CAAACGCCGCTAGAGACTCATACTATAGTGGCGTTTTTATACAAACGCCACTATAGACTCATGA-
* * * *
1614092 TTTAGTGGCGTTT-CTATA-AAAGCGCCGCTAAAGATTGTACTTTAGTGGCATTTTTATACAAAC
65 TTTAGTGGCGTTTGTTTTACAAA-CGCCGCTAAAGATTATACCTTAGTGGCATTTTTATACAAAC
* ** *
1614155 GCCGCTATAGAATCGTACTTTAGTGGCATTTTTATAT
129 GCCGCTAAAGAATCAAACTTTAGTGGCATTTGTAT-T
* *
1614192 -AAACGCCGCTATAGACT-ACTACCTATAGTGGC-TTTTTATACAAACGCCGCTATAGACTCATG
1 CAAACGCCGCTAGAGACTCA-TA-CTATAGTGGCGTTTTTATACAAACGCCACTATAGACTCATG
* * *
1614254 ATTTAGTGGCGTTTGTGTTTACAAACGCCGCTATAGATTCATACCTTAGTGG-GTTTTTATATAA
64 ATTTAGTGGCGTTTGT-TTTACAAACGCCGCTAAAGATT-ATACCTTAGTGGCATTTTTATACAA
* *
1614318 ACGCCGCTAAAGACTCAAACTTTAGTGGCGTTTGTATT
127 ACGCCGCTAAAGAATCAAACTTTAGTGGCATTTGTATT
* * * *
1614356 CAAACGCCGCTAGAGACTCATACTTTAGTGGCGTTTTTATGCAAACGCCACTATAGACTCGTGTT
1 CAAACGCCGCTAGAGACTCATACTATAGTGGCGTTTTTATACAAACGCCACTATAGACTCATGAT
1614421 TTAGTGGCGTTTGTTTTACAAACGCCGC
66 TTAGTGGCGTTTGTTTTACAAACGCCGC
1614449 AAGTTTACAA
Statistics
Matches: 218, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
160 1 0.00
161 24 0.11
162 22 0.10
163 15 0.07
164 25 0.11
165 117 0.54
166 14 0.06
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (164 bp):
CAAACGCCGCTAGAGACTCATACTATAGTGGCGTTTTTATACAAACGCCACTATAGACTCATGAT
TTAGTGGCGTTTGTTTTACAAACGCCGCTAAAGATTATACCTTAGTGGCATTTTTATACAAACGC
CGCTAAAGAATCAAACTTTAGTGGCATTTGTATT
Found at i:1614444 original size:124 final size:123
Alignment explanation
Indices: 1614017--1614448 Score: 437
Period size: 124 Copynumber: 3.5 Consensus size: 123
1614007 GGTTTATAGC
* * * * * * * *
1614017 GGCGTTTTTAGAACAAACGCGGCTAAAGACTCATACTTTAGCGGTGTTTCTATA-AAACGCCGCT
1 GGCGTTTTTA-TACAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTATATAAACGCCGCT
* * * **
1614081 AAATACT-ATACTTTAGTGGCGTTTCTA-TAAAAGCGCCGCTAAAGA-TTGTACTTTAGT
65 AAAGACTCAAACTTTAGTGGCGTTTCTATTCAAA-CGCCGCTAAAGACTCATACTTTAGT
* *
1614138 GGCATTTTTATACAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTTTATATAAACGCCGCTA
1 GGCGTTTTTATACAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTATATAAACGCCGCTA
* * * * * * *
1614203 TAGACTACTACCTATAGTGGC-TTTTTATACAAACGCCGCTATAGACTCATGA-TTTAGT
66 AAGACT-CAAACTTTAGTGGCGTTTCTATTCAAACGCCGCTAAAGACTCAT-ACTTTAGT
* * * *
1614261 GGCGTTTGTGTTTACAAACGCCGCTATAGATTCATACCTTAGTGG-GTTTTTATATAAACGCCGC
1 GGCGTTT-T-TATACAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTATATAAACGCCGC
* *
1614325 TAAAGACTCAAACTTTAGTGGCGTTTGTATTCAAACGCCGCTAGAGACTCATACTTTAGT
64 TAAAGACTCAAACTTTAGTGGCGTTTCTATTCAAACGCCGCTAAAGACTCATACTTTAGT
* * * ** * *
1614385 GGCGTTTTTATGCAAACGCCACTATAGACTCGTGTTTTAGTGGCGTTTGTTTTACAAACGCCGC
1 GGCGTTTTTATACAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTT-TTATATAAACGCCGC
1614449 AAGTTTACAA
Statistics
Matches: 254, Mismatches: 45, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
120 34 0.13
121 24 0.09
122 43 0.17
123 43 0.17
124 79 0.31
125 31 0.12
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (123 bp):
GGCGTTTTTATACAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTATATAAACGCCGCTA
AAGACTCAAACTTTAGTGGCGTTTCTATTCAAACGCCGCTAAAGACTCATACTTTAGT
Found at i:1617993 original size:43 final size:43
Alignment explanation
Indices: 1617922--1618355 Score: 531
Period size: 43 Copynumber: 10.1 Consensus size: 43
1617912 AAGGAAATTA
*
1617922 GCGGCGTTTGTATCC-AAAAACACCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAAACGCCGCTATAGATCTGACCTTTT
* * * * *
1617965 GCGGTGTTTGTTCCAAAAAACGCTGCTATATATATGATCTTTT
1 GCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCTGACCTTTT
* *
1618008 GCGACGTTTGTTCCAAAAAACGCCGCTATATATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCTGACCTTTT
* * *
1618051 GCGGTGTTTCTTCTAAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCTGACCTTTT
*
1618094 GCGGTGTTTGTTCCAAAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCC-AAAAAACGCCGCTATAGATCTGACCTTTT
* * * * *
1618138 GCTGCGTTTGTTCC-AAAAATGCCACTATATATCTGATCTTTT
1 GCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCTGACCTTTT
* * *
1618180 GCAGTGTTTGTTCCATAAAACGCCGCTATAGATCTGA-CTTATT
1 GCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCTGACCTT-TT
* * *
1618223 GGGGCGTTTGTTCC--AAAACGCCGCTATAGATATCAACCTTTT
1 GCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCT-GACCTTTT
*
1618265 GCGGCGTTTGTTCC-AAAAACGCCGCTATAGATCTCAACCTTTT
1 GCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCT-GACCTTTT
* *
1618308 GCAGCGTTTGTTCC-AAAAACGCCGCTATAGATCTTGACCTATT
1 GCGGCGTTTGTTCCAAAAAACGCCGCTATAGATC-TGACCTTTT
1618351 GCGGC
1 GCGGC
1618356 ATTTTTGGTT
Statistics
Matches: 342, Mismatches: 41, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
41 18 0.05
42 58 0.17
43 224 0.65
44 42 0.12
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:1618528 original size:17 final size:17
Alignment explanation
Indices: 1618508--1618566 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
1618498 TTTAGGGAAG
1618508 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
1618525 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
1618541 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
1618558 TAGTTCATT
1 TAGTTCATT
1618567 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:1618580 original size:18 final size:18
Alignment explanation
Indices: 1618557--1618602 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1618547 ATTCATGCAT
1618557 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
1618575 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
1618593 TTATTTCATT
1 TTAGTTCATT
1618603 AAACAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:1619046 original size:200 final size:202
Alignment explanation
Indices: 1618701--1619102 Score: 790
Period size: 200 Copynumber: 2.0 Consensus size: 202
1618691 TGAACAGTCT
1618701 CAACAGATGCAAGAATATCAGTCAGAATGTATTCTAATTCTGGATGCGATATAGATATTTTTGGG
1 CAACAGATGCAAGAATATCAGTCAGAATGTATTCTAATTCTGGATGCGATATAGATATTTTTGGG
1618766 TCCAGAAACCACTTGGACATTATTCCTCTATCTCTTAGCTTTCCAACGCCTTTTGAATCATCTCA
66 TCCAGAAACCACTTGGACATTATTCCTCTATCTCTTAGCTTTCCAACGCCTTTTGAATCATCTCA
1618831 ATCCGATATCGGGAGCTTGAGATATGATCGAATCACAAAAGAAATTGTAGGCTGGAATTTTCATT
131 ATCCGATATCGGGAGCTTGAGATATGATCGAATCACAAAAGAAATTGTAGGCTGGAATTTTCATT
1618896 ACGGGAA
196 ACGGGAA
1618903 CAACAGATGCAAGAATATCAGTCAGAATGTATTCTAATTCT-GATGCGATATAGATA-TTTTGGG
1 CAACAGATGCAAGAATATCAGTCAGAATGTATTCTAATTCTGGATGCGATATAGATATTTTTGGG
1618966 TCCAGAAACCACTTGGACATTATTCCTCTATCTCTTAGCTTTCCAACGCCTTTTGAATCATCTCA
66 TCCAGAAACCACTTGGACATTATTCCTCTATCTCTTAGCTTTCCAACGCCTTTTGAATCATCTCA
1619031 ATCCGATATCGGGAGCTTGAGATATGATCGAATCACAAAAGAAATTGTAGGCTGGAATTTTCATT
131 ATCCGATATCGGGAGCTTGAGATATGATCGAATCACAAAAGAAATTGTAGGCTGGAATTTTCATT
1619096 ACGGGAA
196 ACGGGAA
1619103 TTTCATGCAT
Statistics
Matches: 200, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
200 144 0.72
201 15 0.08
202 41 0.20
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (202 bp):
CAACAGATGCAAGAATATCAGTCAGAATGTATTCTAATTCTGGATGCGATATAGATATTTTTGGG
TCCAGAAACCACTTGGACATTATTCCTCTATCTCTTAGCTTTCCAACGCCTTTTGAATCATCTCA
ATCCGATATCGGGAGCTTGAGATATGATCGAATCACAAAAGAAATTGTAGGCTGGAATTTTCATT
ACGGGAA
Found at i:1621650 original size:43 final size:43
Alignment explanation
Indices: 1621593--1621747 Score: 166
Period size: 43 Copynumber: 3.6 Consensus size: 43
1621583 TTTTCAGGTA
* * * *
1621593 AAAAACGTCGCTAAATAACAAACATGTTACGGCGTTTGTGCCT
1 AAAAATGTCGCTAAATAACAAACCTTTTACGGCATTTGTGCCT
** * *
1621636 AAAAATGTCGCTAAATAACAAACCCTTTTGTGACATCTGTGCCT
1 AAAAATGTCGCTAAATAACAAA-CCTTTTACGGCATTTGTGCCT
* * * ** *
1621680 AAAAATGCCGTTAAATAATAAACCTTTTACGGTTTTTGTGACT
1 AAAAATGTCGCTAAATAACAAACCTTTTACGGCATTTGTGCCT
*
1621723 AAAAATGTCGCTAAATAACATACCT
1 AAAAATGTCGCTAAATAACAAACCT
1621748 ATTGCGGAGT
Statistics
Matches: 89, Mismatches: 22, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
43 56 0.63
44 33 0.37
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (43 bp):
AAAAATGTCGCTAAATAACAAACCTTTTACGGCATTTGTGCCT
Found at i:1625095 original size:36 final size:35
Alignment explanation
Indices: 1624986--1625226 Score: 252
Period size: 36 Copynumber: 6.7 Consensus size: 35
1624976 ATATTTTTAA
1624986 AAAAACATATAATATATAGTTTTTAAAATATTTTT
1 AAAAACATATAATATATAGTTTTTAAAATATTTTT
*
1625021 GAAAACATATATATAATATAGGTTTTTAAAACGTATTTTT
1 AAAAACATATA-AT-ATATA-GTTTTTAAAA--TATTTTT
* *
1625061 AAAAACATATAGTATATAGTTTTTAAAATAATTTT
1 AAAAACATATAATATATAGTTTTTAAAATATTTTT
* * *
1625096 -GAAACATAAAATATATAGTTTTGAAAATATTTTT
1 AAAAACATATAATATATAGTTTTTAAAATATTTTT
* * ** *
1625130 -AAAACGTGTATAATATATAGTTTTGAAAACGTTTTA
1 AAAAAC--ATATAATATATAGTTTTTAAAATATTTTT
* * *
1625166 AAAAACGCATATAATATATAGTTTTGAAATTTTTTTT
1 AAAAA--CATATAATATATAGTTTTTAAAATATTTTT
1625203 GAAAAACATATAATATATAGTTTT
1 -AAAAACATATAATATATAGTTTT
1625227 GAAACCGTTA
Statistics
Matches: 175, Mismatches: 20, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
34 33 0.19
35 16 0.09
36 44 0.25
37 43 0.25
38 20 0.11
39 2 0.01
40 17 0.10
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (35 bp):
AAAAACATATAATATATAGTTTTTAAAATATTTTT
Found at i:1625112 original size:109 final size:107
Alignment explanation
Indices: 1624987--1625230 Score: 305
Period size: 109 Copynumber: 2.2 Consensus size: 107
1624977 TATTTTTAAA
* *
1624987 AAAACATATAATATATAGTTTTTAAAATATTTTTGAAAACATATAT-ATAATATAGGTTTTTAAA
1 AAAACATATAATATATAGTTTTGAAAATATTTTT-AAAACATATATAAT-ATATA-GTTTTGAAA
* * *
1625051 ACGTATTTTTAAAAA-CATATAGTATATAGTTTTTAAAATAATTTTG
63 ACG--TTTTAAAAAACCATATAATATATAGTTTTGAAAATAATTTTG
* * *
1625097 -AAACATAAAATATATAGTTTTGAAAATATTTTTAAAACGTGTATAATATATAGTTTTGAAAACG
1 AAAACATATAATATATAGTTTTGAAAATATTTTTAAAACATATATAATATATAGTTTTGAAAACG
* **
1625161 TTTTAAAAAACGCATATAATATATAGTTTTGAAATTTTTTTTG
66 TTTTAAAAAAC-CATATAATATATAGTTTTGAAAATAATTTTG
1625204 AAAAACATATAATATATAGTTTTGAAA
1 -AAAACATATAATATATAGTTTTGAAA
1625231 CCGTTATATT
Statistics
Matches: 117, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
105 9 0.08
107 37 0.32
108 14 0.12
109 57 0.49
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (107 bp):
AAAACATATAATATATAGTTTTGAAAATATTTTTAAAACATATATAATATATAGTTTTGAAAACG
TTTTAAAAAACCATATAATATATAGTTTTGAAAATAATTTTG
Found at i:1625227 original size:36 final size:36
Alignment explanation
Indices: 1624976--1625230 Score: 254
Period size: 37 Copynumber: 7.0 Consensus size: 36
1624966 ATTTTATAAC
* *
1624976 ATATTTTTAAAAAAACATATAATATATAGTTTTTAAA
1 ATATTTTT-GAAAAACATATAATATATAGTTTTGAAA
*
1625013 ATATTTTTG-AAAACATATATATAATATAGGTTTTTAAA
1 ATATTTTTGAAAAACATATA-AT-ATATA-GTTTTGAAA
* *
1625051 ACGTATTTTT-AAAAACATATAGTATATAGTTTTTAAA
1 A--TATTTTTGAAAAACATATAATATATAGTTTTGAAA
* *
1625088 ATAATTTTG--AAACATAAAATATATAGTTTTGAAA
1 ATATTTTTGAAAAACATATAATATATAGTTTTGAAA
*
1625122 ATATTTTT--AAAACGTGTATAATATATAGTTTTGAAA
1 ATATTTTTGAAAAAC--ATATAATATATAGTTTTGAAA
** *
1625158 A-CGTTTTAAAAAACGCATATAATATATAGTTTTGAAA
1 ATATTTTTGAAAAA--CATATAATATATAGTTTTGAAA
* *
1625195 TTTTTTTTGAAAAACATATAATATATAGTTTTGAAA
1 ATATTTTTGAAAAACATATAATATATAGTTTTGAAA
1625231 CCGTTATATT
Statistics
Matches: 187, Mismatches: 16, Indels: 31
0.80 0.07 0.13
Matches are distributed among these distances:
34 33 0.18
35 20 0.11
36 44 0.24
37 47 0.25
38 24 0.13
39 2 0.01
40 17 0.09
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (36 bp):
ATATTTTTGAAAAACATATAATATATAGTTTTGAAA
Found at i:1625304 original size:4 final size:4
Alignment explanation
Indices: 1625271--1625330 Score: 52
Period size: 4 Copynumber: 14.5 Consensus size: 4
1625261 ACGTAATATA
* *
1625271 TTAT ATTAT ATAT TTAT ATAT TTCAT TTAT TTAT ATTAAT TTA- TTA-
1 TTAT -TTAT TTAT TTAT TTAT TT-AT TTAT TTAT -TT-AT TTAT TTAT
1625317 TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TT
1625331 TTCAGGTCCA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
3 6 0.13
4 27 0.57
5 12 0.26
6 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:1625325 original size:10 final size:9
Alignment explanation
Indices: 1625267--1625330 Score: 64
Period size: 8 Copynumber: 7.1 Consensus size: 9
1625257 GGAAACGTAA
1625267 TATATTATAT
1 TATATTAT-T
1625277 TATA-TATT
1 TATATTATT
1625285 TATA-TATT
1 TATATTATT
1625293 TCAT-TTATT
1 T-ATATTATT
1625302 TATATTAATT
1 TATATT-ATT
1625312 TATTATTATT
1 TA-TATTATT
1625322 TAT-TTATT
1 TATATTATT
1625330 T
1 T
1625331 TTCAGGTCCA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
8 18 0.37
9 13 0.27
10 14 0.29
11 4 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
TATATTATT
Found at i:1626344 original size:45 final size:46
Alignment explanation
Indices: 1626269--1626359 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
1626259 TTTTGAAAGC
* * *
1626269 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATCGATGCATAAAATGCA
1626315 CTGAGTGCATCGATGCATGGT-ATATGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATCGATGCATAAAATGCA
1626360 TTCGATGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.50
46 21 0.50
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATATGCATCGATGCATAAAATGCA
Found at i:1626403 original size:20 final size:20
Alignment explanation
Indices: 1626378--1626415 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1626368 TTGAAATTTA
1626378 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
1626398 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
1626416 CACTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:1626801 original size:17 final size:17
Alignment explanation
Indices: 1626779--1626812 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1626769 CTTCTCCCTT
1626779 AAAAAAAACTTAATTAC
1 AAAAAAAACTTAATTAC
1626796 AAAAAAAACTTAATTAC
1 AAAAAAAACTTAATTAC
1626813 TTTGACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAAAACTTAATTAC
Found at i:1630804 original size:54 final size:53
Alignment explanation
Indices: 1630746--1630987 Score: 278
Period size: 54 Copynumber: 4.5 Consensus size: 53
1630736 GTATTCCTTC
* * *
1630746 AGGGAGTAGA-AACTTGAACAATCTTTTGCCTACGGGTTCGCTCCCTCTTTCTTT
1 AGGGAGTATAGAACTCGAACAATCTTTT--CTACGGGTTCGCTCCCTCTTTCTCT
*
1630800 AGGGAGTATAGAACTCGAAC-ATTTTCTTCTTACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATAGAACTCGAACAATCTT-TTC-TACGGGTTCGCTCCCTCTTTCTCT
** * * *
1630854 ATAGAGTATAGAACTCGAACACAT-TCTTCTCACGCGTTCGCTCCCTCATTCTCT
1 AGGGAGTATAGAACTCGAACA-ATCTTTTCT-ACGGGTTCGCTCCCTCTTTCTCT
* *
1630908 AGGGAGTATAGTACTCGAACACATTCTTTT-TACGGGTTCGCTCCCTCTTTCTTT
1 AGGGAGTATAGAACTCGAACA-A-TCTTTTCTACGGGTTCGCTCCCTCTTTCTCT
1630962 AGGGAGTATAGAACTCGAAC-ATCTTT
1 AGGGAGTATAGAACTCGAACAATCTTT
1630988 ATCAATCGCG
Statistics
Matches: 163, Mismatches: 17, Indels: 19
0.82 0.09 0.10
Matches are distributed among these distances:
51 5 0.03
52 1 0.01
53 2 0.01
54 137 0.84
55 13 0.08
56 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (53 bp):
AGGGAGTATAGAACTCGAACAATCTTTTCTACGGGTTCGCTCCCTCTTTCTCT
Found at i:1630941 original size:108 final size:108
Alignment explanation
Indices: 1630781--1630982 Score: 323
Period size: 108 Copynumber: 1.9 Consensus size: 108
1630771 TTGCCTACGG
* * **
1630781 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATTTTCTTCTTACGGGTTCGCTCCCT
1 GTTCGCTCCCTCATTCTCTAGGGAGTATAGAACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
*
1630846 CTTTCTCTATAGAGTATAGAACTCGAACACATTCTTCTCACGC
66 CTTTCTCTAGAGAGTATAGAACTCGAACACATTCTTCTCACGC
* *
1630889 GTTCGCTCCCTCATTCTCTAGGGAGTATAGTACTCGAACACATTCTTTTTACGGGTTCGCTCCCT
1 GTTCGCTCCCTCATTCTCTAGGGAGTATAGAACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
* *
1630954 CTTTCTTTAGGGAGTATAGAACTCGAACA
66 CTTTCTCTAGAGAGTATAGAACTCGAACA
1630983 TCTTTATCAA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 85 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (108 bp):
GTTCGCTCCCTCATTCTCTAGGGAGTATAGAACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
CTTTCTCTAGAGAGTATAGAACTCGAACACATTCTTCTCACGC
Found at i:1631024 original size:108 final size:107
Alignment explanation
Indices: 1630781--1631036 Score: 254
Period size: 108 Copynumber: 2.4 Consensus size: 107
1630771 TTGCCTACGG
* * * ** **
1630781 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATTTTCTTCTTACGGGTTCGCTCCCT
1 GTTCGCTCCCTCATGCTCTAGAAAGTATAG-ACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
* *
1630846 CTTTCTCTATAGAGTATAGAACTCGAACACATTCTTCTCACGC
65 CTTTCTCTAGAGAGTATAGAACTCGAACACATTCTTCTAACGC
* ** *
1630889 GTTCGCTCCCTCATTCTCTAGGGAGTATAGTACTCGAACACATTCTTTTTACGGGTTCGCTCCCT
1 GTTCGCTCCCTCATGCTCTAGAAAGTATAG-ACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
* *
1630954 CTTTCTTTAGGGAGTATAGAACTCGAACATC-TT-TATC-AATCGC
65 CTTTCTCTAGAGAGTATAGAACTCGAACA-CATTCT-TCTAA-CGC
1630997 G-TCTGCTCCCT-ATCGCT-TCAGAAAGTATAAGACTCGAACA
1 GTTC-GCTCCCTCAT-GCTCT-AGAAAGTAT-AGACTCGAACA
1631037 ATCTTCAACA
Statistics
Matches: 128, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
107 7 0.05
108 118 0.92
109 3 0.02
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (107 bp):
GTTCGCTCCCTCATGCTCTAGAAAGTATAGACTCGAACACATTCTTCTTACGGGTTCGCTCCCTC
TTTCTCTAGAGAGTATAGAACTCGAACACATTCTTCTAACGC
Found at i:1631071 original size:55 final size:55
Alignment explanation
Indices: 1630947--1631589 Score: 902
Period size: 55 Copynumber: 11.8 Consensus size: 55
1630937 TTACGGGTTC
* * * * * * *
1630947 GCTCCCTCTTTCTTTAGGGAGTAT-AGAACTCGAAC-ATCTTTATCAATCGCGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCT
* *
1631001 GCTCCCTA-TCGCTTCAGAAAGTATAAGACTCGAACAATCTTCAACAATAGTGTCT
1 GCTCCCTATTC-CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* * * * *
1631056 ACTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAACCTTCAATAATTGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* * * * *
1631111 GCTCTCTATTTCTTCAGAGAGTATAAGACTCGAAC-ATCTTCATCAAACGGGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* * *
1631165 GCTCCATATTCCTTCAGAGAGTATAAGACTCGAACAACCTTCAACAATCGTGTTT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
*
1631220 GCTCCCTATTCCTTCAGAGAGTATAAAACTCGAACAATCTTCAACAATCGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
*
1631275 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATATTCAACAATCGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* *
1631330 GCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
*
1631385 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
** * ** *
1631440 GCTCTTTATTTCTTCAGAGAGTATAAGACTCGAAC-ATCTTCTTCAATTGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
**
1631494 ATTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
*
1631549 GCTCTCTATTCCTTCAGAGAGTATAAGACTCGAAC-ATCTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTC
1631590 TTCAAACGGA
Statistics
Matches: 520, Mismatches: 63, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.00
54 121 0.23
55 396 0.76
56 2 0.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
Found at i:1631167 original size:164 final size:164
Alignment explanation
Indices: 1630955--1631589 Score: 961
Period size: 164 Copynumber: 3.9 Consensus size: 164
1630945 TCGCTCCCTC
* * * *
1630955 TTTCTTTAGGGAGTAT-AGAACTCGAACATCTTTATCAATCGCGTCTGCTCCCTA-TCGCTTCAG
1 TTTCTTCAGAGAGTATAAG-ACTCGAACATCTTCATCAATCGTGTCTGCTCCCTATTC-CTTCAG
* * *
1631018 AAAGTATAAGACTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGAGAGTATAAG
64 AGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* * *
1631083 ACTCAAACAACCTTCAATAATTGTGTCTGCTCTCTA
129 ACTCGAACAATCTTCAATAATCGTGTCTGCTCTCTA
* * *
1631119 TTTCTTCAGAGAGTATAAGACTCGAACATCTTCATCAAACGGGTCTGCTCCATATTCCTTCAGAG
1 TTTCTTCAGAGAGTATAAGACTCGAACATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAG
* * *
1631184 AGTATAAGACTCGAACAACCTTCAACAATCGTGTTTGCTCCCTATTCCTTCAGAGAGTATAAAAC
66 AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
* *
1631249 TCGAACAATCTTCAACAATCGTGTCTGCTCCCTA
131 TCGAACAATCTTCAATAATCGTGTCTGCTCTCTA
* * * *
1631283 TTCCTTCAGAGAGTATAAGACTCGAACAATATTCAACAATCGTGTCTGCTCTCTATTCCTTCAGA
1 TTTCTTCAGAGAGTATAAGACTCGAAC-ATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGA
*
1631348 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTTTGCTCCCTATTCCTTCAGAGAGTATAAGA
65 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGA
*
1631413 CTCGAACAATCTTCAATAATCGTGTCTGCTCTTTA
130 CTCGAACAATCTTCAATAATCGTGTCTGCTCTCTA
* * **
1631448 TTTCTTCAGAGAGTATAAGACTCGAACATCTTCTTCAATTGTGTCTATTCCCTATTCCTTCAGAG
1 TTTCTTCAGAGAGTATAAGACTCGAACATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAG
*
1631513 AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGAC
66 AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
1631578 TCGAAC-ATCTTC
131 TCGAACAATCTTC
1631590 TTCAAACGGA
Statistics
Matches: 429, Mismatches: 39, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
163 6 0.01
164 267 0.62
165 156 0.36
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (164 bp):
TTTCTTCAGAGAGTATAAGACTCGAACATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAG
AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
TCGAACAATCTTCAATAATCGTGTCTGCTCTCTA
Found at i:1631289 original size:219 final size:219
Alignment explanation
Indices: 1630965--1631598 Score: 952
Period size: 219 Copynumber: 2.9 Consensus size: 219
1630955 TTTCTTTAGG
* * * *
1630965 GAGTAT-AGAACTCGAAC-ATCTTTATCAATCGCGTCTGCTCCCTA-TCGCTTCAGAAAGTATAA
1 GAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC-CTTCAGAGAGTATAA
*
1631027 GACTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCAAACA
64 GACTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * * *
1631092 ACCTTCAATAATTGTGTCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAACATCTTCATCAA
129 ATCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCATCAA
1631157 ACGGGTCTGCTCCATATTCCTTCAGA
194 ACGGGTCTGCTCCATATTCCTTCAGA
* * *
1631183 GAGTATAAGACTCGAACAACCTTCAACAATCGTGTTTGCTCCCTATTCCTTCAGAGAGTATAAAA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGA
* *
1631248 CTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
66 CTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
* * *
1631313 ATTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
131 CTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAAC-ATCTTCATCAAA
* * *
1631378 CGTGTTTGCTCCCTATTCCTTCAGA
195 CGGGTCTGCTCCATATTCCTTCAGA
* ** *
1631403 GAGTATAAGACTCGAACAATCTTCAATAATCGTGTCTGCTCTTTATTTCTTCAGAGAGTATAAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGA
** * *
1631468 CTCGAAC-ATCTTCTTCAATTGTGTCTATTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
66 CTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
*
1631532 CTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCTTCAAAC
131 CTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCATCAAAC
1631597 GG
196 GG
1631599 ATTCACTCCC
Statistics
Matches: 375, Mismatches: 37, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
218 25 0.07
219 251 0.67
220 99 0.26
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (219 bp):
GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGA
CTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
CTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCATCAAAC
GGGTCTGCTCCATATTCCTTCAGA
Found at i:1631367 original size:329 final size:327
Alignment explanation
Indices: 1630947--1631589 Score: 984
Period size: 329 Copynumber: 2.0 Consensus size: 327
1630937 TTACGGGTTC
* * * * * * *
1630947 GCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTTATCAATCGCGTCTGCTCCCTATCG
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACATATTCAACAATCGCGTCTGCTCCCTATCG
1631012 CTTCAGAAAGTATAAGACTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGAGAG
66 CTTCAGAAAGTATAAGACTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGAGAG
*
1631077 TATAAGACTCAAACAACCTTCAATAATTGTGTCTGCTCTCTATTTCTTCAGAGAGTATAAGACTC
131 TATAAGACTCAAACAACCTTCAATAATCGTGTCTGCTCTCTATTTCTTCAGAGAGTATAAGACTC
*
1631142 GAACATCTTCATCAAACGGGTCTGCTCCATATTCCTTCAGAGAGTATAAGACTCGAACAACCTTC
196 GAACATCTTCATCAAACGGGTCTACTCCATATTCCTTCAGAGAGTATAAGACTCGAACAACCTTC
*
1631207 AACAATCGTGTTTGCTCCCTATTCCTTCAGAGAGTATAAAACTCGAACAATCTTCAACAATCGTG
261 AACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAAACTCGAAC-ATCTTCAACAATCGTG
1631272 TCT
325 TCT
* *
1631275 GCTCCCTATTCCTTCAGAGAGTATA-AGACTCGAACAATATTCAACAATCGTGTCTGCTCTCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC-ATATTCAACAATCGCGTCTGCTCCCTA-
* * * *
1631339 TC-CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTTGCTCCCTATTCCTTCAGA
63 TCGCTTCAGAAAGTATAAGACTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGA
* * *
1631403 GAGTATAAGACTCGAACAATCTTCAATAATCGTGTCTGCTCTTTATTTCTTCAGAGAGTATAAGA
128 GAGTATAAGACTCAAACAACCTTCAATAATCGTGTCTGCTCTCTATTTCTTCAGAGAGTATAAGA
* ** * * * *
1631468 CTCGAACATCTTCTTCAATTGTGTCTATTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATC
193 CTCGAACATCTTCATCAAACGGGTCTACTCCATATTCCTTCAGAGAGTATAAGACTCGAACAACC
* *
1631533 TTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTC
258 TTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAAACTCGAACATCTTC
1631590 TTCAAACGGA
Statistics
Matches: 284, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
327 1 0.00
328 35 0.12
329 246 0.87
330 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (327 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACATATTCAACAATCGCGTCTGCTCCCTATCG
CTTCAGAAAGTATAAGACTCGAACAATCTTCAACAATAGTGTCTACTCCCTATTCCTTCAGAGAG
TATAAGACTCAAACAACCTTCAATAATCGTGTCTGCTCTCTATTTCTTCAGAGAGTATAAGACTC
GAACATCTTCATCAAACGGGTCTACTCCATATTCCTTCAGAGAGTATAAGACTCGAACAACCTTC
AACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAAACTCGAACATCTTCAACAATCGTGT
CT
Found at i:1632168 original size:37 final size:37
Alignment explanation
Indices: 1632038--1632179 Score: 196
Period size: 37 Copynumber: 3.8 Consensus size: 37
1632028 TTGCTCCAAC
* *
1632038 ACTCTTCCGAGAAGGCTTAA-ATGGATTTGCTTCATT
1 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATT
* * *
1632074 ACTCTTCAGTGAAGGCTTAAAATGGATTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATT
**
1632111 ACTCTTCGGTGAAGGCTTAAGATGTTTTTGCTTCATT
1 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATT
*
1632148 ACTCTTCGGTGAAGGCTTAAGATTGACTTTGC
1 ACTCTTCGGTGAAGGCTTAAGATGGA-TTTGC
1632180 CCCAATCTCA
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 18 0.19
37 70 0.75
38 5 0.05
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATT
Found at i:1637254 original size:6 final size:6
Alignment explanation
Indices: 1637241--1637283 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
1637231 TAAAATGCTT
*
1637241 ATGC-A ATGAAA ATGCAA ATGCAA ATGCCAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA ATG-CAA ATGCAA ATGCAA A
1637284 AGGTGTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 3 0.09
6 25 0.74
7 6 0.18
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGCAA
Found at i:1637273 original size:13 final size:13
Alignment explanation
Indices: 1637245--1637280 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1637235 ATGCTTATGC
*
1637245 AATGAAAATG-CA
1 AATGCAAATGCCA
1637257 AATGCAAATGCCA
1 AATGCAAATGCCA
1637270 AATGCAAATGC
1 AATGCAAATGC
1637281 AAAAGGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (13 bp):
AATGCAAATGCCA
Found at i:1641617 original size:23 final size:22
Alignment explanation
Indices: 1641583--1641661 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
1641573 ACCCGACGGA
1641583 TGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCACATTCAAGG-G
* *
1641606 TGCATC-AGTGCACCTTC-ATGG
1 TGCATCGA-TGCACATTCAAGGG
* *
1641627 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGG
*
1641649 TGCATCAATGCAC
1 TGCATCGATGCAC
1641662 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
21 14 0.31
22 17 0.38
23 14 0.31
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGG
Found at i:1641644 original size:21 final size:20
Alignment explanation
Indices: 1641583--1641680 Score: 65
Period size: 21 Copynumber: 4.6 Consensus size: 20
1641573 ACCCGACGGA
1641583 TGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCACATTC-A-G-G
*
1641606 TGCATC-AGTGCACCTTCATGG
1 TGCATCGA-TGCACATTCA-GG
*
1641627 TGTATCGATGCACATTCAAGG
1 TGCATCGATGCACATTC-AGG
* *
1641648 ATGCATCAATGCAC-TGTTAGG
1 -TGCATCGATGCACAT-TCAGG
*
1641669 TGTATCGATGCA
1 TGCATCGATGCA
1641681 TGAAGCACAA
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
20 10 0.16
21 20 0.33
22 17 0.28
23 14 0.23
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACATTCAGG
Found at i:1647602 original size:45 final size:46
Alignment explanation
Indices: 1647514--1647604 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
1647504 TTTGAAAAGC
* *
1647514 CTAAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTAAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
1647560 CTAAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTAAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
1647605 TTCGATGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (46 bp):
CTAAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:1647649 original size:20 final size:20
Alignment explanation
Indices: 1647624--1647661 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1647614 TGAATAAATA
1647624 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
1647644 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
1647662 CACTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:1649757 original size:13 final size:13
Alignment explanation
Indices: 1649739--1649781 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1649729 TCTCACTAAC
1649739 TTTTTTATTTCAT
1 TTTTTTATTTCAT
*
1649752 TTTTTTATTTTAT
1 TTTTTTATTTCAT
*
1649765 TTTATTTTTTATCAT
1 TTT-TTTATT-TCAT
1649780 TT
1 TT
1649782 ACATCATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 15 0.60
14 5 0.20
15 5 0.20
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTATTTCAT
Found at i:1653177 original size:74 final size:74
Alignment explanation
Indices: 1653051--1653482 Score: 699
Period size: 74 Copynumber: 5.9 Consensus size: 74
1653041 TGTTTGTTTG
* *
1653051 TTGATAATGCTCAA--TTGAGTATTGGATAATGCTCATTCAACTAGCATGGTAAATATGCTCAAA
1 TTGATAATGCTCAATTTTGA-TAAT-GATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAA
1653114 ATTGTCATTTC
64 ATTGTCATTTC
* * * *
1653125 TTAATAATGCTCAATGTTGATAAAGAGAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1653190 TGTCATTTC
66 TGTCATTTC
* * *
1653199 TTTATAATGCTCAATTTTGATAATTATAATGCTCATTCAACTAGCATTATAAATATGCTCAAAAT
1 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1653264 TGTCATTTC
66 TGTCATTTC
*
1653273 TTGATAATGCTTAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1653338 TGTCATTTC
66 TGTCATTTC
* *
1653347 TTGATAATGCTCAATTTTAATAATGATAATGCTCATTCAACTAGCATTGTAAA-ATGCTTAAAAT
1 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1653411 TGTCATTTC
66 TGTCATTTC
* *
1653420 TTGATAATGCTCAATTTTGATAATGATAATGCTAATTCAACTAGCATTGTAAAAATGCTCAAA
1 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAA
1653483 TTAGGTTATT
Statistics
Matches: 334, Mismatches: 21, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
73 70 0.21
74 258 0.77
75 2 0.01
76 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (74 bp):
TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
TGTCATTTC
Found at i:1656872 original size:3 final size:3
Alignment explanation
Indices: 1656864--1656978 Score: 203
Period size: 3 Copynumber: 38.3 Consensus size: 3
1656854 TTAATATATT
*
1656864 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1656912 TAA TGA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1656960 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
1656979 GATATGGGTA
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 106 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1660642 original size:16 final size:14
Alignment explanation
Indices: 1660621--1660661 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1660611 AGGGCTAAAC
1660621 ATATATATTCTTTT
1 ATATATATTCTTTT
1660635 ATATATATTCTTTT
1 ATATATATTCTTTT
* *
1660649 GTATATACTCTTT
1 ATATATATTCTTT
1660662 GTAGACACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (14 bp):
ATATATATTCTTTT
Found at i:1661026 original size:74 final size:74
Alignment explanation
Indices: 1660905--1661231 Score: 559
Period size: 74 Copynumber: 4.4 Consensus size: 74
1660895 TGGGGGAATG
*
1660905 TTGATAATGCTCAA--TTGAGTATTGGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAA
1 TTGATAATGCTCAATTTTGA-TAAT-GATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAA
1660968 ATTGTCATTTC
64 ATTGTCATTTC
* *
1660979 TTGATAATGCTCAATGTTGATAAAGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1661044 TGTCATTTC
66 TGTCATTTC
1661053 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
*
1661118 TGTTATTTC
66 TGTCATTTC
* *
1661127 TTGATAATGCTCAATTTTGATAATGATAATGCTAATTCAACTAGCATTGTAAAAATGCTCAAAAT
1 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1661192 TGTCATTTC
66 TGTCATTTC
*
1661201 GTGATAATGCTCAATTTTGATAATGATAATG
1 TTGATAATGCTCAATTTTGATAATGATAATG
1661232 TTCAAATTAG
Statistics
Matches: 242, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
74 236 0.98
75 2 0.01
76 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (74 bp):
TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
TGTCATTTC
Found at i:1663705 original size:19 final size:19
Alignment explanation
Indices: 1663681--1663789 Score: 83
Period size: 19 Copynumber: 5.3 Consensus size: 19
1663671 ACTATCGCAA
1663681 TGCGATTTTCCAAATTCGC
1 TGCGATTTTCCAAATTCGC
* *
1663700 TGCGATTGTCCAAGTTCGC
1 TGCGATTTTCCAAATTCGC
*
1663719 GTTGCGATTTATTCCAAATTCGT
1 --TGCGA-TT-TTCCAAATTCGC
** *
1663742 TGCGATAGTCCAAGTTCGC
1 TGCGATTTTCCAAATTCGC
*
1663761 GTTGCGATTTATTCCAAATTCGT
1 --TGCGA-TT-TTCCAAATTCGC
1663784 TGCGAT
1 TGCGAT
1663790 AGTCCAAGTT
Statistics
Matches: 69, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
19 26 0.38
20 2 0.03
21 20 0.29
22 3 0.04
23 18 0.26
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (19 bp):
TGCGATTTTCCAAATTCGC
Found at i:1663734 original size:42 final size:42
Alignment explanation
Indices: 1663681--1663822 Score: 243
Period size: 42 Copynumber: 3.4 Consensus size: 42
1663671 ACTATCGCAA
* *
1663681 TGCGA-TT-TTCCAAATTCGCTGCGATTGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1663721 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1663763 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
*
1663805 TACGATTTATTCCAAATT
1 TGCGATTTATTCCAAATT
1663823 ATTGCATTTG
Statistics
Matches: 97, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
40 5 0.05
41 2 0.02
42 90 0.93
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:1663742 original size:21 final size:21
Alignment explanation
Indices: 1663681--1663822 Score: 109
Period size: 21 Copynumber: 6.8 Consensus size: 21
1663671 ACTATCGCAA
*
1663681 TGCGATT-TTCCAAATT-CGC
1 TGCGATTATTCCAAATTCCGT
* *
1663700 TGCGATT-GTCCAAGTTCGCGT
1 TGCGATTATTCCAAATTC-CGT
1663721 TGCGATTTATTCCAAATT-CGT
1 TGCGA-TTATTCCAAATTCCGT
* *
1663742 TGCGA-TAGTCCAAGTTCGCGT
1 TGCGATTATTCCAAATTC-CGT
1663763 TGCGATTTATTCCAAATT-CGT
1 TGCGA-TTATTCCAAATTCCGT
* *
1663784 TGCGA-TAGTCCAAGTTCGCGT
1 TGCGATTATTCCAAATTC-CGT
*
1663805 TACGATTTATTCCAAATT
1 TGCGA-TTATTCCAAATT
1663823 ATTGCATTTG
Statistics
Matches: 97, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
19 32 0.33
21 38 0.39
22 2 0.02
23 25 0.26
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (21 bp):
TGCGATTATTCCAAATTCCGT
Found at i:1664712 original size:21 final size:21
Alignment explanation
Indices: 1664688--1664761 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
1664678 TTTGGAATAA
1664688 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* * **
1664709 ATCGCAA--CTAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
1664728 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
1664749 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1664762 TATGTAAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
19 15 0.36
21 27 0.64
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:1664741 original size:40 final size:42
Alignment explanation
Indices: 1664660--1664755 Score: 169
Period size: 40 Copynumber: 2.3 Consensus size: 42
1664650 CATTGCGATT
1664660 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
*
1664702 TTGGACTATCGCAACTAATTTGG-A-AAATCGCAACGCGAAC
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
1664742 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1664756 TGCGAATATG
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
40 30 0.57
41 1 0.02
42 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
Found at i:1665452 original size:52 final size:52
Alignment explanation
Indices: 1665390--1665492 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
1665380 TTATAATATT
1665390 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
* *
1665442 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATG
1665493 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
Found at i:1670050 original size:52 final size:52
Alignment explanation
Indices: 1669988--1670090 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
1669978 TTATAATATT
1669988 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
* *
1670040 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATG
1670091 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
Found at i:1670529 original size:51 final size:51
Alignment explanation
Indices: 1670432--1670529 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
1670422 ACCCTTTACA
* * **
1670432 GTAAGGCGCGCCCCCTGCAGTGCGTTTTACGCTGATATGGTGCCACGTGGG
1 GTAAGGCGCGCCCCCTGCAGCGCGCTTTACGCTGATATGGCACCACGTGGG
* * *
1670483 GTAAGGTGCGCCCCCTGCAGCGCGCTTTACGTTGATCTGGCACCACG
1 GTAAGGCGCGCCCCCTGCAGCGCGCTTTACGCTGATATGGCACCACG
1670530 GCGTGCCTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.22
Consensus pattern (51 bp):
GTAAGGCGCGCCCCCTGCAGCGCGCTTTACGCTGATATGGCACCACGTGGG
Found at i:1677679 original size:10 final size:10
Alignment explanation
Indices: 1677664--1677703 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1677654 GTAAAATTAA
*
1677664 TAATAATAGT
1 TAATAATAAT
1677674 TAATAATAAT
1 TAATAATAAT
1677684 TAATAATAAT
1 TAATAATAAT
* *
1677694 AAAGAATAAT
1 TAATAATAAT
1677704 AAAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (10 bp):
TAATAATAAT
Found at i:1677695 original size:13 final size:14
Alignment explanation
Indices: 1677658--1677695 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1677648 TAATATGTAA
1677658 AATTAATAATAA-T
1 AATTAATAATAATT
*
1677671 AGTTAATAATAATT
1 AATTAATAATAATT
1677685 AA-TAATAATAA
1 AATTAATAATAA
1677696 AGAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
AATTAATAATAATT
Found at i:1677927 original size:43 final size:40
Alignment explanation
Indices: 1677873--1677976 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
1677863 GACGACACTG
* *
1677873 CTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGGTGACACGG
1 CTCATACGTGATGAAGAGTTCGGGTCG---AAGGATGACACGA
* * ** *
1677916 TTCATACGTGATGAGGAAATCTGGTCGAAGGATGACACGA
1 CTCATACGTGATGAAGAGTTCGGGTCGAAGGATGACACGA
*
1677956 CTCATGCGTGATGAAGAGTTC
1 CTCATACGTGATGAAGAGTTC
1677977 TTGGCCATCT
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
40 27 0.55
43 22 0.45
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (40 bp):
CTCATACGTGATGAAGAGTTCGGGTCGAAGGATGACACGA
Found at i:1678186 original size:130 final size:134
Alignment explanation
Indices: 1677900--1678208 Score: 364
Period size: 135 Copynumber: 2.3 Consensus size: 134
1677890 GTTCGGGTCG
** * *
1677900 TCTAAGGGTGACACGGTTCATACGTGATGAGGAAATCTGGTC-GAAGGATGACACGACTCATGCG
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAAATCTGGTCAGAAGGATGACACGACTCATACG
* *
1677964 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
66 TGATGAAGAGTTCTTGGCCATCTTTA-GAA-GGTGATAACTCAGTTCCTACGCAATGAGGACGGC
1678029 TGGTTA
129 TGGTTA
* * * *
1678035 TCTAAGGGTGACACGACTCCTACGTGATGAGGATATCTAGTCAG-GGGATGACACTG-CTCCTAC
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAAATCTGGTCAGAAGGATGACAC-GACTCATAC
* *
1678098 GTGATGAAGAGTTCTTGGCCAT-TTTA-TA-GTGATAACAT-AGTTCCTACGTAATGAGGACGGC
65 GTGATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAAC-TCAGTTCCTACGCAATGAGGACGGC
1678159 TGGTTA
129 TGGTTA
* * ** *
1678165 TCTAATGTTGACGTTG-CTCCTACGTGATGAGGAGATCTGGTCAG
1 TCTAAGGGTGAC-ACGACTCCTACGTGATGAGGAAATCTGGTCAG
1678209 CTGATGTTGA
Statistics
Matches: 152, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
130 70 0.46
131 2 0.01
132 1 0.01
134 4 0.03
135 73 0.48
136 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (134 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAGGAAATCTGGTCAGAAGGATGACACGACTCATACG
TGATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAACTCAGTTCCTACGCAATGAGGACGGCTG
GTTA
Found at i:1692031 original size:26 final size:27
Alignment explanation
Indices: 1691965--1692043 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 27
1691955 AGATGCCTCC
*
1691965 CTTTTTTTTTCTTTTCTGTTTCGAATCT
1 CTTTTTTTTTCTTTTC-GTTTCCAATCT
*
1691993 CTCTCTGTCTTTTTCTTTTCGTTTCCTAT-T
1 CT-T-T-T-TTTTTCTTTTCGTTTCCAATCT
* *
1692023 CTTTTTTTTTTTTTTGGTTTC
1 CTTTTTTTTTCTTTTCGTTTC
1692044 GTTCCCTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 14 0.33
27 1 0.02
28 3 0.07
29 2 0.05
30 4 0.09
31 8 0.19
32 11 0.26
ACGTcount: A:0.04, C:0.19, G:0.08, T:0.70
Consensus pattern (27 bp):
CTTTTTTTTTCTTTTCGTTTCCAATCT
Found at i:1696556 original size:3 final size:3
Alignment explanation
Indices: 1696550--1696652 Score: 199
Period size: 3 Copynumber: 34.7 Consensus size: 3
1696540 TAAAAAAATG
1696550 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1696598 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1696645 TAA TAA TA
1 TAA TAA TA
1696653 TAAGTAACAA
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 97 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1698138 original size:22 final size:22
Alignment explanation
Indices: 1698113--1698220 Score: 153
Period size: 22 Copynumber: 4.9 Consensus size: 22
1698103 GGCATGTGAA
*
1698113 ATATGTCCCGAAGGACCTATGT
1 ATATGTCCCGAAGGACCTATAT
** **
1698135 ATATGTTTCGAAGGACCTGCAT
1 ATATGTCCCGAAGGACCTATAT
1698157 ATATGTCCCGAAGGACCTATAT
1 ATATGTCCCGAAGGACCTATAT
*
1698179 ATATGTCCCGAAGGACCTGTAT
1 ATATGTCCCGAAGGACCTATAT
*
1698201 ATATGTCCCGAAGAACCTAT
1 ATATGTCCCGAAGGACCTAT
1698221 GTAACCCTCG
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (22 bp):
ATATGTCCCGAAGGACCTATAT
Found at i:1698176 original size:44 final size:44
Alignment explanation
Indices: 1698113--1698223 Score: 177
Period size: 44 Copynumber: 2.5 Consensus size: 44
1698103 GGCATGTGAA
**
1698113 ATATGTCCCGAAGGACCTATGTATATGTTTCGAAGGACCTGCAT
1 ATATGTCCCGAAGGACCTATGTATATGTCCCGAAGGACCTGCAT
* *
1698157 ATATGTCCCGAAGGACCTATATATATGTCCCGAAGGACCTGTAT
1 ATATGTCCCGAAGGACCTATGTATATGTCCCGAAGGACCTGCAT
*
1698201 ATATGTCCCGAAGAACCTATGTA
1 ATATGTCCCGAAGGACCTATGTA
1698224 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (44 bp):
ATATGTCCCGAAGGACCTATGTATATGTCCCGAAGGACCTGCAT
Found at i:1700612 original size:20 final size:20
Alignment explanation
Indices: 1700587--1700660 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
1700577 TTTGGTTCAC
1700587 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
1700607 GGAATGTAAGATTACAAGTG
1 GGAATGTAAGATTACCAGTG
1700627 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1700647 GGAATGTAAGATTA
1 GGAATGTAAGATTA
1700661 TCAGGGAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.38, C:0.07, G:0.30, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1706237 original size:59 final size:59
Alignment explanation
Indices: 1706145--1706504 Score: 558
Period size: 59 Copynumber: 6.1 Consensus size: 59
1706135 TTTCTCTAAA
* *
1706145 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTACCGATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* *
1706204 ATGAAATGTTAAATGCCTAATTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
*
1706263 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATACAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * * * * *
1706322 ATGAAAGGTTAAATGACTAATTGTGCATTTGGCATAAAGGTTCCAATAATACAAGGTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* *
1706381 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAAAAAGGTTCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * * * *
1706440 ATGAAAGGTTAAATGACTAACTGTGCATTTGGTAGAAATGTGTCACTAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
1706499 ATGAAA
1 ATGAAA
1706505 AATAGTGTAT
Statistics
Matches: 277, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 277 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (59 bp):
ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
Found at i:1718700 original size:59 final size:59
Alignment explanation
Indices: 1718595--1718836 Score: 371
Period size: 59 Copynumber: 4.1 Consensus size: 59
1718585 TTTCTTTAAA
* *
1718595 ATGAAAGGTTAAATGCCTAACTGTGGATTTGGCAGAAAGGTTCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGAATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * *
1718654 ATGAAAGGTTAAATGCCTAACTGTTAATTTGG-ACGAAATGTGCCAATAATGGAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGAATTTGGCA-GAAAGGTGCCAATAATGCAAGTTAG
*
1718713 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGAATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * *
1718772 ATGAAATGTTAAATGCCTAACTGT-ACATTTGGCAGAAAGGTGCCACTAATGAAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGA-ATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
1718831 ATGAAA
1 ATGAAA
1718837 AATAGTGTAT
Statistics
Matches: 167, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
58 1 0.01
59 165 0.99
60 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (59 bp):
ATGAAAGGTTAAATGCCTAACTGTGAATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
Found at i:1719078 original size:59 final size:59
Alignment explanation
Indices: 1719009--1719329 Score: 482
Period size: 59 Copynumber: 5.4 Consensus size: 59
1718999 TGACAGGAAT
* *
1719009 GTGCCAATAATGCAAGTTAGATGGAAA-GTTAAATGCCTAACTGTGCATTTGGCAAAAAG
1 GTGCCAATAATGCAAGTTAGAT-GAAAGGTTAAATGCCTAACTGTGCATTTGGTAGAAAG
* * *
1719068 GTGCCAATAATGCAAGTTAAATGAAAGGTTAAATGCCTAACTGTGCATTTGGAAGAAAT
1 GTGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAACTGTGCATTTGGTAGAAAG
* * *
1719127 GTGCCAATAATACAAGTTAGATGAAAGGTTAAATGCCTAATTGTACATTTGGTAGAAAG
1 GTGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAACTGTGCATTTGGTAGAAAG
* *
1719186 GTGCCAATAATGCAAGTTAGATGAAAAGTTATATGCCTAACTGTGCATTTGGTAGAAAG
1 GTGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAACTGTGCATTTGGTAGAAAG
* * * * *
1719245 GTGCCAAAAATGCAGGTTAGATGAAAGGTTAAATGCATAATTGTGTATTTGGTAGAAAG
1 GTGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAACTGTGCATTTGGTAGAAAG
*
1719304 GTGCCACTAATGCAAGTTAGATGAAA
1 GTGCCAATAATGCAAGTTAGATGAAA
1719330 AATAGTGTAT
Statistics
Matches: 236, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
58 4 0.02
59 232 0.98
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (59 bp):
GTGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAACTGTGCATTTGGTAGAAAG
Found at i:1723453 original size:17 final size:17
Alignment explanation
Indices: 1723431--1723465 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1723421 ATTTACGCTC
1723431 AGGGTATCATCAGTTGA
1 AGGGTATCATCAGTTGA
1723448 AGGGTATCATCAGTTGA
1 AGGGTATCATCAGTTGA
1723465 A
1 A
1723466 TTTTCAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (17 bp):
AGGGTATCATCAGTTGA
Found at i:1727502 original size:23 final size:23
Alignment explanation
Indices: 1727469--1727553 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
1727459 AGTCGAGGGT
*
1727469 TCTACGCGGTCCTTCAGGACAAA
1 TCTACGTGGTCCTTCAGGACAAA
* ** **
1727492 TCTATGTGGTCCTTTGGGACATT
1 TCTACGTGGTCCTTCAGGACAAA
*
1727515 TCTACGTGGTCCTTC-GATACAAA
1 TCTACGTGGTCCTTCAG-GACAAA
*
1727538 TTCTACGCGGTCCTTC
1 -TCTACGTGGTCCTTC
1727554 GGAAAAAATT
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
22 1 0.02
23 33 0.69
24 14 0.29
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (23 bp):
TCTACGTGGTCCTTCAGGACAAA
Found at i:1727562 original size:24 final size:24
Alignment explanation
Indices: 1727514--1727566 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1727504 TTTGGGACAT
* *
1727514 TTCTACGTGGTCCTTCGATACAAA
1 TTCTACGCGGTCCTTCGATAAAAA
1727538 TTCTACGCGGTCCTTCGGA-AAAAA
1 TTCTACGCGGTCCTTC-GATAAAAA
1727562 TTCTA
1 TTCTA
1727567 AGTGGTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGATAAAAA
Found at i:1730741 original size:21 final size:20
Alignment explanation
Indices: 1730684--1730744 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
1730674 CTATAAGTTT
*
1730684 TCTTTATCTCAGTTTATTTA
1 TCTTTATCTCATTTTATTTA
*
1730704 T-TTTAT-TTATTTGTTTATTTAA
1 TCTTTATCTCA--T-TTTATTT-A
1730726 TCTTTATCTCATTTTATTT
1 TCTTTATCTCATTTTATTT
1730745 CTTTAAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
18 2 0.06
19 5 0.16
20 1 0.03
21 14 0.44
22 3 0.09
23 5 0.16
24 2 0.06
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (20 bp):
TCTTTATCTCATTTTATTTA
Found at i:1732329 original size:21 final size:21
Alignment explanation
Indices: 1732305--1732372 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
1732295 AATTTCACAA
**
1732305 GAAAAGCTGGTTATATCCCAT
1 GAAAAGCTGGTTGCATCCCAT
** *
1732326 GAAAAATTGGTTGCATCCCAA
1 GAAAAGCTGGTTGCATCCCAT
1732347 GAAAAGCTGGTTGCATCCCAT
1 GAAAAGCTGGTTGCATCCCAT
1732368 GAAAA
1 GAAAA
1732373 ATTCAAAAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (21 bp):
GAAAAGCTGGTTGCATCCCAT
Found at i:1736422 original size:11 final size:11
Alignment explanation
Indices: 1736406--1736452 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1736396 AGGCAACCCG
1736406 TTTCGTTTTAT
1 TTTCGTTTTAT
*
1736417 TTTCGTTTTAA
1 TTTCGTTTTAT
*
1736428 TTTCATTTTA-
1 TTTCGTTTTAT
*
1736438 ATTCTGTTTTAT
1 TTTC-GTTTTAT
1736450 TTT
1 TTT
1736453 TAGCAAACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
10 3 0.10
11 24 0.83
12 2 0.07
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.70
Consensus pattern (11 bp):
TTTCGTTTTAT
Found at i:1742418 original size:3 final size:3
Alignment explanation
Indices: 1742410--1742443 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1742400 AAAATATTAA
1742410 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1742444 ATTAGTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1744891 original size:19 final size:19
Alignment explanation
Indices: 1744852--1744891 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1744842 TCCTCTTTTT
*
1744852 AAATAATTAATTTGAAGTA
1 AAATAATTAATTTCAAGTA
1744871 AAATAATTAAATTTCAA-TA
1 AAATAATT-AATTTCAAGTA
1744890 AA
1 AA
1744892 TGGATCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
AAATAATTAATTTCAAGTA
Found at i:1756155 original size:8 final size:8
Alignment explanation
Indices: 1756122--1756197 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 8
1756112 TATGCTTGAA
*
1756122 GAAAAAAG
1 GAAAAAAT
*
1756130 GAACAAAT
1 GAAAAAAT
1756138 -AAAAAGAT
1 GAAAAA-AT
1756146 GAAAAAAT
1 GAAAAAAT
*
1756154 GAAAAAGAAA
1 G-AAAA-AAT
*
1756164 AAAAAAAT
1 GAAAAAAT
1756172 G-AAAAA-
1 GAAAAAAT
*
1756178 -AAGAAAT
1 GAAAAAAT
1756185 GAAAAAAT
1 GAAAAAAT
1756193 GAAAA
1 GAAAA
1756198 GAGAAAAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
6 4 0.08
7 9 0.17
8 24 0.46
9 13 0.25
10 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:1756167 original size:26 final size:25
Alignment explanation
Indices: 1756138--1756191 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
1756128 AGGAACAAAT
* *
1756138 AAAAAGATGAAAAAATGAAAAAGAAA
1 AAAAAAATGAAAAAAAG-AAAAGAAA
*
1756164 AAAAAAATGAAAAAAAGAAATGAAA
1 AAAAAAATGAAAAAAAGAAAAGAAA
1756189 AAA
1 AAA
1756192 TGAAAAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (25 bp):
AAAAAAATGAAAAAAAGAAAAGAAA
Found at i:1756196 original size:13 final size:13
Alignment explanation
Indices: 1756144--1756206 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
1756134 AAATAAAAAG
1756144 ATGAAAAAATGAAA
1 ATGAAAAAATG-AA
* *
1756158 AAGAAAAAA-AAA
1 ATGAAAAAATGAA
*
1756170 ATGAAAAAAAGAA
1 ATGAAAAAATGAA
1756183 ATGAAAAAATGAA
1 ATGAAAAAATGAA
*
1756196 AAGAGAAAAAT
1 ATGA-AAAAAT
1756207 AAGGGTTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 10 0.24
13 17 0.41
14 14 0.34
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (13 bp):
ATGAAAAAATGAA
Found at i:1757323 original size:136 final size:135
Alignment explanation
Indices: 1757070--1757424 Score: 487
Period size: 136 Copynumber: 2.6 Consensus size: 135
1757060 AGAAAGAGAT
* * * *
1757070 GGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCGTCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGGAGAAGAAGTT
* * * * * *** * * *
1757135 CATAATGAGAAGAGC-CGATTTGACTTATCACTCGATTCATGGCGTTTTGAATCAGTGACACCTC
65 CATAATGAGAAGAACTTG-TTCGACCTATCACTAGATTCACAACATTTAGAATCAATGACACCTC
1757199 GCTTGAG
129 GCTTGAG
* *
1757206 GGGTCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTAATAGAGGGAGAAGAAGTT
1 GGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAA-AGAGGGAGAAGAAGTT
1757271 CATAATGAGAAGAACTTGTTCGACCTATCACTAGATTCACAACATTTAGAATCAATGACACCTCG
65 CATAATGAGAAGAACTTGTTCGACCTATCACTAGATTCACAACATTTAGAATCAATGACACCTCG
1757336 CTTGAG
130 CTTGAG
* * * *
1757342 GGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAGAACTTATCCAACGAGGAAGAAGAAGTTC
1 GGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGGAGAAGAAGTTC
1757407 ATAATGAGAAGAACTTGT
66 ATAATGAGAAGAACTTGT
1757425 CCAACTTCGC
Statistics
Matches: 194, Mismatches: 23, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
135 34 0.18
136 159 0.82
137 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (135 bp):
GGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCGACCTATCACTAGATTCACAACATTTAGAATCAATGACACCTCGC
TTGAG
Found at i:1757459 original size:91 final size:92
Alignment explanation
Indices: 1757344--1757516 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 92
1757334 CGCTTGAGGG
* * *
1757344 ATCAACATTTTCAGTGAAGAGTTCATAATGAGAAGAACTTATCC-AACGAG-GAAGAAGAAGTTC
1 ATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGAG-AGAAGAAGTTC
1757407 ATAATGAGAAGAACTTGTCCAACTTCGC
65 ATAATGAGAAGAACTTGTCCAACTTCGC
* *
1757435 ATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGAGAGAATAAGTTCA
1 ATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGAGAGAAGAAGTTCA
*
1757500 TAATGAGAAGAGCTTGT
66 TAATGAGAAGAACTTGT
1757517 TCGACCTATC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
91 41 0.55
92 32 0.43
93 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (92 bp):
ATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGAGAGAAGAAGTTCA
TAATGAGAAGAACTTGTCCAACTTCGC
Found at i:1760387 original size:19 final size:19
Alignment explanation
Indices: 1760348--1760387 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1760338 TCCTCTTTTT
*
1760348 AAATAATTAATTTGAAGTA
1 AAATAATTAATTTCAAGTA
1760367 AAATAATTAAATTTCAA-TA
1 AAATAATT-AATTTCAAGTA
1760386 AA
1 AA
1760388 TGAATCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
AAATAATTAATTTCAAGTA
Found at i:1761353 original size:45 final size:45
Alignment explanation
Indices: 1761267--1761353 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
1761257 ATGGTTATTA
** *
1761267 TGACAAAATAAATTTGTTATAATATTTTATTTTGAGAAAATATAG
1 TGACAAAATAAATTTGACATAATATTTTATTTTGACAAAATATAG
* *
1761312 TGACTAAATAAATTTGACATAAT-TTCTTATTTTGACTAAATA
1 TGACAAAATAAATTTGACATAATATT-TTATTTTGACAAAATA
1761354 AATTTGTTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 2 0.06
45 34 0.94
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (45 bp):
TGACAAAATAAATTTGACATAATATTTTATTTTGACAAAATATAG
Found at i:1761368 original size:32 final size:32
Alignment explanation
Indices: 1761312--1761374 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1761302 GAAAATATAG
*
1761312 TGACTAAATAAATTTGACATAATTTCTTATTT
1 TGACTAAATAAATTTGACACAATTTCTTATTT
** *
1761344 TGACTAAATAAATTTGTTACAATTTGTTATT
1 TGACTAAATAAATTTGACACAATTTCTTATT
1761375 ATGAAAGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (32 bp):
TGACTAAATAAATTTGACACAATTTCTTATTT
Found at i:1761455 original size:175 final size:175
Alignment explanation
Indices: 1761155--1761511 Score: 497
Period size: 175 Copynumber: 2.0 Consensus size: 175
1761145 TATATTACTT
* * *
1761155 ATAATTTCTTTTTTGTGACTAAATAACTTTGTTACAATTTGTTATTGTGAAAGAATAATAGTTAT
1 ATAATTTCTTATTTGTGACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATAATAGTTAT
* *
1761220 CATAATTTTTATATTGAGAAATCAATATTTATTATAAATGGTTATTATGACAAAATAAATTTGTT
66 CATAATTTTTATATTCAGAAATCAATATTTATTATAAATGGTTATTATGACAAAATAAATTTGTC
* * *
1761285 ATAA-TATTTTATTTTGAG-AA-AATATAGTGACTAAATAAATTTGAC
131 AAAAGT-TTTTATTTTGAGAAACAAT-TA-TGAATAAATAAATTAGAC
* * *
1761330 ATAATTTCTTATTT-TGACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATATTATTTTT
1 ATAATTTCTTATTTGTGACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATAATAGTTAT
* * * * *
1761394 CATAATTTTTTATATTCAGAAATTACTATTTGTTATAAATTGTTATTATGACTAAATAAATTTGT
66 CATAA-TTTTTATATTCAGAAATCAATATTTATTATAAATGGTTATTATGACAAAATAAATTTGT
*
1761459 CAAAAGTTTTTATTTTTAGAAACAATTATGAATAAATAAATTAGAC
130 CAAAAGTTTTTATTTTGAGAAACAATTATGAATAAATAAATTAGAC
1761505 ATAATTT
1 ATAATTT
1761512 TTTTTTTATT
Statistics
Matches: 161, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
174 50 0.31
175 103 0.64
176 5 0.03
177 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.46
Consensus pattern (175 bp):
ATAATTTCTTATTTGTGACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATAATAGTTAT
CATAATTTTTATATTCAGAAATCAATATTTATTATAAATGGTTATTATGACAAAATAAATTTGTC
AAAAGTTTTTATTTTGAGAAACAATTATGAATAAATAAATTAGAC
Found at i:1761587 original size:32 final size:31
Alignment explanation
Indices: 1761551--1761641 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 31
1761541 TATTGTTACT
*
1761551 AAATAAATTTGTTACAATTTTTTATTTTGAAA
1 AAATAAATTTGTTATAA-TTTTTATTTTGAAA
* * * *
1761583 AAATATTATTTGTCATAAATTTTATTTTGAGA
1 AAATA-AATTTGTTATAATTTTTATTTTGAAA
* *
1761615 AATTAATATTTATTATAAATTTTTATT
1 AAATAA-ATTTGTTAT-AATTTTTATT
1761642 ATGATTAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
32 28 0.61
33 18 0.39
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (31 bp):
AAATAAATTTGTTATAATTTTTATTTTGAAA
Found at i:1762359 original size:20 final size:20
Alignment explanation
Indices: 1762334--1762387 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1762324 TAAATGACTA
1762334 GGGGTATCGGTACCTCTAAG
1 GGGGTATCGGTACCTCTAAG
*
1762354 GGGGTATCGGTATCTCTAAG
1 GGGGTATCGGTACCTCTAAG
1762374 GGGGTATCGGTACC
1 GGGGTATCGGTACC
1762388 CATTGGGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGTATCGGTACCTCTAAG
Found at i:1762648 original size:14 final size:15
Alignment explanation
Indices: 1762629--1762661 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1762619 TAATTTAATC
*
1762629 AAATATATAAT-TTA
1 AAATATAAAATCTTA
1762643 AAATATAAAATCTTA
1 AAATATAAAATCTTA
1762658 AAAT
1 AAAT
1762662 TCATTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATAAAATCTTA
Found at i:1765075 original size:20 final size:22
Alignment explanation
Indices: 1765046--1765118 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 22
1765036 TAAACCCGAC
*
1765046 AGGGGATATCGATAC-C-CTTAT
1 AGGGG-TATCGATACACACTTAA
*
1765067 AGGGGTATCGATACACATTTAA
1 AGGGGTATCGATACACACTTAA
* *
1765089 AGAGGGTATCGATACAC-GTTGA
1 AG-GGGTATCGATACACACTTAA
1765111 AGGGGTAT
1 AGGGGTAT
1765119 TGTTGAGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.20
21 12 0.27
22 10 0.22
23 14 0.31
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.26
Consensus pattern (22 bp):
AGGGGTATCGATACACACTTAA
Found at i:1766558 original size:15 final size:15
Alignment explanation
Indices: 1766532--1766579 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
1766522 TTCAAATATC
1766532 CAAACAAATCCAAAAT
1 CAAAC-AATCCAAAAT
*
1766548 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
*
1766565 CAAACATTCCAAAAT
1 CAAACAATCCAAAAT
1766580 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.00, T:0.17
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:1767744 original size:21 final size:21
Alignment explanation
Indices: 1767715--1767790 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 21
1767705 CATGGGAGGT
1767715 ATCGATTCCC-TCAAGGAGGGA
1 ATCGATTCCCTTCAAGG-GGGA
*
1767736 ATCGGTTCCCATTCAAAGGGGGA
1 ATCGATTCCC-TTC-AAGGGGGA
* *
1767759 ATCGGTTCCCCTTCAAGGGGGT
1 ATCGATT-CCCTTCAAGGGGGA
1767781 ATCGATTCCC
1 ATCGATTCCC
1767791 ACTACACTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 12 0.25
22 13 0.27
23 16 0.33
24 7 0.15
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (21 bp):
ATCGATTCCCTTCAAGGGGGA
Found at i:1767779 original size:22 final size:22
Alignment explanation
Indices: 1767725--1767791 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
1767715 ATCGATTCCC
1767725 TCAAGGAGGGAATCGGTTCCCAT
1 TCAAGG-GGGAATCGGTTCCCAT
*
1767748 TCAAAGGGGGAATCGGTTCCCCT
1 TC-AAGGGGGAATCGGTTCCCAT
* *
1767771 TCAAGGGGGTATCGATTCCCA
1 TCAAGGGGGAATCGGTTCCCA
1767792 CTACACTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
22 16 0.41
23 19 0.49
24 4 0.10
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.22
Consensus pattern (22 bp):
TCAAGGGGGAATCGGTTCCCAT
Found at i:1773897 original size:20 final size:21
Alignment explanation
Indices: 1773853--1773906 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1773843 GTTTTCAACA
*
1773853 GGTATCGATACCTAGCAAGGG
1 GGTATCGATACCTAGCAAAGG
* *
1773874 GGTATTGATACCTA-TAAAGG
1 GGTATCGATACCTAGCAAAGG
1773894 GGTATCGATACCT
1 GGTATCGATACCT
1773907 GGTGCACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (21 bp):
GGTATCGATACCTAGCAAAGG
Found at i:1777332 original size:17 final size:17
Alignment explanation
Indices: 1777288--1777335 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 17
1777278 TAAAAATATT
1777288 TTTCTCTCTAAAACTCAG
1 TTTC-CTCTAAAACTCAG
*
1777306 TTTCCCTCTAAAATTCAG
1 TTT-CCTCTAAAACTCAG
1777324 TTTCCTCTAAAA
1 TTTCCTCTAAAA
1777336 GAAAAGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 9 0.32
18 18 0.64
19 1 0.04
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40
Consensus pattern (17 bp):
TTTCCTCTAAAACTCAG
Found at i:1777462 original size:14 final size:16
Alignment explanation
Indices: 1777434--1777465 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1777424 TTTCTTTGAT
1777434 TAATATAATATTAAAA
1 TAATATAATATTAAAA
1777450 TAATA-AATA-TAAAA
1 TAATATAATATTAAAA
1777464 TA
1 TA
1777466 TATCAATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATATAATATTAAAA
Found at i:1777579 original size:3 final size:3
Alignment explanation
Indices: 1777571--1777606 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1777561 AGAAAATACA
1777571 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1777607 TAAAGCATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1778528 original size:16 final size:15
Alignment explanation
Indices: 1778505--1778534 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1778495 TAATTAGGAC
1778505 TTTATTTATTTTAAA
1 TTTATTTATTTTAAA
1778520 TTTACTTTATTTTAA
1 TTTA-TTTATTTTAA
1778535 CTTTCCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTTATTTTAAA
Found at i:1780587 original size:33 final size:33
Alignment explanation
Indices: 1780504--1780589 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
1780494 ATGCATTGCA
* * * *
1780504 ACAAGAAACAAATGAAACAATTTATGCACTTCG
1 ACAAGAAACAAAAGAGACAATTCATGCACTCCG
*
1780537 ACAAGAAACAAAAGAGACAATTCATTCACTCCG
1 ACAAGAAACAAAAGAGACAATTCATGCACTCCG
* *
1780570 ATAAGAAACAAAGGAGACAA
1 ACAAGAAACAAAAGAGACAA
1780590 GAGAATTGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.52, C:0.19, G:0.14, T:0.15
Consensus pattern (33 bp):
ACAAGAAACAAAAGAGACAATTCATGCACTCCG
Found at i:1781541 original size:2 final size:2
Alignment explanation
Indices: 1781534--1781564 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1781524 TAATTAAAAT
1781534 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 T
1781565 TAATTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1790901 original size:13 final size:13
Alignment explanation
Indices: 1790885--1790929 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1790875 AATCAATTTA
1790885 AAATATAAAAATT
1 AAATATAAAAATT
1790898 AAATATAAAAATACT
1 AAATATAAAAAT--T
* *
1790913 AAAAATAAATATT
1 AAATATAAAAATT
1790926 AAAT
1 AAAT
1790930 TACTAGACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 16 0.59
15 11 0.41
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAAAAATT
Found at i:1790908 original size:21 final size:21
Alignment explanation
Indices: 1790884--1790934 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1790874 AAATCAATTT
1790884 AAAATA-TAAAAATTAAATATA
1 AAAATACTAAAAA-TAAATATA
*
1790905 AAAATACTAAAAATAAATATT
1 AAAATACTAAAAATAAATATA
*
1790926 AAATTACTA
1 AAAATACTA
1790935 GACATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATACTAAAAATAAATATA
Found at i:1791495 original size:20 final size:21
Alignment explanation
Indices: 1791463--1791508 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1791453 ATTGTTCAAT
*
1791463 TTTTTAGTAATTTAATTTTTA
1 TTTTTAGTAATTTAATATTTA
*
1791484 TTTTTAGT-ATTTCATATTTA
1 TTTTTAGTAATTTAATATTTA
1791504 TTTTT
1 TTTTT
1791509 TATATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTAGTAATTTAATATTTA
Found at i:1791509 original size:21 final size:22
Alignment explanation
Indices: 1791461--1791510 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
1791451 ATATTGTTCA
*
1791461 ATTTTTTAGTAATTTAATTTTT
1 ATTTTTTAGTAATTTAATATTT
*
1791483 A-TTTTTAGT-ATTTCATATTT
1 ATTTTTTAGTAATTTAATATTT
1791503 ATTTTTTA
1 ATTTTTTA
1791511 TATATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.40
21 14 0.56
22 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (22 bp):
ATTTTTTAGTAATTTAATATTT
Found at i:1792088 original size:42 final size:42
Alignment explanation
Indices: 1792041--1792135 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
1792031 TTCCCCGAAA
* *
1792041 TACCGTGTTTGTTTCATATAATTCATTTTTCGGAAAATATTT
1 TACCGTGTTTGTTTCACATAATTCATTTTCCGGAAAATATTT
* ** *
1792083 TACCGTGTTTGTTTCACGTAATTTGTTTTCCGGAAAATGTTT
1 TACCGTGTTTGTTTCACATAATTCATTTTCCGGAAAATATTT
1792125 T-CCAGTGTTTG
1 TACC-GTGTTTG
1792136 GTTGGAGGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 2 0.04
42 44 0.96
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (42 bp):
TACCGTGTTTGTTTCACATAATTCATTTTCCGGAAAATATTT
Found at i:1792394 original size:22 final size:22
Alignment explanation
Indices: 1792369--1792417 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1792359 TTATATTTAT
1792369 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* *
1792391 TAATATTTTTAATATTATAATA
1 TAATATTTATAATAATATAATA
*
1792413 AAATA
1 TAATA
1792418 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:1792411 original size:30 final size:32
Alignment explanation
Indices: 1792361--1792419 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
1792351 TATTTAAATT
*
1792361 ATATTTATTAATATTTATAATAATATAATATA
1 ATATTTATTAATATTTATAATAAAATAATATA
1792393 ATATTT-TTAATA-TTATAATAAAATAAT
1 ATATTTATTAATATTTATAATAAAATAAT
1792420 CAATTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 14 0.54
31 6 0.23
32 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
ATATTTATTAATATTTATAATAAAATAATATA
Found at i:1792552 original size:19 final size:18
Alignment explanation
Indices: 1792484--1792554 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
1792474 TAATTGTTTT
*
1792484 ATATATTTAATAATGAATA
1 ATAT-TTTAATAATTAATA
*
1792503 ATATTATTTATATATTTAATA
1 ATA-T-TTTA-ATAATTAATA
* * *
1792524 TTAATATAATAATCTAATA
1 ATATTTTAATAAT-TAATA
1792543 ATATTTTAATAA
1 ATATTTTAATAA
1792555 AGCTATTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 4 0.10
19 20 0.50
20 6 0.15
21 10 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATATTTTAATAATTAATA
Found at i:1792575 original size:23 final size:23
Alignment explanation
Indices: 1792549--1792593 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1792539 AATAATATTT
*
1792549 TAATAAAGCTATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1792572 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1792594 ATATAACACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1794118 original size:198 final size:196
Alignment explanation
Indices: 1793680--1794557 Score: 879
Period size: 198 Copynumber: 4.6 Consensus size: 196
1793670 AGTAAGTAGA
* * ** ** * *
1793680 AATTAAGTAATATTATATCGTTACTTTTTTAAAAAAAATTTAAACTATATATTATAGTTAATTCG
1 AATTAAGTAATATTATATCATTAATTTTTT-ATTAATTTTTAAATTATATATTATAGTTAATTTG
* * * *
1793745 ATTTTTGATGATGAATGTTACTAAAATTTTAATATTATGCATATAATTTGAGAAGAAGGAAAAAA
65 ATTGTT--T-ATGAATGTTAATATAATTTTAATATTATGCATGTAATTTGAGAAGAAGGAAAAAA
* * * * ** *
1793810 TTGTAAAAGAAAAAAAAAGGAGGAGGAGGAGGAGGAGGAGAAAATATTAGTAAGTAGATGTATAT
127 -TGTAAAAG-AAGAAGAA-GA--AGAAGAATAAGAAGGAGAAAATATTAGTAAGTAGATGTATAT
*
1793875 TTTATTTTTT
187 TTTAATTTTT
** *
1793885 AATTAAGTAATATTATATTGTTAATTTTATTTTTAATTTTTAAATTATATATTATAGTTAATTTG
1 AATTAAGTAATATTATATCATTAATTTT-TTATTAATTTTTAAATTATATATTATAGTTAATTTG
* *
1793950 ATTGTTTATGAATGTTAATATAATTTTAATATTATGAATGTAATTTGAGAAGAATGAAAAAATGT
65 ATTGTTTATGAATGTTAATATAATTTTAATATTATGCATGTAATTTGAGAAGAAGGAAAAAATGT
1794015 AAAAGAAGAAGAAGAAGAAGGAATAAGAAGGAGAAAATATTAGTAAGTAGATGTATATTTTAATT
130 AAAAGAAGAAGAAGAAGAA-GAATAAGAAGGAGAAAATATTAGTAAGTAGATGTATATTTTAATT
1794080 TTT
194 TTT
*
1794083 AATTTAAGTAATATTATATCATTAATTTTTTTTTAATTTTTAAATTATATATTATAGTTAATTTG
1 AA-TTAAGTAATATTATATCATTAATTTTTTATTAATTTTTAAATTATATATTATAGTTAATTTG
* * * * * *
1794148 ATTGTTTATGTATTTTATTAAAATTTTAATATTATGCATCTAATTTGAGAAGAAGGAAAAATTTG
65 ATTGTTTATGAATGTTAATATAATTTTAATATTATGCATGTAATTTGAGAAGAAGGAAAAA-ATG
* *
1794213 TAAAAG-A-AA-AAGAAG-A-AA-AAGAAGGAAAAATATTATTATGTATATGTATATGTATATTT
129 TAAAAGAAGAAGAAGAAGAAGAATAAGAAGGAGAAA-A-TATTA-GTA-A-GTAGATGTATATTT
*
1794272 TATTTTTT
189 TAATTTTT
* *
1794280 AATTAAGGAATATTATATC-----------GTTAA-TTTT--ATT-T-TATTATAGTTAATTTGA
1 AATTAAGTAATATTATATCATTAATTTTTTATTAATTTTTAAATTATATATTATAGTTAATTTGA
* *
1794329 TTGTTGATGAATGTTAATATAATTTTAATATTATGCATGTAATCTT-AGAAGAAGGAAAAATTGT
66 TTGTTTATGAATGTTAATATAATTTTAATATTATGCATGTAAT-TTGAGAAGAAGGAAAAAATGT
*
1794393 --AA-AAGAAGAAGAAGAAGAAT------GAGAAAATATTAGTAAGTAGATGCATATTTT-ATTT
130 AAAAGAAGAAGAAGAAGAAGAATAAGAAGGAGAAAATATTAGTAAGTAGATGTATATTTTAATTT
1794448 TT
195 TT
* * *
1794450 GATTAATTAATATTAT-T-ATT-A----TTATT--TTTTTAAATTATATATTATAGTTAATTTAA
1 AATTAAGTAATATTATATCATTAATTTTTTATTAATTTTTAAATTATATATTATAGTTAATTTGA
*
1794506 TT-TTTGATGAATGTTAATATACTTTTAATATTATGCATGTAATTTGAGAAGA
66 TTGTTT-ATGAATGTTAATATAATTTTAATATTATGCATGTAATTTGAGAAGA
1794558 TTTGGTGAAA
Statistics
Matches: 589, Mismatches: 55, Indels: 86
0.81 0.08 0.12
Matches are distributed among these distances:
169 1 0.00
170 18 0.03
171 13 0.02
172 1 0.00
173 7 0.01
174 7 0.01
175 4 0.01
176 10 0.02
177 63 0.11
178 2 0.00
179 10 0.02
180 69 0.12
181 5 0.01
182 3 0.01
184 4 0.01
185 4 0.01
192 11 0.02
193 3 0.01
194 5 0.01
195 4 0.01
196 23 0.04
197 27 0.05
198 136 0.23
199 34 0.06
200 6 0.01
201 8 0.01
202 50 0.08
203 1 0.00
205 58 0.10
206 2 0.00
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (196 bp):
AATTAAGTAATATTATATCATTAATTTTTTATTAATTTTTAAATTATATATTATAGTTAATTTGA
TTGTTTATGAATGTTAATATAATTTTAATATTATGCATGTAATTTGAGAAGAAGGAAAAAATGTA
AAAGAAGAAGAAGAAGAAGAATAAGAAGGAGAAAATATTAGTAAGTAGATGTATATTTTAATTTT
T
Found at i:1794341 original size:378 final size:372
Alignment explanation
Indices: 1793680--1794557 Score: 963
Period size: 378 Copynumber: 2.3 Consensus size: 372
1793670 AGTAAGTAGA
* * ** ** * *
1793680 AATTAAGTAATATTATATCGTTACTTTTTTAAAAAAAATTTAAACTATATATTATAGTTAATTCG
1 AATTAAGTAATATTATATCATTAATTTTTT-ATTAATTTTTAAATTATATATTATAGTTAATTTG
*
1793745 ATTTTTGATGATGAATGTTACTAAAATTTTAATATTATGCATATAATTTGAGAAGAAGGAAAAAA
65 ATTTTTGATG-T--ATGTTAATAAAATTTTAATATTATGCATATAATTTGAGAAGAAGGAAAAAA
* *
1793810 TTGTAAAAGAAAAAAAAAGGAGGAGGAGGAGGAGGAGGAGAAAATATTAGTAAGTAGATGTATAT
127 TTGTAAAAGAAAAAAAAAGGA-GA-GA-GA-GAGAAGGAAAAAATATTAGTAAGTAGATGTATAT
* *
1793875 TTTATTTTTTAATTAAGTAATATTATATTGTTAATTTTATTTTTAATTTTTAAATTATATATTAT
188 TTTATTTTTTAATTAAGGAATATTATATCG-----------TTTAATTTTT-AATTATATATTAT
*
1793940 AGTTAATTTGATTGTTTATGAATGTTAATATAATTTTAATATTATGAATGTAAT-TTGAGAAGAA
241 AGTTAATTTGATTGTTGATGAATGTTAATATAATTTTAATATTATGAATGTAATCTT-AGAAGAA
* *
1794004 TGAAAAAATGTAAAAGAAGAAGAAGAAGAAGGAATAAGAAGGAGAAAATATTAGTAAGTAGATGT
305 GGAAAAAATGT--AA-AAGAAGAAGAAGAA-GAAT------GAGAAAATATTAGTAAGTAGATGC
1794069 ATATTTTAATTTTT
360 ATATTTT-ATTTTT
*
1794083 AATTTAAGTAATATTATATCATTAATTTTTTTTTAATTTTTAAATTATATATTATAGTTAATTTG
1 AA-TTAAGTAATATTATATCATTAATTTTTTATTAATTTTTAAATTATATATTATAGTTAATTTG
* * * *
1794148 ATTGTTT-ATGTATTTTATTAAAATTTTAATATTATGCATCTAATTTGAGAAGAAGGAAAAATTT
65 ATT-TTTGATGTATGTTAATAAAATTTTAATATTATGCATATAATTTGAGAAGAAGGAAAAAATT
* *
1794212 GTAAAAG-AAAAAGAA-GA-A-A-A-AGAAGGAAAAATATTATTATGTATATGTATATGTATATT
129 GTAAAAGAAAAAAAAAGGAGAGAGAGAGAAGGAAAAA-A-TATTA-GTA-A-GTAGATGTATATT
1794271 TTATTTTTTAATTAAGGAATATTATATCG-TTAA-TTTT-ATT-T-TATTATAGTTAATTTGATT
189 TTATTTTTTAATTAAGGAATATTATATCGTTTAATTTTTAATTATATATTATAGTTAATTTGATT
* *
1794331 GTTGATGAATGTTAATATAATTTTAATATTATGCATGTAATCTTAGAAGAAGGAAAAATTGTAAA
254 GTTGATGAATGTTAATATAATTTTAATATTATGAATGTAATCTTAGAAGAAGGAAAAAATGTAAA
1794396 AGAAGAAGAAGAAGAATGAGAAAATATTAGTAAGTAGATGCATATTTTATTTTT
319 AGAAGAAGAAGAAGAATGAGAAAATATTAGTAAGTAGATGCATATTTTATTTTT
* * *
1794450 GATTAATTAATATTAT-T-ATT-A----TTATT--TTTTTAAATTATATATTATAGTTAATTTAA
1 AATTAAGTAATATTATATCATTAATTTTTTATTAATTTTTAAATTATATATTATAGTTAATTTGA
* * * *
1794506 TTTTTGATGAATGTTAATATACTTTTAATATTATGCATGTAATTTGAGAAGA
66 TTTTTGATGTATGTTAATAAAATTTTAATATTATGCATATAATTTGAGAAGA
1794558 TTTGGTGAAA
Statistics
Matches: 432, Mismatches: 34, Indels: 64
0.82 0.06 0.12
Matches are distributed among these distances:
356 3 0.01
357 71 0.16
359 4 0.01
363 1 0.00
364 3 0.01
365 1 0.00
366 13 0.03
367 7 0.02
368 30 0.07
374 4 0.01
375 14 0.03
376 2 0.00
378 74 0.17
379 3 0.01
380 3 0.01
382 4 0.01
383 4 0.01
390 9 0.02
391 1 0.00
392 6 0.01
393 3 0.01
394 2 0.00
395 39 0.09
396 1 0.00
398 2 0.00
399 7 0.02
400 56 0.13
402 1 0.00
403 35 0.08
404 29 0.07
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (372 bp):
AATTAAGTAATATTATATCATTAATTTTTTATTAATTTTTAAATTATATATTATAGTTAATTTGA
TTTTTGATGTATGTTAATAAAATTTTAATATTATGCATATAATTTGAGAAGAAGGAAAAAATTGT
AAAAGAAAAAAAAAGGAGAGAGAGAGAAGGAAAAAATATTAGTAAGTAGATGTATATTTTATTTT
TTAATTAAGGAATATTATATCGTTTAATTTTTAATTATATATTATAGTTAATTTGATTGTTGATG
AATGTTAATATAATTTTAATATTATGAATGTAATCTTAGAAGAAGGAAAAAATGTAAAAGAAGAA
GAAGAAGAATGAGAAAATATTAGTAAGTAGATGCATATTTTATTTTT
Found at i:1794491 original size:29 final size:27
Alignment explanation
Indices: 1794438--1794494 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
1794428 AGTAGATGCA
1794438 TATTTTATTTTTGATTAATTAATATTAT
1 TATTTTATTTTT-ATTAATTAATATTAT
1794466 TATTATTATTTTT-TTAAATTATATATTAT
1 TATT-TTATTTTTATT-AATTA-ATATTAT
1794495 AGTTAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 2 0.08
28 9 0.35
29 15 0.58
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
TATTTTATTTTTATTAATTAATATTAT
Found at i:1794578 original size:177 final size:175
Alignment explanation
Indices: 1794026--1794557 Score: 560
Period size: 180 Copynumber: 2.9 Consensus size: 175
1794016 AAAGAAGAAG
*
1794026 AAGAAGAAGGAATAAGAAGGAGAAAATATTAGTAAGTAGATGTATATTTTAATTTTTAATTTAAG
1 AAGAAGAA-GAAGAAGAAGGAGAAAATATTAGTAAGTAGATGTATATTTT-ATTTTTAA-TTAAG
*
1794091 TAATATTATATCATTAATTTTTTTTTAATTTTTAAATTATATATTATAGTTAATTTGATTGTTTA
63 TAATATTAT-T-ATT-A----TTATT--TTTTTAAATTATATATTATAGTTAATTTGATTGTTTA
* * * * *
1794156 TGTATTTTATTAAAATTTTAATATTATGCATCTAATTTGAGAAGAAGGAAAAATTTGTAA
119 TGAATGTTAATATAATTTTAATATTATGCATGTAATTTGAGAAGAAGGAAAAA--T-TAA
* * *
1794216 AAGAAAAAGAAGAAAAAGAAGGAAAAATATTATTATGTATATGTATATGTATATTTTATTTTTTA
1 AAG---AAGAAGAAGAAGAAGGAGAAA-A-TATTA-GTA-A-GTAGATGTATATTTTA-TTTTTA
* ** * *
1794281 ATTAAGGAATATTA-TATCGTTA--ATTTT--ATT-T-TATTATAGTTAATTTGATTGTTGATGA
57 ATTAAGTAATATTATTATTATTATTTTTTTAAATTATATATTATAGTTAATTTGATTGTTTATGA
1794339 ATGTTAATATAATTTTAATATTATGCATGTAATCTT-AGAAGAAGGAAAAATTGTAA
122 ATGTTAATATAATTTTAATATTATGCATGTAAT-TTGAGAAGAAGGAAAAA-T-TAA
* * * *
1794395 AAGAAGAAGAAGAAGAATGAGAAAATATTAGTAAGTAGATGCATATTTTATTTTTGATTAATTAA
1 AAGAAGAAGAAGAAGAAGGAGAAAATATTAGTAAGTAGATGTATATTTTATTTTTAATTAAGTAA
*
1794460 TATTATTATTATTATTTTTTTAAATTATATATTATAGTTAATTTAATT-TTTGATGAATGTTAAT
66 TATTATTATTATTATTTTTTTAAATTATATATTATAGTTAATTTGATTGTTT-ATGAATGTTAAT
*
1794524 ATACTTTTAATATTATGCATGTAATTTGAGAAGA
130 ATAATTTTAATATTATGCATGTAATTTGAGAAGA
1794558 TTTGGTGAAA
Statistics
Matches: 295, Mismatches: 28, Indels: 51
0.79 0.07 0.14
Matches are distributed among these distances:
170 17 0.06
171 20 0.07
172 1 0.00
173 7 0.02
174 5 0.02
175 4 0.01
176 23 0.08
177 60 0.20
179 9 0.03
180 68 0.23
181 3 0.01
182 3 0.01
184 4 0.01
188 2 0.01
190 3 0.01
192 14 0.05
193 8 0.03
194 6 0.02
195 3 0.01
196 14 0.05
197 21 0.07
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (175 bp):
AAGAAGAAGAAGAAGAAGGAGAAAATATTAGTAAGTAGATGTATATTTTATTTTTAATTAAGTAA
TATTATTATTATTATTTTTTTAAATTATATATTATAGTTAATTTGATTGTTTATGAATGTTAATA
TAATTTTAATATTATGCATGTAATTTGAGAAGAAGGAAAAATTAA
Found at i:1801403 original size:19 final size:20
Alignment explanation
Indices: 1801364--1801419 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
1801354 GAAATCCCTT
*
1801364 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATCTTTAA
1801384 TGAAAATACATGA-CTTTAA
1 TGAAAATACATGATCTTTAA
* *
1801403 TGAACATACATGCTCTT
1 TGAAAATACATGATCTT
1801420 GGATGAATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATCTTTAA
Found at i:1804603 original size:14 final size:14
Alignment explanation
Indices: 1804584--1804616 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1804574 AGTGCTTCAA
1804584 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTATT
1804598 CTTTTCTTTTTATT
1 CTTTTCTTTTTATT
1804612 CTTTT
1 CTTTT
1804617 GAATACTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTATT
Found at i:1818118 original size:24 final size:24
Alignment explanation
Indices: 1818075--1818124 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1818065 TTTGTTTTCT
*
1818075 TTTTCTTCTTTTGAATGCTTGAAA
1 TTTTCTTCTTTTGAACGCTTGAAA
* *
1818099 TTTTCTTCTTTTGAGCGCTTGCAA
1 TTTTCTTCTTTTGAACGCTTGAAA
1818123 TT
1 TT
1818125 CCTTTGCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.54
Consensus pattern (24 bp):
TTTTCTTCTTTTGAACGCTTGAAA
Done.