Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008180.1 Hibiscus syriacus cultivar Beakdansim tig00110777_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: 2670214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 14
Found at i:1375024 original size:20 final size:20
Alignment explanation
Indices: 1374972--1375016 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1374962 ACTTTTATAT
1374972 TTATTACTATTA-A-TATTTA
1 TTATTA-TATTATATTATTTA
1374991 TTATTATATTATATTATTTA
1 TTATTATATTATATTATTTA
1375011 TT-TTAT
1 TTATTAT
1375017 TTTAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.21
19 11 0.46
20 8 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTATATTATATTATTTA
Found at i:1378326 original size:21 final size:21
Alignment explanation
Indices: 1378302--1378370 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
1378292 ACTCGCATAT
1378302 TAACAGACTGAATTGATATGA
1 TAACAGACTGAATTGATATGA
*
1378323 TAACATG--TAAATAGTCGCATAT--
1 TAACA-GACTGAAT--T-G-ATATGA
1378345 TAACAGACTGAATTGATATGA
1 TAACAGACTGAATTGATATGA
1378366 TAACA
1 TAACA
1378371 TGTAAATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 18
0.65 0.04 0.32
Matches are distributed among these distances:
19 4 0.11
20 5 0.14
21 12 0.32
22 7 0.19
23 5 0.14
24 4 0.11
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
TAACAGACTGAATTGATATGA
Found at i:1378355 original size:43 final size:43
Alignment explanation
Indices: 1378294--1378379 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
1378284 TTATGATCAC
1378294 TCGCATATTAACAGACTGAATTGATATGATAACATGTAAATAG
1 TCGCATATTAACAGACTGAATTGATATGATAACATGTAAATAG
1378337 TCGCATATTAACAGACTGAATTGATATGATAACATGTAAATAG
1 TCGCATATTAACAGACTGAATTGATATGATAACATGTAAATAG
1378380 ATTTGTTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (43 bp):
TCGCATATTAACAGACTGAATTGATATGATAACATGTAAATAG
Found at i:1381161 original size:29 final size:29
Alignment explanation
Indices: 1381129--1381222 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
1381119 ATTGATTCTT
*
1381129 AAACTTTTGAACATTCTAATTTCATCCCC
1 AAACTTTTGAACATTCTAAATTCATCCCC
* * * *
1381158 AAACAATTACT-ATCATTCTAAATTCGTGCCC
1 AAAC--TT-TTGAACATTCTAAATTCATCCCC
**
1381189 AAACTTTTGAATGTTCTAAATTCATCCCC
1 AAACTTTTGAACATTCTAAATTCATCCCC
1381218 AAACT
1 AAACT
1381223 ATAACCCACA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
28 1 0.02
29 26 0.52
31 22 0.44
32 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (29 bp):
AAACTTTTGAACATTCTAAATTCATCCCC
Found at i:1387683 original size:30 final size:29
Alignment explanation
Indices: 1387638--1387696 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 29
1387628 GCTTCATGAA
1387638 AGTTCTTCCAAAGAGAGTATAATAAATCT
1 AGTTCTTCCAAAGAGAGTATAATAAATCT
1387667 AGTTCTTCCGAAAGAGAGTATAATAAATCT
1 AGTTCTTCC-AAAGAGAGTATAATAAATCT
1387697 TATGAGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (29 bp):
AGTTCTTCCAAAGAGAGTATAATAAATCT
Found at i:1388667 original size:21 final size:22
Alignment explanation
Indices: 1388628--1388668 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1388618 TAAGTACTTA
1388628 AAGTATATTATTATTTTTATTT
1 AAGTATATTATTATTTTTATTT
1388650 AAGTAT-TTAGTT-TTTTTAT
1 AAGTATATTA-TTATTTTTAT
1388669 CAAAATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
AAGTATATTATTATTTTTATTT
Found at i:1388687 original size:20 final size:21
Alignment explanation
Indices: 1388661--1388701 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1388651 AGTATTTAGT
*
1388661 TTTTTTATCAAAATAAGTATC
1 TTTTTAATCAAAATAAGTATC
1388682 TTTTTAATCAAAATAAGTAT
1 TTTTTAATCAAAATAAGTAT
1388702 TTAAAGTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTTTAATCAAAATAAGTATC
Found at i:1388725 original size:29 final size:30
Alignment explanation
Indices: 1388675--1388735 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
1388665 TTATCAAAAT
*
1388675 AAGTATCTTTTTAATCAAAATAAGTATTTA
1 AAGTATCTTTTTAATCAAAATAAGTATGTA
* *
1388705 AAGTATCTTTTT-GTCAAAATAGGTATGTA
1 AAGTATCTTTTTAATCAAAATAAGTATGTA
1388734 AA
1 AA
1388736 ATATTCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (30 bp):
AAGTATCTTTTTAATCAAAATAAGTATGTA
Found at i:1391466 original size:2 final size:2
Alignment explanation
Indices: 1391459--1391525 Score: 98
Period size: 2 Copynumber: 33.0 Consensus size: 2
1391449 CTGATATTTA
1391459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1391501 AT AT CAT TT TT AT AA AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT
1391526 TATTTTTACT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 58 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1394120 original size:21 final size:21
Alignment explanation
Indices: 1394094--1394133 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1394084 GAGAAATTGT
1394094 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
1394115 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
1394134 AAACAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:1397992 original size:20 final size:19
Alignment explanation
Indices: 1397939--1397992 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
1397929 ATAGGGCAGA
*
1397939 GGGAATCGATACCCCCAAG
1 GGGAACCGATACCCCCAAG
1397958 GGGAACCGATACCCCCAAG
1 GGGAACCGATACCCCCAAG
*
1397977 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
1397993 TTTGAATAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.28, C:0.37, G:0.26, T:0.09
Consensus pattern (19 bp):
GGGAACCGATACCCCCAAG
Found at i:1408204 original size:54 final size:52
Alignment explanation
Indices: 1408111--1408263 Score: 164
Period size: 52 Copynumber: 2.9 Consensus size: 52
1408101 CAGAAATCTA
* * *
1408111 TGCAGAAACCACAGAAAGTGTGAATGT-TTGTCAAATGTTTTACGAACATATG
1 TGCAGAAGCCACAAAAAG-ATGAATGTGTTGTCAAATGTTTTACGAACATATG
* *
1408163 TGCAGAAGCCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACAAACATCTG
1 TGCAGAAGCCACA--AAAAGATGAATGTGTTGTCAAATGTTTTACGAACATATG
* **** * *
1408217 TGTAGAAGCCACATCTGGATGAATGTGTTATCAAATATTTTACGAAC
1 TGCAGAAGCCACAAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
1408264 TAGTGATTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
52 39 0.46
53 7 0.08
54 39 0.46
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (52 bp):
TGCAGAAGCCACAAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATATG
Found at i:1408665 original size:20 final size:22
Alignment explanation
Indices: 1408620--1408676 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1408610 ACATATACAT
1408620 TCTTCAAAGATGACAGATTCTC
1 TCTTCAAAGATGACAGATTCTC
*
1408642 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGACAGATTCTC
* *
1408664 TTTTCAAATATGA
1 TCTTCAAAGATGA
1408677 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGACAGATTCTC
Found at i:1409456 original size:36 final size:36
Alignment explanation
Indices: 1409405--1409518 Score: 138
Period size: 36 Copynumber: 3.1 Consensus size: 36
1409395 TTCAAATAGC
1409405 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * * ** ** *
1409441 AATTTGTCTCGCTTGAGATAGTTTCACTCGAAATAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
*
1409477 CAATTTAACTCACTTGAGATTGTTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1409514 AATTT
1 AATTT
1409519 GTTTCTCTTG
Statistics
Matches: 60, Mismatches: 17, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
36 33 0.55
37 27 0.45
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:1409517 original size:73 final size:73
Alignment explanation
Indices: 1409398--1409546 Score: 244
Period size: 73 Copynumber: 2.0 Consensus size: 73
1409388 GGATGTTTTC
* * *
1409398 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGATAGT
1 AAATAACAATTTAACTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGT
*
1409463 TTCACTCG
66 TTCACTAG
* *
1409471 AAATAACAATTTAACTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTTTCTCTTGAGACAGT
1 AAATAACAATTTAACTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGT
1409536 TTCACTAG
66 TTCACTAG
1409544 AAA
1 AAA
1409547 CAGAAATTTC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (73 bp):
AAATAACAATTTAACTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGT
TTCACTAG
Found at i:1409529 original size:36 final size:36
Alignment explanation
Indices: 1409405--1409531 Score: 137
Period size: 36 Copynumber: 3.5 Consensus size: 36
1409395 TTCAAATAGC
*
1409405 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTGTCTCACTTGAGATTGTTTTTCTTAAAACAA
* * ** ** *
1409441 AATTTGTCTCGCTTGAGATAGTTTCACTCGAAATAA
1 AATTTGTCTCACTTGAGATTGTTTTTCTTAAAACAA
**
1409477 CAATTTAACTCACTTGAGATTGTTTTTCTTAAAACAA
1 -AATTTGTCTCACTTGAGATTGTTTTTCTTAAAACAA
* *
1409514 AATTTGTTTCTCTTGAGA
1 AATTTGTCTCACTTGAGA
1409532 CAGTTTCACT
Statistics
Matches: 69, Mismatches: 21, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
36 42 0.61
37 27 0.39
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (36 bp):
AATTTGTCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:1409548 original size:36 final size:36
Alignment explanation
Indices: 1409405--1409555 Score: 117
Period size: 36 Copynumber: 4.1 Consensus size: 36
1409395 TTCAAATAGC
* * **
1409405 AATTTATCTCACTTGAGATTGTTTTTCTTA-AAACAA
1 AATTTGTCTCACTTGAGATAGTTTCAC-TAGAAACAA
* * *
1409441 AATTTGTCTCGCTTGAGATAGTTTCACTCGAAATAA
1 AATTTGTCTCACTTGAGATAGTTTCACTAGAAACAA
** * **
1409477 CAATTTAACTCACTTGAGATTGTTTTTCTTA-AAACAA
1 -AATTTGTCTCACTTGAGATAGTTTCAC-TAGAAACAA
* * *
1409514 AATTTGTTTCTCTTGAGACAGTTTCACTAGAAACAGA
1 AATTTGTCTCACTTGAGATAGTTTCACTAGAAACA-A
1409551 AATTT
1 AATTT
1409556 CCATCACTCG
Statistics
Matches: 87, Mismatches: 23, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
35 3 0.03
36 51 0.59
37 32 0.37
38 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (36 bp):
AATTTGTCTCACTTGAGATAGTTTCACTAGAAACAA
Found at i:1409796 original size:123 final size:123
Alignment explanation
Indices: 1409570--1410149 Score: 917
Period size: 123 Copynumber: 4.7 Consensus size: 123
1409560 CACTCGATGG
* *
1409570 ATCAACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGTAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
1409635 ATGAGAAGAACTTGTTCAACCTTTTGTTCGACTCTATCGCAGAAGGAGATAGATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
* *
1409693 ATCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * *
1409758 ATGAGAAGAACTTGTTCAACCTGTTGCTCAACTGTATCGCAGAATGAGATAGATTAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
* *
1409816 ATCAACATTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
1409881 ATGAGAAGAACTTGTTCAACCTTTTGTTCGACTCTATCGCAGAAGGAGATAGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
* * * * *
1409939 ATCAACATTTCCAAAAGGAGTTCATAATGAAAAGAATTCATCTGAAGATGAAGAAAAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
1410004 ATGAGAAGAACTTGTTCGACCATTTGCTCGATTCTATCGCAGAAGGAGATAGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
** * *
1410062 ATCAACATTTCCAGAAATAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCAAA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
1410127 ATGAGAAGAACTGGTTCAACCTT
66 ATGAGAAGAACTTGTTCAACCTT
1410150 AGTTCAATTC
Statistics
Matches: 414, Mismatches: 43, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
123 414 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
Found at i:1411620 original size:25 final size:24
Alignment explanation
Indices: 1411588--1411655 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 24
1411578 TTGATCATTA
1411588 ATTA-TTTGCAATATTATTTTATT
1 ATTACTTTGCAATATTATTTTATT
*
1411611 ATTACTTTTG--ATATATATTTAAATT
1 ATTAC-TTTGCAATAT-TATTT-TATT
*
1411636 ATTACTTT-CATTATTATTTT
1 ATTACTTTGCAATATTATTTT
1411656 TTTTTATCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
23 8 0.22
24 13 0.36
25 15 0.42
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (24 bp):
ATTACTTTGCAATATTATTTTATT
Found at i:1411713 original size:28 final size:26
Alignment explanation
Indices: 1411675--1411726 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
1411665 TAATCATATA
1411675 AATATATATTTATATATATTTGTTTAAAT
1 AATATATATTTAT-T-TATTT-TTTAAAT
1411704 AATA-ATATTTATTTATTTTTTAA
1 AATATATATTTATTTATTTTTTAA
1411727 TATTAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.22
26 5 0.22
27 1 0.04
28 8 0.35
29 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
AATATATATTTATTTATTTTTTAAAT
Found at i:1412116 original size:2 final size:2
Alignment explanation
Indices: 1412109--1412135 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1412099 TACAAAACTC
1412109 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 T
1412136 TTAATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1418428 original size:33 final size:33
Alignment explanation
Indices: 1418386--1418486 Score: 193
Period size: 33 Copynumber: 3.1 Consensus size: 33
1418376 AATGAATTAC
1418386 ATCTTTTGGAAAACATTTTCTGGAAAATGTTTT
1 ATCTTTTGGAAAACATTTTCTGGAAAATGTTTT
1418419 ATCTTTTGGAAAACATTTTCTGGAAAATGTTTT
1 ATCTTTTGGAAAACATTTTCTGGAAAATGTTTT
*
1418452 ATCTTTTGGAAAATATTTTCTGGAAAATGTTTT
1 ATCTTTTGGAAAACATTTTCTGGAAAATGTTTT
1418485 AT
1 AT
1418487 GGTGTTTGGA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.47
Consensus pattern (33 bp):
ATCTTTTGGAAAACATTTTCTGGAAAATGTTTT
Found at i:1418430 original size:19 final size:19
Alignment explanation
Indices: 1418406--1418470 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
1418396 AAACATTTTC
1418406 TGGAAAATGTTTTATCTTT
1 TGGAAAATGTTTTATCTTT
**
1418425 TGGAAAA-CATTT-TC---
1 TGGAAAATGTTTTATCTTT
1418439 TGGAAAATGTTTTATCTTT
1 TGGAAAATGTTTTATCTTT
*
1418458 TGGAAAATATTTT
1 TGGAAAATGTTTT
1418471 CTGGAAAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 7 0.19
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 19 0.53
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (19 bp):
TGGAAAATGTTTTATCTTT
Found at i:1418451 original size:14 final size:14
Alignment explanation
Indices: 1418401--1418484 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
1418391 TTGGAAAACA
1418401 TTTTCTGGAAAATG
1 TTTTCTGGAAAATG
**
1418415 TTTTATCTTTTGGAAAACA
1 -TTT-TC---TGGAAAATG
1418434 TTTTCTGGAAAATG
1 TTTTCTGGAAAATG
*
1418448 TTTTATCTTTTGGAAAATA
1 -TTT-TC---TGGAAAATG
1418467 TTTTCTGGAAAATG
1 TTTTCTGGAAAATG
1418481 TTTT
1 TTTT
1418485 ATGGTGTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 19
0.68 0.08 0.24
Matches are distributed among these distances:
14 19 0.35
15 6 0.11
16 4 0.07
17 4 0.07
18 6 0.11
19 15 0.28
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (14 bp):
TTTTCTGGAAAATG
Found at i:1418997 original size:26 final size:25
Alignment explanation
Indices: 1418951--1419026 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 25
1418941 TTAAAATAAA
1418951 AATATAA-TAGTATCATATATTATTAT
1 AATATAATTAGTAT-AT-TATTATTAT
* *
1418977 AATATAATTGAGTATATTATTGTAAT
1 AATATAATT-AGTATATTATTATTAT
*
1419003 AATATTATTA-T-TATTATTATTAT
1 AATATAATTAGTATATTATTATTAT
1419026 A
1 A
1419027 TTATTAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
23 11 0.26
24 1 0.02
25 1 0.02
26 22 0.51
27 3 0.07
28 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (25 bp):
AATATAATTAGTATATTATTATTAT
Found at i:1419014 original size:20 final size:20
Alignment explanation
Indices: 1418953--1419032 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 20
1418943 AAAATAAAAA
* *
1418953 TATAATAGTATCATATATTAT
1 TATAATAATATTAT-TATTAT
1418974 TATAAT-ATAATTGAGTATATTAT
1 TATAATAAT-ATT-A-T-TATTAT
*
1418997 TGTAATAATATTATTATTAT
1 TATAATAATATTATTATTAT
* *
1419017 TATTATTATATTATTA
1 TATAATAATATTATTA
1419033 AAAATATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 20 0.41
21 9 0.18
22 2 0.04
23 16 0.33
24 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (20 bp):
TATAATAATATTATTATTAT
Found at i:1419031 original size:23 final size:22
Alignment explanation
Indices: 1418953--1419032 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 22
1418943 AAAATAAAAA
* *
1418953 TATAATAGTATCA-TATATTAT
1 TATAATATTATTAGTATATTAT
*
1418974 TATAATATAATTGAGTATATTAT
1 TATAATATTATT-AGTATATTAT
* * *
1418997 TGTAATAATATTATTATTATTAT
1 TATAATATTATTAGTA-TATTAT
*
1419020 TATTATATTATTA
1 TATAATATTATTA
1419033 AAAATATTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
21 9 0.20
22 4 0.09
23 33 0.72
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (22 bp):
TATAATATTATTAGTATATTAT
Found at i:1419039 original size:12 final size:12
Alignment explanation
Indices: 1419024--1419068 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1419014 TATTATTATT
1419024 ATATTATTAAAA
1 ATATTATTAAAA
*
1419036 ATATTAATAAAA
1 ATATTATTAAAA
*
1419048 ATATT-TTAAAT
1 ATATTATTAAAA
*
1419059 ATGTTATTAA
1 ATATTATTAA
1419069 TTAATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
ATATTATTAAAA
Found at i:1429480 original size:182 final size:182
Alignment explanation
Indices: 1429172--1429845 Score: 992
Period size: 182 Copynumber: 3.7 Consensus size: 182
1429162 TGTCGGTTTA
* * * * * * *
1429172 TGTCGATACTTTATAAAAATGTATCGATCTATATCAATATAACATGTAAAAATATGACAAAATCA
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
* * * * * * *
1429237 GTCTCGAAAAGACAAAAGCGGTAAAGCGCTACC-AGATATATTAAAAGTGTCGATTCTTTAATAT
66 GTCTCGAAATGACAAAACCGGTATAGAGATACCGA-ATATATTGAAAGTGTCGATACTTTAATAT
* *
1429301 AAGTATCGAAACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCTCCTATAAAG
130 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
1429354 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
* *
1429419 GTCTCGTAATGATAAAACCGGTATAGAGATACCGAATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCGAAATGACAAAACCGGTATAGAGATACCGAATATATTGAAAGTGTCGATACTTTAATATA
*
1429484 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCATTTTTAGCGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
* * * * * * * *
1429536 TATCAATACTTTATAACAATGTATCGACCCACAATGATATAATAGGTAAAAATATAACAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
* * *
1429601 GTCTCGAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCGAAATGACAAAACCGGTATAGAGATACCGAATATATTGAAAGTGTCGATACTTTAATATA
* * *
1429666 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCTTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
* *
1429718 TGTCGATACTTTATAACAATGTATCGATCCACAATGATATAACACGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
*
1429783 GTCTCGAAATGACAAAACCGGTATAGA-ACTACCGGATATATTGAAAGTGTCGATACTTTAATA
66 GTCTCGAAATGACAAAACCGGTATAGAGA-TACCGAATATATTGAAAGTGTCGATACTTTAATA
1429846 AGTACGTGTA
Statistics
Matches: 446, Mismatches: 44, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
182 445 1.00
183 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (182 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
GTCTCGAAATGACAAAACCGGTATAGAGATACCGAATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
Found at i:1431826 original size:19 final size:22
Alignment explanation
Indices: 1431778--1431832 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
1431768 TTTTTGTTTT
1431778 TTTTATATAAAATGATAGTATAA
1 TTTTATATAAAAT-ATAGTATAA
1431801 TTATTATATAAAAT-TA-TA-AA
1 TT-TTATATAAAATATAGTATAA
1431821 TTTTATTATAAA
1 TTTTA-TATAAA
1431833 TGCATATTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 2 0.07
22 2 0.07
23 2 0.07
24 11 0.37
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTTATATAAAATATAGTATAA
Found at i:1432520 original size:18 final size:18
Alignment explanation
Indices: 1432497--1432532 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1432487 GAAAAAATAT
*
1432497 GAAGAAGAAAATATGGAG
1 GAAGAAGAAAAGATGGAG
1432515 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1432533 AAAATGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1434110 original size:19 final size:19
Alignment explanation
Indices: 1434086--1434130 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1434076 AATGTAAGGT
1434086 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1434105 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1434124 TAATTTT
1 TAATTTT
1434131 ATATGTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1434466 original size:15 final size:15
Alignment explanation
Indices: 1434446--1434514 Score: 129
Period size: 15 Copynumber: 4.6 Consensus size: 15
1434436 GTCCAGTATG
1434446 GTTCCCAAACGTAAA
1 GTTCCCAAACGTAAA
1434461 GTTCCCAAACGTAAA
1 GTTCCCAAACGTAAA
1434476 GTTCCCAAACGTAAA
1 GTTCCCAAACGTAAA
1434491 GTTCCCAAACGTAAA
1 GTTCCCAAACGTAAA
*
1434506 GTTTCCAAA
1 GTTCCCAAA
1434515 AAATAGATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (15 bp):
GTTCCCAAACGTAAA
Found at i:1434886 original size:200 final size:200
Alignment explanation
Indices: 1434531--1435494 Score: 1290
Period size: 200 Copynumber: 4.8 Consensus size: 200
1434521 ATAAGCAGAT
* *
1434531 GTGTCGATACATTTATACAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * **
1434596 AGTAATTTTGTAATATAACTGGTATAAATATACCAATTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTGCAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * * *
1434661 ATCAACACTTTTGAAATTAGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAATGC
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGAACGC
1434726 ATAAA
196 ATAAA
* * * *
1434731 GTGTCGATACATTTGTAAAAAGTATCGATCCCAGAAACATCGAAACACAAAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
1434796 GGTAAATTTT-CAATGTAACCGGTATAACTATACCGGTTTTATGAGAGAACAAGTCTACATAATG
66 GGT-AATTTTGCAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATG
* *
1434860 TATCGACACTTTTGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGCACG
130 TATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGAACG
1434925 CATAAA
195 CATAAA
* * * *
1434931 GTGTCAATACATTTATAAAAAAGTATCGATACCAAAAACATCGAAACCCATAATTGTAATATAAT
1 GTGTCGATACATTTAT-AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * *
1434996 AGGTAATTTTACAATGTAACCGGTATAAATATATCAGTTTTATGTGAAAATAGGTCT-CATAATG
65 AGGTAATTTTGCAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATG
* * * *
1435060 TATCGACACTTGTG-GATCTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAAC
130 TATCGACACTTTTGAAAT-TTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGAAC
1435124 GCATAAA
194 GCATAAA
* *
1435131 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
1435196 GGTAATTTTGTAATGTAACTGGTATAAATATATCGATTTTATGTGAGAATATGTCTACAAAATGT
66 GGTAATTTTGCAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * * * * * *
1435261 ATTGACACTTGTGTATTTTGTGTCGATAATTTTTGTCTAGAAGGAATGCCCAAAAGGGTGCACCC
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGAACGC
1435326 ATAAA
196 ATAAA
* ***
1435331 GTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAATTGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
1435396 GGTAAATTTCCAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTC-AGCATAAAG
66 GGTAATTTTGCAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTA-CATAATG
* *
1435460 TGTCGACAAATTTT-AAATTTGTGTCGATACTTTTT
130 TATCGAC-ACTTTTGAAATTTGTGTCGATACTTTTT
1435495 TAAATATCGC
Statistics
Matches: 668, Mismatches: 88, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
199 96 0.14
200 476 0.71
201 96 0.14
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGCAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATGT
ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGAACGC
ATAAA
Found at i:1435838 original size:15 final size:15
Alignment explanation
Indices: 1435818--1435846 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1435808 TCTTTCTCAA
1435818 AGCTCTTCTCAACCC
1 AGCTCTTCTCAACCC
1435833 AGCTCTTCTCAACC
1 AGCTCTTCTCAACC
1435847 ACAACCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.45, G:0.07, T:0.28
Consensus pattern (15 bp):
AGCTCTTCTCAACCC
Found at i:1437042 original size:6 final size:6
Alignment explanation
Indices: 1437008--1437060 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
1436998 CAAGCGGTCA
* * * * * *
1437008 ATGAAG ATGAAG ATGACG ATGAAG ATGATG ATGATA ATGGTG ATGATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
1437056 ATGAT
1 ATGAT
1437061 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.40, C:0.02, G:0.32, T:0.26
Consensus pattern (6 bp):
ATGATG
Found at i:1448278 original size:200 final size:200
Alignment explanation
Indices: 1447935--1448961 Score: 1361
Period size: 200 Copynumber: 5.1 Consensus size: 200
1447925 TTAACTCAAC
1447935 AATAGGTCTACA-AATTGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAA
1 AATAGGTCTACATAA-TGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAA
*
1447999 TGTCCAAAAGGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCAATCCCAGAAACATC
65 TGTCCAAAAGGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATC
* *
1448064 GAAACTGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTA
130 GAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTA
* *
1448129 TGTGAG
195 TGAGAA
* * * *
1448135 AATAGGTCTACATAATGTATCGACACTTCTGGATTTTGTGTCGATACTTTTTGTCCATAATGATT
1 AATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAAT
* * * *
1448200 GTCCAAAAGGGTGCACACATAAAGTGTTGATACATTTATAAAAAGTATCTATCCCAGAAATATCG
66 GTCCAAAAGGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCG
* * *
1448265 AAACCGATAATTATAATGTATTAGGTAAATTTACAATGTAACCGGTATAAATAAACCGGTTTTAT
131 AAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTAT
1448330 GAGAA
196 GAGAA
*
1448335 AAT-GGTCTACA-AATTGTATCGACACTTGTGGAATTTATGTCGATACTTTTTGTCCAGAATGAA
1 AATAGGTCTACATAA-TGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAA
*
1448398 TGTCCAAAAGGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAGAAACATC
65 TGTCCAAAAGGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATC
*
1448463 GAAACCGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTATAAATATACCGATTTTA
130 GAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTA
1448528 TGAGAA
195 TGAGAA
* * ** * * * *
1448534 AATAGAT-TAGCATAAAGTATCGACACCTT-TTAAATTTGTGTCAATACATTTTGTCCAAAACGA
1 AATAGGTCTA-CATAATGTATCGACA-CTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGA
* * * * * * *
1448597 TTG-CCAAATGGGGTGCACGCATAAAGTGTCGATACATTTATTAAGAGTGTCGATCCAAAAAAAC
64 ATGTCCAAA-AGGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCC-CAGAAAC
* * * *
1448661 ATCAAAACCGAAAATTATAATGTAATAGGTAAATTTCCAATGTAACTGGTATAAATATACCGATT
127 ATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATT
1448726 TTATGAGAA
192 TTATGAGAA
* * * ** * * *
1448735 AATATGTC-AGCATAAAGTATCGACACTTTTTAAATTTGTGTCGATACATTTTGTCCTGAACGAA
1 AATAGGTCTA-CATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAA
* * * * ** * *
1448799 TG-CCAAATGGGGTGCACGTATAAAGTGTCGATACATTTATTAAGAGCGTCGATCCAAAAAACAT
65 TGTCCAAA-AGGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACAT
* * * *
1448863 CGAAACCGAAAATTATAATGTAATAGGTAAATTTACAATGTAACCGATATAAATGTATC-AGTTT
129 CGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGA-TTT
1448927 TATGAGAA
193 TATGAGAA
* * *
1448935 AATAGATATACATAATATATCGACACT
1 AATAGGTCTACATAATGTATCGACACT
1448962 GTTTAAATTT
Statistics
Matches: 747, Mismatches: 68, Indels: 24
0.89 0.08 0.03
Matches are distributed among these distances:
198 2 0.00
199 190 0.25
200 365 0.49
201 190 0.25
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (200 bp):
AATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAAT
GTCCAAAAGGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCG
AAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTAT
GAGAA
Found at i:1450614 original size:20 final size:20
Alignment explanation
Indices: 1450589--1450638 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1450579 ACTACGAGAT
1450589 GAAATTTTGTTAATTTAGGG
1 GAAATTTTGTTAATTTAGGG
1450609 GAAATTTTGTTAATTTAGGG
1 GAAATTTTGTTAATTTAGGG
1450629 GAAATTTTGT
1 GAAATTTTGT
1450639 ATACGATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (20 bp):
GAAATTTTGTTAATTTAGGG
Found at i:1450655 original size:19 final size:19
Alignment explanation
Indices: 1450631--1450678 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1450621 ATTTAGGGGA
1450631 AATTTTGTATACGATTCAT
1 AATTTTGTATACGATTCAT
*
1450650 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTCAT
*
1450669 ATTTTTGTAT
1 AATTTTGTAT
1450679 GTGAATGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.54
Consensus pattern (19 bp):
AATTTTGTATACGATTCAT
Found at i:1453662 original size:199 final size:198
Alignment explanation
Indices: 1453306--1453829 Score: 716
Period size: 199 Copynumber: 2.6 Consensus size: 198
1453296 GTGTCGATAC
* *
1453306 ATTTGTGTCAATACTTATTGTCCAGAATGAATGCCCAAACGAA-GTGCACACATAAAGTGTCGAT
1 ATTTGTGTCGATACTT-TTGTCCAGAATGAATG-CCAAAC-AAGGTGCACGCATAAAGTGTCGAT
1453370 ACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATT
63 ACATTTATT-AAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATT
* * *
1453435 TACAATGCAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTC-AGCATAAAGTATCAACA
127 TACAATGCAACCGATATAAATATATCGGTTTTATAAGAAAATAGGTCTA-AATAAAGTATCAACA
1453499 CTTGTTAA
191 CTTGTTAA
* * * * * * *
1453507 ATTTGTGTCGATACATTTTGTCTATAATGAATGTCAAACAGGGTGCATGCATAGAGTGTCGATAT
1 ATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACAAGGTGCACGCATAAAGTGTCGATAC
* * *
1453572 ATTTATTGAAAGTATCAATCCCAAAAACATCGAAA-CGAAAATTATAATGTGATAGGTAAATTTA
65 ATTTATT-AAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTA
* * * *
1453636 CAATGTACCCGATATAAATATATCGGTTTTATAAGAAAATAGGTCTAAATAATGTATCGACACTT
129 CAATGCAACCGATATAAATATATCGGTTTTATAAGAAAATAGGTCTAAATAAAGTATCAACACTT
*
1453701 TTTAA
194 GTTAA
* * *
1453706 GTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACAAGGTGCACGCATAAAGTGTCGATACA
1 ATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACAAGGTGCACGCATAAAGTGTCGATACA
*
1453771 TTTA--AAAGTGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAA
66 TTTATTAAA--GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAA
1453830 ATTTGTAATG
Statistics
Matches: 282, Mismatches: 35, Indels: 15
0.85 0.11 0.05
Matches are distributed among these distances:
195 3 0.01
197 22 0.08
198 69 0.24
199 101 0.36
200 58 0.21
201 27 0.10
202 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (198 bp):
ATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACAAGGTGCACGCATAAAGTGTCGATACA
TTTATTAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACA
ATGCAACCGATATAAATATATCGGTTTTATAAGAAAATAGGTCTAAATAAAGTATCAACACTTGT
TAA
Found at i:1453928 original size:23 final size:23
Alignment explanation
Indices: 1453872--1453928 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1453862 TTACTTAGAA
*
1453872 AATATGTCAATATAAGCGCTACCT
1 AATATGT-TATATAAGCGCTACCT
* ** *
1453896 ATTACATTATATAAGCGTTACCT
1 AATATGTTATATAAGCGCTACCT
1453919 AATATGTTAT
1 AATATGTTAT
1453929 TGTACTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (23 bp):
AATATGTTATATAAGCGCTACCT
Found at i:1454015 original size:23 final size:23
Alignment explanation
Indices: 1453965--1454009 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1453955 TGTCTATTTT
* *
1453965 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
1453988 ATTATATAAACGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
1454010 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:1454027 original size:87 final size:87
Alignment explanation
Indices: 1453881--1454043 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
1453871 AAATATGTCA
* *
1453881 ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
1453946 CCGATTAAATGTCTATTTTATT
66 CCGATTAAATGTCTATTTTATT
1453968 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
* *
1454033 TCGGTTAAATG
66 CCGATTAAATG
1454044 ATATAAAATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGATTAAATGTCTATTTTATT
Found at i:1459680 original size:22 final size:23
Alignment explanation
Indices: 1459655--1459697 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1459645 AATAATTACT
*
1459655 AAAATAT-CATTTTTTTAAAAAA
1 AAAATATGAATTTTTTTAAAAAA
1459677 AAAATATGAATTTTTTTAAAA
1 AAAATATGAATTTTTTTAAAA
1459698 TTACGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAATATGAATTTTTTTAAAAAA
Found at i:1459728 original size:29 final size:29
Alignment explanation
Indices: 1459703--1459772 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1459693 TAAAATTACG
1459703 AAAATA-ATACCCTTTTCAAAATAATTATC
1 AAAATAGA-ACCCTTTTCAAAATAATTATC
* * *
1459732 AGAATAGAACCCTTTTCCAAATAATTAGC
1 AAAATAGAACCCTTTTCAAAATAATTATC
* *
1459761 AGAATAGCACCC
1 AAAATAGAACCC
1459773 AGTCAACGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.27
Consensus pattern (29 bp):
AAAATAGAACCCTTTTCAAAATAATTATC
Found at i:1459805 original size:18 final size:18
Alignment explanation
Indices: 1459782--1459820 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1459772 CAGTCAACGA
1459782 TCGGGTCAACGGGTCGGG
1 TCGGGTCAACGGGTCGGG
*
1459800 TCGGGTCAACGGGTTGGG
1 TCGGGTCAACGGGTCGGG
1459818 TCG
1 TCG
1459821 TAACCGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.49, T:0.21
Consensus pattern (18 bp):
TCGGGTCAACGGGTCGGG
Found at i:1466973 original size:29 final size:28
Alignment explanation
Indices: 1466940--1467075 Score: 88
Period size: 29 Copynumber: 5.0 Consensus size: 28
1466930 AAAAAATACC
1466940 AAAATATCACCATTTTCAAAATAATTACT
1 AAAATATCA-CATTTTCAAAATAATTACT
* * *
1466969 AAAATATCATTCTTTTTTAAAAAAATTACT
1 AAAATATCA--CATTTTCAAAATAATTACT
** *
1466999 -AAAT-T---ATTTT-TTAA-AATTACA
1 AAAATATCACATTTTCAAAATAATTACT
* *
1467020 AAAATAGCACATTTTCAAAATAATTACC
1 AAAATATCACATTTTCAAAATAATTACT
* * *
1467048 ATAATAACACCCTTTTCAAAATAATTAC
1 AAAATATCA-CATTTTCAAAATAATTAC
1467076 CAGAATAGCA
Statistics
Matches: 83, Mismatches: 15, Indels: 18
0.72 0.13 0.16
Matches are distributed among these distances:
21 6 0.07
22 6 0.07
23 4 0.05
26 5 0.06
27 2 0.02
28 14 0.17
29 30 0.36
30 16 0.19
ACGTcount: A:0.48, C:0.15, G:0.01, T:0.37
Consensus pattern (28 bp):
AAAATATCACATTTTCAAAATAATTACT
Found at i:1466998 original size:30 final size:29
Alignment explanation
Indices: 1466925--1467001 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
1466915 AATAGCATCA
* *
1466925 TTTAAAAAAAATACCAAAATATCACCATT
1 TTTAAAAAAATTACTAAAATATCACCATT
* * * *
1466954 TTCAAAATAATTACTAAAATATCATTCTTT
1 TTTAAAAAAATTACTAAAATATCA-CCATT
1466984 TTTAAAAAAATTACTAAA
1 TTTAAAAAAATTACTAAA
1467002 TTATTTTTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (29 bp):
TTTAAAAAAATTACTAAAATATCACCATT
Found at i:1467053 original size:28 final size:29
Alignment explanation
Indices: 1467013--1467116 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
1467003 TATTTTTTAA
* *
1467013 AATTACAAAAATAGCA-CATTTTCAAAAT
1 AATTACCAGAATAGCACCATTTTCAAAAT
* * *
1467041 AATTACCATAATAACACCCTTTTCAAAAT
1 AATTACCAGAATAGCACCATTTTCAAAAT
* *
1467070 AATTACCAGAATAGCACCCTTTTTC-AATT
1 AATTACCAGAATAGCA-CCATTTTCAAAAT
1467099 AATTACCAGAATAGCACC
1 AATTACCAGAATAGCACC
1467117 CGGTCAACGG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 15 0.23
29 44 0.67
30 7 0.11
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (29 bp):
AATTACCAGAATAGCACCATTTTCAAAAT
Found at i:1467076 original size:29 final size:30
Alignment explanation
Indices: 1467031--1467117 Score: 133
Period size: 29 Copynumber: 3.0 Consensus size: 30
1467021 AAATAGCACA
* *
1467031 TTTTCAAAATAATTACCATAATAACACCC-
1 TTTTCAAAATAATTACCAGAATAGCACCCT
1467060 TTTTCAAAATAATTACCAGAATAGCACCCT
1 TTTTCAAAATAATTACCAGAATAGCACCCT
*
1467090 TTTTC-AATTAATTACCAGAATAGCACCC
1 TTTTCAAAATAATTACCAGAATAGCACCC
1467118 GGTCAACGGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 49 0.91
30 5 0.09
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (30 bp):
TTTTCAAAATAATTACCAGAATAGCACCCT
Found at i:1468594 original size:17 final size:17
Alignment explanation
Indices: 1468572--1468610 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1468562 TGAATCAAAT
1468572 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1468589 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1468606 -AATTA
1 TAATTA
1468611 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1471717 original size:28 final size:27
Alignment explanation
Indices: 1471677--1471761 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 27
1471667 TTCCGTTTAT
**
1471677 ATTATACTATCGAGCTGGTGCTTGAAAG
1 ATTATACTATCGAGC-ACTGCTTGAAAG
*
1471705 ATTATACTATCGAGACACTGCTTGAGAG
1 ATTATACTATCGAG-CACTGCTTGAAAG
1471733 ATTATACTATCGAGCCACTGCTTGAAAG
1 ATTATACTATCGAG-CACTGCTTGAAAG
1471761 A
1 A
1471762 AACGACAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 50 0.98
29 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (27 bp):
ATTATACTATCGAGCACTGCTTGAAAG
Found at i:1471959 original size:60 final size:60
Alignment explanation
Indices: 1471882--1471994 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
1471872 GAACATATGA
* *
1471882 ATAGTCGGGTGACCATTTTGTAA-CTTTTAATAGTCG-GATGACTCAACAAAGCAACATTAT
1 ATAGTCGAGTGACCATTTTGTAATC-TTTAATAGTCGAG-GGACTCAACAAAGCAACATTAT
*
1471942 ATAGTCGAGTGATCATTTTGTAATCTTTAATAGTCGAGGGACTCAACAAAGCA
1 ATAGTCGAGTGACCATTTTGTAATCTTTAATAGTCGAGGGACTCAACAAAGCA
1471995 TCACCCCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
60 46 0.96
61 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (60 bp):
ATAGTCGAGTGACCATTTTGTAATCTTTAATAGTCGAGGGACTCAACAAAGCAACATTAT
Found at i:1476923 original size:16 final size:16
Alignment explanation
Indices: 1476896--1476941 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1476886 TTTCTCTATC
1476896 TTTTTTT-T-TTCTCT
1 TTTTTTTCTGTTCTCT
*
1476910 TTTTTTTCTGTTCTGT
1 TTTTTTTCTGTTCTCT
1476926 TTTTTTGTC-GTTCTCT
1 TTTTTT-TCTGTTCTCT
1476942 GCCGTCTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 7 0.26
15 1 0.04
16 17 0.63
17 2 0.07
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTTTTCTGTTCTCT
Found at i:1477412 original size:3 final size:3
Alignment explanation
Indices: 1477404--1477528 Score: 124
Period size: 3 Copynumber: 41.0 Consensus size: 3
1477394 TTATTTATTA
*
1477404 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * * * * * *
1477451 AAT AAT TAT TAT TAT TAT TAT TAT AAT AAT ACT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
1477499 ACT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1477529 TTTAAATAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
3 100 0.94
4 6 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:1477833 original size:60 final size:59
Alignment explanation
Indices: 1477740--1477854 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 59
1477730 TTTTGGAAAC
* *
1477740 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCAAAG
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCAAAG
1477800 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1477855 TCCCGAAGGC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
59 19 0.36
60 34 0.64
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (59 bp):
ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCAAAG
Found at i:1477926 original size:76 final size:76
Alignment explanation
Indices: 1477800--1478357 Score: 1071
Period size: 76 Copynumber: 7.3 Consensus size: 76
1477790 AAAAGCAAAG
1477800 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1477865 TTTTTGGAAAC
66 TTTTTGGAAAC
*
1477876 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1477941 TTTTTGGAAAC
66 TTTTTGGAAAC
1477952 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
1478017 TTTTTGGAAAT
66 TTTTTGGAAAC
*
1478028 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1478093 TTTTTGGAAAC
66 TTTTTGGAAAC
1478104 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1478169 TTTTTGGAAAC
66 TTTTTGGAAAC
*
1478180 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1478245 TTTTTGGAAAC
66 TTTTTGGAAAC
1478256 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1478321 TTTTTGGAAAC
66 TTTTTGGAAAC
*
1478332 ATCATGCACTGAAGGACTTATAGATG
1 ATCATGCACTGAAGGACTTACAGATG
1478358 TGAGAAATAG
Statistics
Matches: 473, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 473 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAAC
Found at i:1479057 original size:22 final size:22
Alignment explanation
Indices: 1479032--1479086 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1479022 CATAAAGCTT
1479032 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1479054 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1479076 TCATCTTTGAA
1 TCATCTTTGAA
1479087 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1483978 original size:17 final size:16
Alignment explanation
Indices: 1483937--1483980 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1483927 TTGATTTAAT
*
1483937 TTTTTTTTTG-TTTTG
1 TTTTTTTTTGCTTTTC
*
1483952 TTTTGTTTTGCTTTTC
1 TTTTTTTTTGCTTTTC
1483968 TTTTTTCTTTGCT
1 TTTTTT-TTTGCT
1483981 GGATGAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 9 0.38
16 9 0.38
17 6 0.25
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (16 bp):
TTTTTTTTTGCTTTTC
Found at i:1490813 original size:20 final size:19
Alignment explanation
Indices: 1490756--1490818 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 19
1490746 TTATCATTAT
1490756 TATTTTATTTAATAATAATAA
1 TATTTTA-TTAATAATAAT-A
*
1490777 TATATATATATATATAATAATA
1 TAT-TTTAT-TA-ATAATAATA
1490799 TATTTTAGTTAATAATAATA
1 TATTTTA-TTAATAATAATA
1490819 AATAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 9 0.25
21 9 0.25
22 10 0.28
23 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATTTTATTAATAATAATA
Found at i:1492671 original size:12 final size:12
Alignment explanation
Indices: 1492654--1492684 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1492644 AAACCCACAT
1492654 GTGAGTGCATGA
1 GTGAGTGCATGA
1492666 GTGAGTGCATGA
1 GTGAGTGCATGA
1492678 GTGAGTG
1 GTGAGTG
1492685 AGATGTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.06, G:0.45, T:0.26
Consensus pattern (12 bp):
GTGAGTGCATGA
Found at i:1494397 original size:60 final size:59
Alignment explanation
Indices: 1494324--1494439 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 59
1494314 TTATTATATA
* *
1494324 ATTATAAAATATTGATTTT-TTGAATT-CTTTA-ATTATTAAAAGTTATAAAATAATTTATCG
1 ATTATAAAATATTG-TTTTATTGAATTAC--TAGACTATTAAAAGTTACAAAAT-ATTTATCG
* *
1494384 ATTATATATTATTGTTTTATTGAATTACTAGACTATTAAAAGTTACAAAATATTTA
1 ATTATAAAATATTGTTTTATTGAATTACTAGACTATTAAAAGTTACAAAATATTTA
1494440 CTTAACTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
59 11 0.22
60 37 0.76
61 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (59 bp):
ATTATAAAATATTGTTTTATTGAATTACTAGACTATTAAAAGTTACAAAATATTTATCG
Found at i:1495085 original size:32 final size:32
Alignment explanation
Indices: 1495046--1495120 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
1495036 TAAATACAAT
*
1495046 AAAAATTTCTTATTAAATATTTAGCACTTTTG
1 AAAAATTTCTTATTAAATATTTAACACTTTTG
*
1495078 AAAAATTTCTTATTAAATATTTAATACTTTTG
1 AAAAATTTCTTATTAAATATTTAACACTTTTG
*
1495110 AAAAAATTCTT
1 AAAAATTTCTT
1495121 CCTCTTTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (32 bp):
AAAAATTTCTTATTAAATATTTAACACTTTTG
Found at i:1499429 original size:32 final size:32
Alignment explanation
Indices: 1499388--1499451 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1499378 TCCTTCTTTG
1499388 TCAACTCAAACATTACCCAACTTGTAACATGT
1 TCAACTCAAACATTACCCAACTTGTAACATGT
1499420 TCAACTCAAACATTACCCAACTTGTAACATGT
1 TCAACTCAAACATTACCCAACTTGTAACATGT
1499452 CTCTTTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (32 bp):
TCAACTCAAACATTACCCAACTTGTAACATGT
Found at i:1501681 original size:24 final size:24
Alignment explanation
Indices: 1501649--1501709 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
1501639 GAAAAGGTAT
1501649 AAAAAATAAATAAAT-ATAAATTAA
1 AAAAAAT-AATAAATAATAAATTAA
*
1501673 AAAAAATAATAAATAATGAATTAA
1 AAAAAATAATAAATAATAAATTAA
* *
1501697 AAATAGTAATAAA
1 AAAAAATAATAAA
1501710 GATAAAAGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (24 bp):
AAAAAATAATAAATAATAAATTAA
Found at i:1502468 original size:32 final size:32
Alignment explanation
Indices: 1502426--1502545 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 32
1502416 TTTACACTAA
1502426 AATA-CCTAAAACAAAGATAAAATATAAAAAT
1 AATATCCTAAAACAAAGATAAAATATAAAAAT
*
1502457 AATATCCTAAAACTTAATTAAAATACTAAA-ACCTAATTAAACT
1 AATATCCTAAAAC---A--AAGATA--AAATA--TAA--AAA-T
*
1502500 AAAATACCTAAAACAAAGATAAAATATAAAAAT
1 AATAT-CCTAAAACAAAGATAAAATATAAAAAT
1502533 AATATCCTAAAAC
1 AATATCCTAAAAC
1502546 TTAATTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 29
0.68 0.04 0.28
Matches are distributed among these distances:
31 4 0.06
32 16 0.23
33 5 0.07
34 3 0.04
35 1 0.01
36 3 0.04
37 8 0.11
38 2 0.03
39 8 0.11
40 3 0.04
41 1 0.01
42 3 0.04
43 5 0.07
44 8 0.11
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (32 bp):
AATATCCTAAAACAAAGATAAAATATAAAAAT
Found at i:1502501 original size:76 final size:76
Alignment explanation
Indices: 1502381--1502604 Score: 378
Period size: 76 Copynumber: 2.9 Consensus size: 76
1502371 AACAAGCTAA
* * * * *
1502381 AATATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTACACTAAAATACCTAAAACAAAGATA
1 AATATCCTAAAACTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATA
1502445 AAATATAAAAAT
65 AAATATAAAAAT
*
1502457 AATATCCTAAAACTTAATTAAAATACTAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAA
1 AATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA
1502522 AATATAAAAAT
66 AATATAAAAAT
1502533 AATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA
1 AATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA
1502598 AATATAA
66 AATATAA
1502605 TATTTAAAAT
Statistics
Matches: 140, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
75 5 0.04
76 135 0.96
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.26
Consensus pattern (76 bp):
AATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA
AATATAAAAAT
Found at i:1502511 original size:44 final size:44
Alignment explanation
Indices: 1502457--1502589 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 44
1502447 ATATAAAAAT
1502457 AATATCCTAAAACTTAATTAAAATACTAAAACCTAATTAAACTAA
1 AATA-CCTAAAACTTAATTAAAATACTAAAACCTAATTAAACTAA
*
1502502 AATACCTAAAAC---A--AAGATA--AAATA--TAA--AAA-TAA
1 AATACCTAAAACTTAATTAAAATACTAAA-ACCTAATTAAACTAA
* *
1502535 TAT-CCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
1 AATACCTAAAACTTAATTAAAATACTAAAACCTAATTAAACTAA
1502578 AATACCTAAAAC
1 AATACCTAAAAC
1502590 AAAGATAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 29
0.67 0.05 0.28
Matches are distributed among these distances:
32 8 0.12
33 5 0.07
34 3 0.04
35 1 0.01
36 3 0.04
37 8 0.12
38 2 0.03
39 8 0.12
40 2 0.03
41 1 0.01
42 3 0.04
43 5 0.07
44 16 0.23
45 4 0.06
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.26
Consensus pattern (44 bp):
AATACCTAAAACTTAATTAAAATACTAAAACCTAATTAAACTAA
Found at i:1504438 original size:24 final size:24
Alignment explanation
Indices: 1504405--1504463 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
1504395 TCAAATTAAT
* * *
1504405 TTTTTATGCACTGTTCTGTTCGAA
1 TTTTTCTGCACTGTTATGTTCAAA
1504429 TTTTTCTGCACTGTTATGTTCAAA
1 TTTTTCTGCACTGTTATGTTCAAA
*
1504453 CTTTTCTGCAC
1 TTTTTCTGCAC
1504464 ATTTCGAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (24 bp):
TTTTTCTGCACTGTTATGTTCAAA
Found at i:1504569 original size:5 final size:5
Alignment explanation
Indices: 1504560--1504609 Score: 73
Period size: 5 Copynumber: 9.8 Consensus size: 5
1504550 AGTTTGCTAA
* *
1504560 AAATA AAATA AAATG AAATG AAAATG AAATG AAATG AAATG AAATG AAAT
1 AAATG AAATG AAATG AAATG -AAATG AAATG AAATG AAATG AAATG AAAT
1504610 AGAACAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
5 38 0.88
6 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (5 bp):
AAATG
Found at i:1504583 original size:21 final size:21
Alignment explanation
Indices: 1504559--1504603 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1504549 AAGTTTGCTA
1504559 AAAATAAAATAAAATGAAATG
1 AAAATAAAATAAAATGAAATG
* *
1504580 AAAATGAAATGAAATGAAATG
1 AAAATAAAATAAAATGAAATG
1504601 AAA
1 AAA
1504604 TGAAATAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (21 bp):
AAAATAAAATAAAATGAAATG
Found at i:1507466 original size:21 final size:22
Alignment explanation
Indices: 1507426--1507467 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1507416 TGAAAAGGTA
* *
1507426 TAAAAAATAAATAATTATAAAT
1 TAAAAAAGAAATAATAATAAAT
1507448 TAAAAAAGAAA-AATAATAAA
1 TAAAAAAGAAATAATAATAAA
1507468 ATAATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAAAAGAAATAATAATAAAT
Found at i:1507571 original size:17 final size:17
Alignment explanation
Indices: 1507546--1507579 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1507536 AATGAGATAA
*
1507546 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
1507563 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
1507580 TGGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:1508268 original size:19 final size:19
Alignment explanation
Indices: 1508244--1508354 Score: 70
Period size: 19 Copynumber: 5.8 Consensus size: 19
1508234 AAATAATATC
*
1508244 CTAAAACTTAATTAAAATA
1 CTAAAACCTAATTAAAATA
*
1508263 CTAAAACCTAATTAAACTA
1 CTAAAACCTAATTAAAATA
* *
1508282 --AAATACCTAA-AACAAAGA
1 CTAAA-ACCTAATTA-AAATA
** *
1508300 -TAAAATATAA-AAATAATA
1 CTAAAACCTAATTAA-AATA
*
1508318 TCCTAAAACTTAATTAAAATA
1 --CTAAAACCTAATTAAAATA
1508339 CTAAAACCTAATTAAA
1 CTAAAACCTAATTAAA
1508355 CTAAAATACC
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
17 5 0.07
18 18 0.25
19 35 0.49
21 12 0.17
22 2 0.03
ACGTcount: A:0.59, C:0.14, G:0.01, T:0.26
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:1508463 original size:76 final size:76
Alignment explanation
Indices: 1508176--1508439 Score: 458
Period size: 76 Copynumber: 3.5 Consensus size: 76
1508166 TCTTAAATCC
* * * *
1508176 TAATTAAAACACTTAAAA-CTATTTAAACTAAAATATCTAAAACAAATATAAAATATAAAAATAA
1 TAATTAAAATAC-TAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
1508240 TATCCTAAAACT
65 TATCCTAAAACT
1508252 TAATTAAAATACTAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1508317 ATCCTAAAACT
66 ATCCTAAAACT
1508328 TAATTAAAATACTAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1508393 ATCCTAAAACT
66 ATCCTAAAACT
* *
1508404 TAATTAAAATACTAAAACATATTTAAACTAAAATAC
1 TAATTAAAATACTAAAACCTAATTAAACTAAAATAC
1508440 AAAGATAAAA
Statistics
Matches: 181, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
75 5 0.03
76 176 0.97
ACGTcount: A:0.60, C:0.12, G:0.01, T:0.27
Consensus pattern (76 bp):
TAATTAAAATACTAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
ATCCTAAAACT
Found at i:1517168 original size:21 final size:21
Alignment explanation
Indices: 1517142--1517194 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1517132 AGTATTAAAA
* *
1517142 TAAAAATATTATTAAAAATTT
1 TAAAAATATAATTAAAAATAT
* *
1517163 TAAAAATAAAATTAAAGATAT
1 TAAAAATATAATTAAAAATAT
1517184 TAAAAATATAA
1 TAAAAATATAA
1517195 AATGTTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAAATATAATTAAAAATAT
Found at i:1517213 original size:24 final size:25
Alignment explanation
Indices: 1517174--1517221 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
1517164 AAAAATAAAA
*
1517174 TTAAAGATATTAAAAATATAAAATG
1 TTAAAGATATTAAAAATACAAAATG
*
1517199 TTAAA-ATATTGAAAATACAAAAT
1 TTAAAGATATTAAAAATACAAAAT
1517222 AAAAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (25 bp):
TTAAAGATATTAAAAATACAAAATG
Found at i:1517506 original size:21 final size:20
Alignment explanation
Indices: 1517482--1517533 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1517472 ATACGTTAAT
* *
1517482 TATCACATCAGTATCGTAGAA
1 TATCACATCAATATAGTA-AA
*
1517503 TATCATATCAATATAGTAAA
1 TATCACATCAATATAGTAAA
1517523 TCATCACATCA
1 T-ATCACATCA
1517534 TCACAGTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (20 bp):
TATCACATCAATATAGTAAA
Found at i:1517779 original size:27 final size:27
Alignment explanation
Indices: 1517748--1517800 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1517738 TTTCTCCTAA
1517748 GTTATTTTTTATGATTATTCTATGTGG
1 GTTATTTTTTATGATTATTCTATGTGG
1517775 GTTATTTTTTATGATTATTCTATGTG
1 GTTATTTTTTATGATTATTCTATGTG
1517801 AGAATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.04, G:0.17, T:0.60
Consensus pattern (27 bp):
GTTATTTTTTATGATTATTCTATGTGG
Found at i:1519205 original size:20 final size:19
Alignment explanation
Indices: 1519136--1519249 Score: 68
Period size: 20 Copynumber: 5.7 Consensus size: 19
1519126 AACACAGAAG
*
1519136 TCAAATTCGCAA-TGCGATT
1 TCAAATTCGCAACT-CAATT
*
1519155 TCCACATTCGCAACACTCAATT
1 T-CAAATTCGC-A-ACTCAATT
*
1519177 TCAAATTCGTAACTCAATT
1 TCAAATTCGCAACTCAATT
* *
1519196 TCTGAATTCGCAACTCGATTT
1 TC-AAATTCGCAACTC-AATT
* * *
1519217 TCGAATTTGCAACACAAATT
1 TCAAATTCGCAACTC-AATT
* *
1519237 TTAATTTCGCAAC
1 TCAAATTCGCAAC
1519250 AGGTTTTATT
Statistics
Matches: 74, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.15
20 43 0.58
21 13 0.18
22 6 0.08
23 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (19 bp):
TCAAATTCGCAACTCAATT
Found at i:1519250 original size:20 final size:20
Alignment explanation
Indices: 1519220--1519273 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 20
1519210 TCGATTTTCG
1519220 AATTT-GCAACACAAATTTT
1 AATTTCGCAACACAAATTTT
**
1519239 AATTTCGC-A-ACAGGTTTT
1 AATTTCGCAACACAAATTTT
*
1519257 ATTTTCGCAACACAAAT
1 AATTTCGCAACACAAAT
1519274 ATTTTGGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
18 14 0.52
19 7 0.26
20 6 0.22
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (20 bp):
AATTTCGCAACACAAATTTT
Found at i:1524285 original size:21 final size:21
Alignment explanation
Indices: 1524260--1524311 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1524250 GTGAATCGGG
1524260 CTCTTGAACGGT-GTGAGGGAC
1 CTCTTGAACGGTAG-GAGGGAC
* *
1524281 CTCTTGAATGGTAGGAGGGGC
1 CTCTTGAACGGTAGGAGGGAC
1524302 CTCTTGAACG
1 CTCTTGAACG
1524312 ATGACAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTAGGAGGGAC
Found at i:1524753 original size:21 final size:21
Alignment explanation
Indices: 1524729--1524769 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1524719 GTCGTCATGT
*
1524729 AAAGTACCGACCTCATCACGC
1 AAAGCACCGACCTCATCACGC
*
1524750 AAAGCACTGACCTCATCACG
1 AAAGCACCGACCTCATCACG
1524770 TAACTCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.37, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAGCACCGACCTCATCACGC
Found at i:1526191 original size:16 final size:15
Alignment explanation
Indices: 1526172--1526209 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1526162 ATCTAATAAT
1526172 AATAAAAAAAATTCAA
1 AATAAAAAAAATT-AA
*
1526188 AATAAAAATAATTAA
1 AATAAAAAAAATTAA
1526203 AA-AAAAA
1 AATAAAAA
1526210 CTAACCCTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 4 0.19
16 12 0.57
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AATAAAAAAAATTAA
Found at i:1526312 original size:22 final size:22
Alignment explanation
Indices: 1526282--1526329 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1526272 GATGGAGATA
*
1526282 GACGGATTTCACCAGAGATGGG
1 GACGAATTTCACCAGAGATGGG
* *
1526304 GACGAATTTCGCCGGAGATGGG
1 GACGAATTTCACCAGAGATGGG
1526326 GACG
1 GACG
1526330 GATGTCGTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.40, T:0.17
Consensus pattern (22 bp):
GACGAATTTCACCAGAGATGGG
Found at i:1529295 original size:2 final size:2
Alignment explanation
Indices: 1529288--1529323 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1529278 TAAAATATTC
1529288 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1529324 TGTTTCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1533263 original size:29 final size:29
Alignment explanation
Indices: 1533231--1533291 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1533221 TGTTACCAAC
*
1533231 CGTCAATTGATTTTGATTATGACAGACCA
1 CGTCAATTAATTTTGATTATGACAGACCA
* *
1533260 CGTCAATTAATTTTGATTCTGACAGATCA
1 CGTCAATTAATTTTGATTATGACAGACCA
1533289 CGT
1 CGT
1533292 GTTGTCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (29 bp):
CGTCAATTAATTTTGATTATGACAGACCA
Found at i:1533405 original size:12 final size:12
Alignment explanation
Indices: 1533388--1533414 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1533378 AACAAAGCTA
1533388 ATCAAATAGACT
1 ATCAAATAGACT
1533400 ATCAAATAGACT
1 ATCAAATAGACT
1533412 ATC
1 ATC
1533415 TGTATCATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (12 bp):
ATCAAATAGACT
Found at i:1535139 original size:14 final size:14
Alignment explanation
Indices: 1535120--1535149 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1535110 ATCAAAGTCC
1535120 CTGACTTTGTGTCT
1 CTGACTTTGTGTCT
1535134 CTGACTTTGTGTCT
1 CTGACTTTGTGTCT
1535148 CT
1 CT
1535150 CTTGATCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (14 bp):
CTGACTTTGTGTCT
Found at i:1543937 original size:149 final size:150
Alignment explanation
Indices: 1543748--1544063 Score: 555
Period size: 150 Copynumber: 2.1 Consensus size: 150
1543738 GGGTAGAGGG
* * *
1543748 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAGGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
1543812 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1543877 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
1543897 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1543962 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1544027 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
1544047 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1544064 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 51 0.32
150 108 0.68
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:1550938 original size:150 final size:149
Alignment explanation
Indices: 1550668--1550983 Score: 533
Period size: 150 Copynumber: 2.1 Consensus size: 149
1550658 GGGTAGAGGG
* * *
1550668 TCTACGCGGTCCTTCGGGACATATGCATATTCTTTGGAACATGTGTGAGGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATACATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
1550733 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
*
1550798 TATGGCACTACGGTATAAT
131 TATGGCACTACGGTACAAT
* *
1550817 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATACATATTCTGTGGAACATGTGTGAAGTCTT-GAAAGACACA
1550882 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
*
1550947 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTACAAT
*
1550967 TCTACGCGGTACTTCGG
1 TCTACGCGGTCCTTCGG
1550984 TGCATTTATA
Statistics
Matches: 156, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
149 49 0.31
150 107 0.69
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATACATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTACAAT
Found at i:1555529 original size:30 final size:29
Alignment explanation
Indices: 1555483--1555541 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1555473 TAGTACATGG
*
1555483 GGAAGCCAACCGGAGCA-TCTGACGTCTTCA
1 GGAAACCAACCGGAGCACTC-GAC-TCTTCA
*
1555513 GGAAACCAATCGGAGCACTCGACTCTTCA
1 GGAAACCAACCGGAGCACTCGACTCTTCA
1555542 AGCTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.23
30 18 0.69
31 2 0.08
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.17
Consensus pattern (29 bp):
GGAAACCAACCGGAGCACTCGACTCTTCA
Found at i:1561443 original size:56 final size:56
Alignment explanation
Indices: 1561382--1561524 Score: 205
Period size: 58 Copynumber: 2.5 Consensus size: 56
1561372 TTTTATTAAG
* *
1561382 TAATTTATTTATTGAACATGATTAATTAAATTAATTATAATCATTACAACTTAAAA
1 TAATTTATTTATTGAATATGATTAATTAAATTAATTATAATCATTAAAACTTAAAA
* * *
1561438 TAATTTATTGGAATTGAATATGAATAATTAAATTAATTATAATCATTAAAAGTTAAAA
1 TAATTTATT--TATTGAATATGATTAATTAAATTAATTATAATCATTAAAACTTAAAA
* *
1561496 CAATTTATTTATTGAATATGATGAATTAA
1 TAATTTATTTATTGAATATGATTAATTAA
1561525 CTAATTAATT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
56 26 0.34
58 50 0.66
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (56 bp):
TAATTTATTTATTGAATATGATTAATTAAATTAATTATAATCATTAAAACTTAAAA
Found at i:1562863 original size:22 final size:23
Alignment explanation
Indices: 1562838--1562889 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1562828 CTGGTGGAAA
*
1562838 AAATAAAGAAAACAAAAT-AATT
1 AAATAAAGAAAACAAAATAAAAT
* * *
1562860 AAATTATGAAAACATAATAAAAT
1 AAATAAAGAAAACAAAATAAAAT
1562883 AAATAAA
1 AAATAAA
1562890 ATTGAATATG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (23 bp):
AAATAAAGAAAACAAAATAAAAT
Found at i:1563127 original size:40 final size:40
Alignment explanation
Indices: 1563083--1563352 Score: 129
Period size: 40 Copynumber: 6.8 Consensus size: 40
1563073 TCATTTTCCA
*
1563083 AAATCGCAACGCGAATATGAAAATCACAACGCG-AACACAT
1 AAATCGCAACGCGAATACGAAAATCACAACGCGTAAC-CAT
* * * * * *
1563123 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCACAACGCGTAACCAT
* ** * * * * *
1563163 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCACAACGCGTAACCAT
* * * * * * * *
1563203 ATATCGCAACGCGTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCACAACGCGTAACCAT
* * * * *
1563243 AAATCGCAACGAGAAT-CTGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGAATAC-GAAAATCACAACGCGTAA-CCAT
* * * * *
1563283 AAATCGCAACGAGAAT-CTGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGAATAC-GAAAATCACAACGCGTAA-CCAT
* *
1563323 AAATCGCAACGAGAAT-CTGTAAATCACAAC
1 AAATCGCAACGCGAATAC-GAAAATCACAAC
1563353 ACTGAAATTT
Statistics
Matches: 205, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 3 0.01
40 200 0.98
41 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGAATACGAAAATCACAACGCGTAACCAT
Found at i:1563145 original size:20 final size:20
Alignment explanation
Indices: 1563122--1563352 Score: 277
Period size: 20 Copynumber: 11.6 Consensus size: 20
1563112 CGCGAACACA
1563122 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
1563142 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
**
1563162 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
1563182 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1563202 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1563222 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* * *
1563242 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
1563262 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
1563282 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
1563302 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
1563322 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
1563342 TAAATCACAAC
1 TAAATCGCAAC
1563353 ACTGAAATTT
Statistics
Matches: 183, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
20 183 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:1563147 original size:60 final size:59
Alignment explanation
Indices: 1563083--1563352 Score: 263
Period size: 60 Copynumber: 4.5 Consensus size: 59
1563073 TCATTTTCCA
** * * *
1563083 AAATCGCAACGCGAATATGAAAATCACAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAACGCGTATCCGT
* *** *
1563143 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAACGCGTATCCGT
* * * * * * *
1563203 ATATCGCAACGCGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAACGCGTATCCGT
** * * *
1563263 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAACGCGT-ATCCGT
* * *
1563323 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGAATCCGTAAATCGCAAC
1563353 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.01
60 173 0.99
61 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (59 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAACGCGTATCCGT
Found at i:1564268 original size:12 final size:12
Alignment explanation
Indices: 1564251--1564275 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1564241 ATATAATCCT
1564251 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1564263 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1564275 G
1 G
1564276 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1566651 original size:19 final size:19
Alignment explanation
Indices: 1566611--1566708 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1566601 GATTCTCTCG
1566611 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1566631 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1566650 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1566664 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1566683 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1566702 TTGCGAT
1 TTGCGAT
1566709 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1566705 original size:52 final size:53
Alignment explanation
Indices: 1566592--1566708 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1566582 GAAATGAAAA
1566592 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1566645 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1566697 TCGCATTGCGAT
1 TCGCATTGCGAT
1566709 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1566804 original size:14 final size:14
Alignment explanation
Indices: 1566785--1566839 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1566775 CGGAAATGAA
1566785 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1566799 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1566818 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1566832 AATCGCAA
1 AATCGCAA
1566840 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1566819 original size:33 final size:33
Alignment explanation
Indices: 1566767--1566858 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
1566757 CCATTACATT
1566767 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
1566801 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1566834 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
1566859 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 49 0.84
34 9 0.16
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:1566858 original size:52 final size:52
Alignment explanation
Indices: 1566799--1566915 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
1566789 GCAACGAGAG
1566799 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
1566851 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
1566903 AATCGCATTGCGA
1 AATCGCAATGCGA
1566916 TTCTCCCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1566946 original size:19 final size:18
Alignment explanation
Indices: 1566922--1567019 Score: 132
Period size: 19 Copynumber: 5.5 Consensus size: 18
1566912 GCGATTCTCC
1566922 CATTGCGATTTCATTTCCG
1 CATTGCGATTTCATTT-CG
1566941 CATTGCGATTTCATTTCG
1 CATTGCGATTTCATTTCG
*
1566959 CATTGCGA-TTC-TCTCG
1 CATTGCGATTTCATTTCG
1566975 --TTGCGATTTTCATTTCG
1 CATTGCGA-TTTCATTTCG
1566992 CATTGCGATTTTCATTTCG
1 CATTGCGA-TTTCATTTCG
1567011 CATTGCGAT
1 CATTGCGAT
1567020 AGTCAATTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
18 11 0.15
19 41 0.57
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.44
Consensus pattern (18 bp):
CATTGCGATTTCATTTCG
Found at i:1566965 original size:51 final size:52
Alignment explanation
Indices: 1566905--1567019 Score: 189
Period size: 51 Copynumber: 2.2 Consensus size: 52
1566895 GAAATTAAAA
1566905 TCGCATTGCGATTCTCCCATTGCGA-TTTCATTTCCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTT-CGCATTGCGATTTTCATT
* *
1566956 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1567008 TCGCATTGCGAT
1 TCGCATTGCGAT
1567020 AGTCAATTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 33 0.55
52 27 0.45
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:1567153 original size:13 final size:14
Alignment explanation
Indices: 1567126--1567161 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1567116 CATCAATTAC
1567126 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1567140 ACAAATCATC-TTT
1 ACAAATCAACTTTT
1567153 ACAAATCAA
1 ACAAATCAA
1567162 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1569146 original size:14 final size:14
Alignment explanation
Indices: 1569129--1569185 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1569119 GCAAAATGAA
*
1569129 AATCGCAACGACAG
1 AATCGCAACGAAAG
1569143 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1569160 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1569176 AATCGCAACG
1 AATCGCAACG
1569186 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1569147 original size:33 final size:33
Alignment explanation
Indices: 1569110--1569202 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1569100 GCGAAACCAA
* *
1569110 AATCGCAACGCAAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1569143 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1569176 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1569203 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1569167 original size:19 final size:19
Alignment explanation
Indices: 1569073--1569207 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1569063 TAGTTTACTT
* *
1569073 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1569093 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
1569112 TCGCAACGCAAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1569131 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1569145 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1569164 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1569178 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1569197 TCGCAATGCGA
1 TCGCAACGCGA
1569208 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 10 0.11
19 46 0.48
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1569199 original size:52 final size:51
Alignment explanation
Indices: 1569073--1569207 Score: 130
Period size: 52 Copynumber: 2.6 Consensus size: 51
1569063 TAGTTTACTT
* * *
1569073 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCAAAA
1 TCGCAACACGAAA-TGAAAATCGCAATGCGAAACCAAAATCGCAACGAAAAA
* * * **
1569125 T-G-AAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGAAAGAA
1 TCGCAACA-CGAAATGA-A-AATCGCAATGCGAAACCAAAATCGCAACGAAA-AA
*
1569178 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAACACGAAATGAAAATCGCAATGCGA
1569208 TTTTGGTTTC
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
50 4 0.06
51 6 0.09
52 42 0.65
53 4 0.06
54 7 0.11
55 2 0.03
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (51 bp):
TCGCAACACGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAAAAA
Found at i:1569225 original size:19 final size:19
Alignment explanation
Indices: 1569203--1569331 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1569193 AAAATCGCAA
1569203 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1569222 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1569236 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1569255 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1569269 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1569288 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1569307 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1569327 TGCGA
1 TGCGA
1569332 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1569245 original size:33 final size:33
Alignment explanation
Indices: 1569203--1569294 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1569193 AAAATCGCAA
1569203 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1569236 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1569269 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1569295 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1569534 original size:93 final size:93
Alignment explanation
Indices: 1569375--1569948 Score: 1022
Period size: 93 Copynumber: 6.1 Consensus size: 93
1569365 TTGAATGGAT
1569375 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1569440 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1569468 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1569533 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1569561 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT
1 AAATTTACTTTCAA-C------C---A-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTT
1569626 AAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
55 AAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
*
1569665 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1569730 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1569758 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1569823 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1569851 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1569916 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1569944 AAATT
1 AAATT
1569949 ACTAAGCAAT
Statistics
Matches: 465, Mismatches: 5, Indels: 22
0.95 0.01 0.04
Matches are distributed among these distances:
93 370 0.80
94 2 0.00
97 1 0.00
100 1 0.00
103 2 0.00
104 89 0.19
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1569594 original size:11 final size:11
Alignment explanation
Indices: 1569578--1569608 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1569568 CTTTCAACCA
1569578 AAAGACAAAAC
1 AAAGACAAAAC
1569589 AAAGACAAAAC
1 AAAGACAAAAC
1569600 AAAGACAAA
1 AAAGACAAA
1569609 TACTATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAGACAAAAC
Found at i:1571672 original size:14 final size:14
Alignment explanation
Indices: 1571653--1571742 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1571643 TTGAAATGAA
1571653 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1571667 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1571684 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1571700 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1571719 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1571733 AATCGCAACG
1 AATCGCAACG
1571743 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1571690 original size:33 final size:33
Alignment explanation
Indices: 1571645--1571759 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1571635 TCTTTTGGTT
1571645 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1571678 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1571711 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1571744 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1571760 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1571691 original size:19 final size:18
Alignment explanation
Indices: 1571652--1571764 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1571642 GTTGAAATGA
1571652 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1571667 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1571684 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1571700 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1571717 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1571733 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1571750 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1571765 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1571795 original size:14 final size:14
Alignment explanation
Indices: 1571776--1571829 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1571766 TTTGGTTTCG
1571776 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1571790 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1571809 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1571823 CGTTGCG
1 CGTTGCG
1571830 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1571808 original size:33 final size:33
Alignment explanation
Indices: 1571760--1571840 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1571750 AAAATCGCAA
**
1571760 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1571793 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1571826 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
1571841 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.23, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1571863 original size:20 final size:21
Alignment explanation
Indices: 1571816--1571893 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
1571806 TCGCGTTGCG
**
1571816 ATTCTCTCGTTGCG-CTTTTC
1 ATTCTCTCGTTGCGACTAGTC
1571836 ATTTCTCTCGTTGCGAC-AGTC
1 A-TTCTCTCGTTGCGACTAGTC
*
1571857 ATTCTCTCGTTGCGA-T-TTC
1 ATTCTCTCGTTGCGACTAGTC
*
1571876 ATTTATCTCGTTGCGACT
1 A-TTCTCTCGTTGCGACT
1571894 CTTCTGCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.06
20 28 0.57
21 17 0.35
22 1 0.02
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (21 bp):
ATTCTCTCGTTGCGACTAGTC
Done.