Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008721.1 Hibiscus syriacus cultivar Beakdansim tig00111779_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: 2464137
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1469461 original size:25 final size:25
Alignment explanation
Indices: 1469428--1469507 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
1469418 AAGAGAATAG
1469428 AAAAAGAAAGAAAAAAG-AAAAAGAA
1 AAAAAGAAA-AAAAAAGCAAAAAGAA
*
1469453 AAAAAGAAAAGAAAAGCAAAAAGAA
1 AAAAAGAAAAAAAAAGCAAAAAGAA
* * * *
1469478 AAACA-AAGAAAATAGCAAAGAATAA
1 AAAAAGAAAAAAAAAGCAAA-AAGAA
1469503 AAAAA
1 AAAAA
1469508 TGACAAAGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 17 0.37
25 29 0.63
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.03
Consensus pattern (25 bp):
AAAAAGAAAAAAAAAGCAAAAAGAA
Found at i:1473536 original size:2 final size:2
Alignment explanation
Indices: 1473529--1473553 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1473519 TATCATTGGA
1473529 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 A
1473554 ATAATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1478684 original size:4 final size:4
Alignment explanation
Indices: 1478677--1479047 Score: 715
Period size: 4 Copynumber: 92.8 Consensus size: 4
1478667 TACATATGTT
1478677 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1478725 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1478773 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
1478821 CATA CATA CATA CATA CATA CATA CATG CATG CATG CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1478869 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1478917 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1478965 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1479013 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1479048 GATACATAAA
Statistics
Matches: 365, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 365 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:1479573 original size:153 final size:154
Alignment explanation
Indices: 1479334--1479654 Score: 387
Period size: 153 Copynumber: 2.1 Consensus size: 154
1479324 GTGTTTTTTT
* * * *
1479334 CTTGAAACAAAATTTTGTCTCGCTTGAGACATTTTTCCACAAATTTTGAGAATTTTAAAACAAAT
1 CTTGAAACAAAATTTTGTCTCGCTTGAGACATTTTCCCACAAATTTTGAGAATTTAAAAAAAAAA
* * * * *
1479399 TTTGTCTCGCTTGAGACAATTTATATCAAAGCAAATTTCGTCTCACTTGAGACATTTTTTCTCTA
66 ATTGTCTCACTTAAGACAATTTATATCAAAACAAACTTCGTCTCACTTGAGACATTTTTTCTCTA
1479464 AGATACAAATTTAAATTTATTGTA
131 AGATACAAATTTAAATTTATTGTA
* *
1479488 CTTGTAACAAAATTCTT-TCTCGCTTGAGACA-TTTCCCATAAATTTTGAGAATTTAAAAAAAAA
1 CTTGAAACAAAATT-TTGTCTCGCTTGAGACATTTTCCCACAAATTTTGAGAATTTAAAAAAAAA
* * * * ** *
1479551 AATTGTCTCATTTAAGACAATTTCTCTTAAAACAAACTTCGTCTTGCTTGAGACATTTTTTCCTT
65 AATTGTCTCACTTAAGACAATTTATATCAAAACAAACTTCGTCTCACTTGAGACATTTTTT-CTC
* * * *
1479616 TGATATACAAATTTCGAATTTGATT-CA
129 TAAGATACAAATTT-AAATTT-ATTGTA
1479643 CTTGAAACAAAA
1 CTTGAAACAAAA
1479655 ATTAATCTCA
Statistics
Matches: 140, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
153 77 0.55
154 41 0.29
155 19 0.14
156 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (154 bp):
CTTGAAACAAAATTTTGTCTCGCTTGAGACATTTTCCCACAAATTTTGAGAATTTAAAAAAAAAA
ATTGTCTCACTTAAGACAATTTATATCAAAACAAACTTCGTCTCACTTGAGACATTTTTTCTCTA
AGATACAAATTTAAATTTATTGTA
Found at i:1479709 original size:107 final size:106
Alignment explanation
Indices: 1479570--1479815 Score: 288
Period size: 107 Copynumber: 2.3 Consensus size: 106
1479560 ATTTAAGACA
* *
1479570 ATTTCTCTTAAAACAAACTTCGTCTTGCTTGAGACATTTTTTCCTTTGA-TATACAAATTTCGAA
1 ATTTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA-TTTTTCCTTTGAGAATACAAATTTCGAA
1479634 TTTGATTCAC-TTGAAACAAAAATTAATCTCACTTGAGATTGTT
65 TTTGATTCACATT-AAAC-AAAATTAATCTCACTTGAGATTGTT
* * * *
1479677 ATTTCT-TTCAAAACAAATTTCGTCTCGTTTGAGGCATTTTTCCTTTGAGAATGCAAATTTCGAA
1 ATTTCTCTT-AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGAATACAAATTTCGAA
* * * * *
1479741 TTTGTTTCACATTAAACAAAGTTGATCTCACTTGATATCG-T
65 TTTGATTCACATTAAACAAAATTAATCTCACTTGAGATTGTT
* **
1479782 -TTTCTC-AAAAACAAACTTTATCTCGCTTGAGACA
1 ATTTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1479816 ATTTCTCTAA
Statistics
Matches: 118, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
103 22 0.19
104 5 0.04
105 1 0.01
106 33 0.28
107 55 0.47
108 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (106 bp):
ATTTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGAATACAAATTTCGAAT
TTGATTCACATTAAACAAAATTAATCTCACTTGAGATTGTT
Found at i:1479828 original size:36 final size:35
Alignment explanation
Indices: 1479782--1479893 Score: 136
Period size: 36 Copynumber: 3.1 Consensus size: 35
1479772 TTGATATCGT
*
1479782 TTTCTC-AAAAACAAACTTTATCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAA-TTTGTCTCGCTTGAGACAA
* * *
1479817 TTTCTCTAAAAATAATTTTTGTCTCGTTTGAGACAA
1 TTTCTCTAAAAACAA-ATTTGTCTCGCTTGAGACAA
*
1479853 TTTCTCTAAAAACAAATGTTGTCTCACTTGAGACAAA
1 TTTCTCTAAAAACAAAT-TTGTCTCGCTTGAGAC-AA
1479890 TTTC
1 TTTC
1479894 CAAATTATGA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 7 0.11
36 52 0.80
37 6 0.09
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.38
Consensus pattern (35 bp):
TTTCTCTAAAAACAAATTTGTCTCGCTTGAGACAA
Found at i:1480240 original size:29 final size:27
Alignment explanation
Indices: 1480181--1480241 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
1480171 TGAGAAAGTT
* * *
1480181 TTTCGTAAAAAAAAATCTTTGAGTTTG
1 TTTCTTAAAAAAAAATCTTTGAGTCTA
1480208 TTTCTTAAAAAAAATCATCTTTGAGTCTA
1 TTTCTTAAAAAAAA--ATCTTTGAGTCTA
1480237 TTTCT
1 TTTCT
1480242 ATTAAAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 13 0.45
29 16 0.55
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (27 bp):
TTTCTTAAAAAAAAATCTTTGAGTCTA
Found at i:1480548 original size:30 final size:30
Alignment explanation
Indices: 1480514--1480573 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1480504 CCTTGAGACA
1480514 GTTTCT-CTAGAAATACAAA-ATCTTTGAGTT
1 GTTTCTCCT-GAAATA-AAACATCTTTGAGTT
1480544 GTTTCTCCTGAAATAAAACTATCTTTGAGT
1 GTTTCTCCTGAAATAAAAC-ATCTTTGAGT
1480574 CATTTCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 3 0.11
30 12 0.44
31 12 0.44
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (30 bp):
GTTTCTCCTGAAATAAAACATCTTTGAGTT
Found at i:1480988 original size:31 final size:33
Alignment explanation
Indices: 1480921--1480989 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 33
1480911 CCTTGAAATA
* * *
1480921 AAACAAACAAAATCTTTGAGTATGTTTTTCTTG
1 AAACAAACAAAATCTTTGAGTATGTCTCTCTCG
* *
1480954 AAACAAA-AACAT-TTTGAGTTTGTCTCTCTCG
1 AAACAAACAAAATCTTTGAGTATGTCTCTCTCG
1480985 AAACA
1 AAACA
1480990 CCGATCTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 20 0.65
32 4 0.13
33 7 0.23
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (33 bp):
AAACAAACAAAATCTTTGAGTATGTCTCTCTCG
Found at i:1481098 original size:172 final size:173
Alignment explanation
Indices: 1480898--1481244 Score: 597
Period size: 173 Copynumber: 2.0 Consensus size: 173
1480888 TTTACCATCT
* * *
1480898 TTGAGTTTGTTTCCCTTGAAATAAAAC-AAACAAAATCTTTGAGTATGTTTTTCTTGAAACAAAA
1 TTGAGTTTGTTTCCCATGAAACAAAACAAAAAAAAATCTTTGAGTATGTTTTTCTTGAAACAAAA
1480962 ACATTTTGAGTTTGTCTCTCTCGAAACACCGATCTTTGAGAACGTTTCCCTTAAACACAAATTTT
66 ACATTTTGAGTTTGTCTCTCTCGAAACACCGATCTTTGAGAACGTTTCCCTTAAACACAAATTTT
*
1481027 ATCTCGCTTGAGACAATTTCCTTTAAACGTCATCTTTGAGTTG
131 ATCTCGCTTGAGACAATTTCCTTTAAACATCATCTTTGAGTTG
1481070 TTGAGTTTGTTTCCCATGAAACAAAACAAAAAAAAATCTTTGAGTATGTTTTTCTTGAAACAAAA
1 TTGAGTTTGTTTCCCATGAAACAAAACAAAAAAAAATCTTTGAGTATGTTTTTCTTGAAACAAAA
* * *
1481135 ACATTTTGAGTTTGTTTCTCTCGAAACACCGATCTTTGAGAACGTTTCCTTTAAATACAAATTTT
66 ACATTTTGAGTTTGTCTCTCTCGAAACACCGATCTTTGAGAACGTTTCCCTTAAACACAAATTTT
* * *
1481200 GTCTCGCTTGAGACAGTTTCTTTTAAACATCATCTTTGAGTTG
131 ATCTCGCTTGAGACAATTTCCTTTAAACATCATCTTTGAGTTG
1481243 TT
1 TT
1481245 TCCCTTGAAA
Statistics
Matches: 164, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
172 25 0.15
173 139 0.85
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (173 bp):
TTGAGTTTGTTTCCCATGAAACAAAACAAAAAAAAATCTTTGAGTATGTTTTTCTTGAAACAAAA
ACATTTTGAGTTTGTCTCTCTCGAAACACCGATCTTTGAGAACGTTTCCCTTAAACACAAATTTT
ATCTCGCTTGAGACAATTTCCTTTAAACATCATCTTTGAGTTG
Found at i:1481143 original size:31 final size:32
Alignment explanation
Indices: 1481099--1481162 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
1481089 AACAAAACAA
* *
1481099 AAAAAAATCTTTGAGTATGTTTTTCTTGAAAC
1 AAAAAAATCTTTGAGTATGTTTCTCTCGAAAC
* *
1481131 AAAAACAT-TTTGAGTTTGTTTCTCTCGAAAC
1 AAAAAAATCTTTGAGTATGTTTCTCTCGAAAC
1481162 A
1 A
1481163 CCGATCTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (32 bp):
AAAAAAATCTTTGAGTATGTTTCTCTCGAAAC
Found at i:1481328 original size:67 final size:63
Alignment explanation
Indices: 1481207--1481329 Score: 147
Period size: 67 Copynumber: 1.9 Consensus size: 63
1481197 TTTGTCTCGC
* * * **
1481207 TTGAGACAGTTTCTTTTAAACATCATCTTTGAGTTGTTTCCCTTGAAATGAATTTTGTCGTTT
1 TTGAGACAGTTGCTTTTAAACATCACCTTTAAGTTGTTTCCCTTGAAACAAATTTTGTCGTTT
**
1481270 TTGAGACAGTTGCTTTTGAAACACATCACCTTTAAGTTTGTTTTTCTTGAAACAAATTTT
1 TTGAGACAGTTGCTTTT--AA-ACATCACCTTTAAG-TTGTTTCCCTTGAAACAAATTTT
1481330 TGAGTCTGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
63 16 0.33
65 2 0.04
66 12 0.24
67 19 0.39
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (63 bp):
TTGAGACAGTTGCTTTTAAACATCACCTTTAAGTTGTTTCCCTTGAAACAAATTTTGTCGTTT
Found at i:1481339 original size:28 final size:28
Alignment explanation
Indices: 1481299--1481378 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
1481289 AACACATCAC
* *
1481299 CTTTAAGTTTGTTTTTCTTGAAACAAAT
1 CTTTGAGTCTGTTTTTCTTGAAACAAAT
*
1481327 TTTTGAGTCTGTTTCTT-TTGAAACAAAT
1 CTTTGAGTCTGTTT-TTCTTGAAACAAAT
* **
1481355 CTTTGAGTCAGTTTCCCTTGAAAC
1 CTTTGAGTCTGTTTTTCTTGAAAC
1481379 CTTAATTCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 41 0.95
29 2 0.05
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (28 bp):
CTTTGAGTCTGTTTTTCTTGAAACAAAT
Found at i:1481584 original size:40 final size:39
Alignment explanation
Indices: 1481527--1481606 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
1481517 TTCCTAAAGA
*
1481527 TGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 TGACCAGAACTCTTCATCACGTAGGAGCCGTGTCA-CCCC
* * *
1481567 TGACCAGATCT-TCTCATCGCGTAGGAGTCGTGTCACCCC
1 TGACCAGAACTCT-TCATCACGTAGGAGCCGTGTCACCCC
1481606 T
1 T
1481607 AGATAACCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 6 0.17
40 29 0.83
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.26
Consensus pattern (39 bp):
TGACCAGAACTCTTCATCACGTAGGAGCCGTGTCACCCC
Found at i:1481699 original size:134 final size:134
Alignment explanation
Indices: 1481384--1481878 Score: 704
Period size: 134 Copynumber: 3.7 Consensus size: 134
1481374 GAAACCTTAA
* * *
1481384 TTCCTAAAGATAACCAGAACTCTTTATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTC
1 TTCCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCTC
** * * * *
1481449 ATTGCGTAGGAGCCGTGTCACCCCTAGATAACTAGTCGTCCTCA-CGTGCAGGAACCGAGTTATC
66 ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
1481513 ACCC
131 ACCC
*
1481517 TTCCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTTCTC
1 TTCCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCTC
* * * *
1481582 ATCGCGTAGGAGTCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTATC
66 ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
*
1481647 TCCC
131 ACCC
* * * * *
1481651 TTCCTAAAGATGGCCATAACTCTTCATCACGTATAAGCTGTGTCATCCCCTGACCATATCTCCTC
1 TTCCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCTC
* * *
1481716 ATCACGTAGGAGCTGTGTCAACCATAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
66 ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
1481781 ACCC
131 ACCC
* * * *
1481785 TTCCTAAAGATGGCCAAGAACTCTTCATCACATATGAGCAGTGTCATCCCCTGACCAGATCTCAT
1 TTCCTAAAGATGACC-AGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCT
* * *
1481850 CATCACGTAAGAGCCGAGTCACCCTTAGA
65 CATCACGTAGGAGCCGTGTCACCCCTAGA
1481879 CGACCAGATC
Statistics
Matches: 322, Mismatches: 38, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
133 100 0.31
134 155 0.48
135 67 0.21
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (134 bp):
TTCCTAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCTC
ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATC
ACCC
Found at i:1482097 original size:3 final size:3
Alignment explanation
Indices: 1482089--1482115 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1482079 ATTTATTTAT
1482089 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1482116 ATATATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1483607 original size:30 final size:29
Alignment explanation
Indices: 1483550--1483795 Score: 135
Period size: 30 Copynumber: 8.3 Consensus size: 29
1483540 CTATATTTTC
* * *
1483550 TATTTTAGCCACTTTAGTTTCT-ATTTTATT
1 TATTTTAGTC-CTTAAGTTTCTGTTTTTA-T
* *
1483580 TATTTTAGTCCTTAACTTTCTGTTTTTAC
1 TATTTTAGTCCTTAAGTTTCTGTTTTTAT
* **
1483609 TATTTATA-CCCTTTAAGTTTC-G-TTTTGC
1 TATTT-TAGTCC-TTAAGTTTCTGTTTTTAT
* * *
1483637 TGTTTTAG-CCATGTAAATTTCTGTTTTTGT
1 TATTTTAGTCC-T-TAAGTTTCTGTTTTTAT
* * * *
1483667 CATATTAGTCCTCTAGGTTTCTATTTTTAT
1 TATTTTAGTCCT-TAAGTTTCTGTTTTTAT
* * * *
1483697 TATTTTAGTCCCTAAGTTTTTATTTTTAC
1 TATTTTAGTCCTTAAGTTTCTGTTTTTAT
* * *
1483726 CATTTTAGTCCCTTTAGTTTCTTTTTTTAT
1 TATTTTAGT-CCTTAAGTTTCTGTTTTTAT
* * *
1483756 TATTTTAGTCCTTCAAATTTATGTTAATT-T
1 TATTTTAGTCCTT-AAGTTTCTGTT-TTTAT
1483786 TATTTTAGTC
1 TATTTTAGTC
1483796 TTGTAAATAT
Statistics
Matches: 167, Mismatches: 38, Indels: 22
0.74 0.17 0.10
Matches are distributed among these distances:
27 5 0.03
28 16 0.10
29 44 0.26
30 98 0.59
31 4 0.02
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.58
Consensus pattern (29 bp):
TATTTTAGTCCTTAAGTTTCTGTTTTTAT
Found at i:1483628 original size:59 final size:57
Alignment explanation
Indices: 1483545--1483793 Score: 186
Period size: 59 Copynumber: 4.2 Consensus size: 57
1483535 AATGTCTATA
*
1483545 TTTTCTATTTTAGCCACTTTAGTTTCTA-TTTTATTTATTTTAGTCCTTAACTTTCTGT
1 TTTTCTATTTTAGCC-CTTTAGTTTCTATTTTTA-TTATTTTAGTCCTTAAATTTCTGT
* ** *
1483603 TTTTACTATTTATA-CCCTTTAAGTTTC--GTTTTGCTGTTTTAG-CCATGTAAATTTCTGT
1 TTTT-CTATTT-TAGCCCTTT-AGTTTCTATTTTTATTATTTTAGTCC-T-TAAATTTCTGT
* * * * * * * *
1483661 TTTTGTCATATTAGTCCTCTAGGTTTCTATTTTTATTATTTTAGTCCCTAAGTTTTTAT
1 TTTTCT-ATTTTAGCCCTTTA-GTTTCTATTTTTATTATTTTAGTCCTTAAATTTCTGT
* * *
1483720 TTTTACCATTTTAGTCCCTTTAGTTTCTTTTTTTATTATTTTAGTCCTTCAAATTTATGT
1 TTTT-CTATTTTAG-CCCTTTAGTTTCTATTTTTATTATTTTAGTCCTT-AAATTTCTGT
1483780 TAATTT-TATTTTAG
1 T--TTTCTATTTTAG
1483794 TCTTGTAAAT
Statistics
Matches: 147, Mismatches: 27, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
56 2 0.01
57 12 0.08
58 38 0.26
59 57 0.39
60 33 0.22
61 2 0.01
62 3 0.02
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.58
Consensus pattern (57 bp):
TTTTCTATTTTAGCCCTTTAGTTTCTATTTTTATTATTTTAGTCCTTAAATTTCTGT
Found at i:1490697 original size:19 final size:19
Alignment explanation
Indices: 1490673--1490717 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1490663 CAAAGCGCCT
1490673 TGCATTTAGCAAGGAATCC
1 TGCATTTAGCAAGGAATCC
1490692 TGCATTTAGCAAGGAATCC
1 TGCATTTAGCAAGGAATCC
*
1490711 AGCATTT
1 TGCATTT
1490718 CATTCAAGGA
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:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (19 bp):
TGCATTTAGCAAGGAATCC
Found at i:1499287 original size:2 final size:2
Alignment explanation
Indices: 1499268--1499318 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
1499258 ATAAGATAAG
*
1499268 TA TA TCA TA TA AA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1499310 TA TA TA TA T
1 TA TA TA TA T
1499319 GTCATGTCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1503953 original size:9 final size:9
Alignment explanation
Indices: 1503939--1503971 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1503929 ACTATTCGAG
1503939 TCTTAATTT
1 TCTTAATTT
1503948 TCTTAATTT
1 TCTTAATTT
1503957 TC-TAATATT
1 TCTTAAT-TT
1503966 TCTTAA
1 TCTTAA
1503972 ATTAAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.18
9 15 0.68
10 3 0.14
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (9 bp):
TCTTAATTT
Found at i:1503992 original size:17 final size:17
Alignment explanation
Indices: 1503970--1504004 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1503960 AATATTTCTT
1503970 AAATTAAAGTTAAATTA
1 AAATTAAAGTTAAATTA
* *
1503987 AAATTATATTTAAATTA
1 AAATTAAAGTTAAATTA
1504004 A
1 A
1504005 TCGAATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AAATTAAAGTTAAATTA
Found at i:1506840 original size:21 final size:22
Alignment explanation
Indices: 1506816--1506859 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1506806 TATTATTATT
1506816 TTTAATATTAAAA-ATAATTTA
1 TTTAATATTAAAATATAATTTA
* *
1506837 TTTATTATTAAAATATATTTTA
1 TTTAATATTAAAATATAATTTA
1506859 T
1 T
1506860 AATTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAATATTAAAATATAATTTA
Found at i:1506874 original size:26 final size:26
Alignment explanation
Indices: 1506837--1506923 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
1506827 AAATAATTTA
* *
1506837 TTTATTATTAAAATATATTTTATAAT
1 TTTATTAATAAAATATATTATATAAT
* **
1506863 TTTATTAATAAAAATAAATTGGAT-AT
1 TTTATTAAT-AAAATATATTATATAAT
1506889 TTTATTGAAATAAAA-ATATTATA-AAT
1 TTTATT--AATAAAATATATTATATAAT
*
1506915 TATATTAAT
1 TTTATTAAT
1506924 TATTTATTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
24 3 0.06
26 28 0.57
27 15 0.31
28 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
TTTATTAATAAAATATATTATATAAT
Found at i:1507153 original size:13 final size:11
Alignment explanation
Indices: 1507126--1507188 Score: 54
Period size: 12 Copynumber: 5.3 Consensus size: 11
1507116 AATAAAAATA
1507126 TATTATATTAT
1 TATTATATTAT
1507137 TATTATAATTGAT
1 TATTAT-ATT-AT
*
1507150 TATTTTATTAT
1 TATTATATTAT
* *
1507161 AATATTAAAATAT
1 --TATTATATTAT
1507174 ATATTATATTAT
1 -TATTATATTAT
1507186 TAT
1 TAT
1507189 AAATATTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 11 0.26
12 16 0.38
13 15 0.36
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TATTATATTAT
Found at i:1507193 original size:29 final size:28
Alignment explanation
Indices: 1507126--1507207 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
1507116 AATAAAAATA
* * *
1507126 TATTATATTATTATTATAAT-TGATTATTT
1 TATTATAATATTAATA-AATAT-ATTATAT
1507155 TATTATAATATTAA-AATATATATTATAT
1 TATTATAATATTAATAA-ATATATTATAT
1507183 TATTATAAATATTAATAAATATATT
1 TATTAT-AATATTAATAAATATATT
1507208 TTAAATATCT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 1 0.02
28 15 0.33
29 28 0.61
30 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
TATTATAATATTAATAAATATATTATAT
Found at i:1507207 original size:21 final size:22
Alignment explanation
Indices: 1507162--1507215 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
1507152 TTTTATTATA
* *
1507162 ATATTA-AAATATATATTATAT
1 ATATTATAAATATATAATAAAT
1507183 -TATTATAAATAT-TAATAAAT
1 ATATTATAAATATATAATAAAT
*
1507203 ATATTTTAAATAT
1 ATATTATAAATAT
1507216 CTTAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTATAAATATATAATAAAT
Found at i:1507712 original size:87 final size:87
Alignment explanation
Indices: 1507566--1507728 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
1507556 TATGTTATAT
* * *
1507566 TATTTAACCGGAAATATTATCAAGTATAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAACAGAT
1507631 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
1507653 TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAACAGGT
1 TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAACAGAT
1507718 AGCGCTTATAT
66 AGCGCTTATAT
1507729 TGACATGTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAACAGAT
AGCGCTTATATAATAAAATAGG
Found at i:1508615 original size:23 final size:23
Alignment explanation
Indices: 1508579--1508650 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
1508569 ATACTTTACA
1508579 ATATAA-CGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
1508601 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1508624 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
1508647 ATAT
1 ATAT
1508651 TTTTATCTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 6 0.12
23 42 0.88
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1512233 original size:19 final size:19
Alignment explanation
Indices: 1512209--1512257 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1512199 TTACATTCAC
1512209 ATACAAAATTATAAATCG-T
1 ATACAAAATTATAAAT-GTT
1512228 ATACAAAATTATAAATGTT
1 ATACAAAATTATAAATGTT
1512247 ATACAAAATTA
1 ATACAAAATTA
1512258 ACCCTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATGTT
Found at i:1514085 original size:33 final size:33
Alignment explanation
Indices: 1514048--1514113 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1514038 CATCTTAAGA
*
1514048 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
1514081 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
1514114 CCATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:1514172 original size:21 final size:21
Alignment explanation
Indices: 1514147--1514211 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1514137 CCCCTTATGC
* *
1514147 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1514168 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1514189 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1514210 CT
1 CT
1514212 TGATTATCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1516519 original size:20 final size:19
Alignment explanation
Indices: 1516464--1516510 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1516454 TCCGGTAGCG
1516464 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1516483 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1516504 TTTTACC
1 TTTTACC
1516511 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1516691 original size:20 final size:19
Alignment explanation
Indices: 1516645--1516691 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1516635 TCCGGTAGCG
1516645 TTTTACCGGTTTCATCATT
1 TTTTACCGGTTTCATCATT
* *
1516664 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTCATCAT-T
1516685 TTTTACC
1 TTTTACC
1516692 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTTACCGGTTTCATCATT
Found at i:1516735 original size:181 final size:182
Alignment explanation
Indices: 1516431--1516903 Score: 822
Period size: 181 Copynumber: 2.6 Consensus size: 182
1516421 CGTAGTTACG
1516431 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1516496 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
* *
1516561 AGGCACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGACACTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* *
1516612 AAAGTATCGATACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1516677 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
* *
1516742 AGACGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATT
131 AGACACTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * * * *
1516794 AAAGTACCGACACTTTAAATATATCCGGTACCGCTTTACCGGTTTTATCATTTTAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1516859 TATCATAGTTTTACCTTTTATATCGTTGTGGATCGATACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
1516904 AATTTGAATC
Statistics
Matches: 276, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
181 174 0.63
182 102 0.37
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
AGACACTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
Found at i:1516873 original size:20 final size:18
Alignment explanation
Indices: 1516828--1516864 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1516818 CCGGTACCGC
1516828 TTTACCGGTTTTATCATT
1 TTTACCGGTTTTATCATT
1516846 TTAATACCGGTTTTATCAT
1 TT--TACCGGTTTTATCAT
1516865 AGTTTTACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
20 15 0.88
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTACCGGTTTTATCATT
Found at i:1517827 original size:27 final size:27
Alignment explanation
Indices: 1517761--1517827 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
1517751 ATCGAGTCAG
* * * *
1517761 TTTCGGGTCGGGTGGATGGTATATATT
1 TTTCGGGTCGGGTGAATGATATAAAAT
* * *
1517788 TTTCGGATTGGGTGAATGATGTAAAAT
1 TTTCGGGTCGGGTGAATGATATAAAAT
1517815 TTTCGGGTCGGGT
1 TTTCGGGTCGGGT
1517828 TACATAACCA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.18, C:0.07, G:0.36, T:0.39
Consensus pattern (27 bp):
TTTCGGGTCGGGTGAATGATATAAAAT
Found at i:1518545 original size:3 final size:3
Alignment explanation
Indices: 1518539--1518571 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1518529 AGTAAAAAAA
1518539 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1518572 AGTCAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1518771 original size:18 final size:18
Alignment explanation
Indices: 1518730--1518764 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1518720 CTGTTTTCTA
*
1518730 TTTTTGCTTTTGCTTTTG
1 TTTTTACTTTTGCTTTTG
*
1518748 TTTTTACTTTTTCTTTT
1 TTTTTACTTTTGCTTTT
1518765 TATTTTATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.11, G:0.09, T:0.77
Consensus pattern (18 bp):
TTTTTACTTTTGCTTTTG
Found at i:1519942 original size:3 final size:3
Alignment explanation
Indices: 1519934--1519963 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1519924 GGGAATTGGG
1519934 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1519964 AACTTAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:1522784 original size:12 final size:10
Alignment explanation
Indices: 1522749--1522780 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
1522739 ATGGTTGAAA
1522749 ATAAAAATTT
1 ATAAAAATTT
1522759 ATAAAAATTT
1 ATAAAAATTT
1522769 ATATAAAATTT
1 ATA-AAAATTT
1522780 A
1 A
1522781 ATATGTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:1532838 original size:36 final size:36
Alignment explanation
Indices: 1532797--1532876 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
1532787 ACCCGTGACC
* *
1532797 CGACCCGATGAAATTAAGGTTTCACCTGACCCGACA
1 CGACCCGACGAAATTAAGGTTTCACCTAACCCGACA
1532833 CGACCCGACGAAATTAAGGTTTCACCTAACCCGACA
1 CGACCCGACGAAATTAAGGTTTCACCTAACCCGACA
1532869 CGACCCGA
1 CGACCCGA
1532877 ATATATGACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.31, C:0.34, G:0.19, T:0.16
Consensus pattern (36 bp):
CGACCCGACGAAATTAAGGTTTCACCTAACCCGACA
Found at i:1545219 original size:16 final size:16
Alignment explanation
Indices: 1545198--1545254 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
1545188 ATAAATGAAA
1545198 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
*
1545214 ATAAACGAACACGAAC
1 ATAAACGAACACAAAC
* * *
1545230 ATAAATGAATACAACC
1 ATAAACGAACACAAAC
1545246 ATAAACGAA
1 ATAAACGAA
1545255 TATAAACGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.11
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:1552211 original size:100 final size:100
Alignment explanation
Indices: 1552058--1552319 Score: 456
Period size: 100 Copynumber: 2.6 Consensus size: 100
1552048 ACGTACACAA
*
1552058 ATTCACTTCTAA-AAAA-TTAAGTTCAATCCTCATATTTAACTTCAAACTCAAGTATGTATACTT
1 ATTCACTTCTAATAAAATTTAAGTTCAATTCTCATATTTAACTTCAAACTCAAGTATGTATACTT
*
1552121 AAAATTAGACTCAACTCGACTATACTTGTTTAGAC
66 AAAATTAGACTCAACTCGACTAAACTTGTTTAGAC
1552156 ATTCACTTCTAATAAAATTTAAGTTCAATTCTCATATTTAACTTCAAACTCAAGTATGTATACTT
1 ATTCACTTCTAATAAAATTTAAGTTCAATTCTCATATTTAACTTCAAACTCAAGTATGTATACTT
* *
1552221 AAAATTCGACTCGACTCGACTAAACTTGTTTAGAC
66 AAAATTAGACTCAACTCGACTAAACTTGTTTAGAC
* *
1552256 GTTCACTTCTAATAAAATTTAAGTTCAATTCTCATATTTAACTTCAAACTCAAGTAAGTATACT
1 ATTCACTTCTAATAAAATTTAAGTTCAATTCTCATATTTAACTTCAAACTCAAGTATGTATACT
1552320 CGAGTTTGAG
Statistics
Matches: 156, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
98 12 0.08
99 4 0.03
100 140 0.90
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (100 bp):
ATTCACTTCTAATAAAATTTAAGTTCAATTCTCATATTTAACTTCAAACTCAAGTATGTATACTT
AAAATTAGACTCAACTCGACTAAACTTGTTTAGAC
Found at i:1553297 original size:39 final size:39
Alignment explanation
Indices: 1553243--1553321 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1553233 GAATACTACC
1553243 CCCATATCATGAGAACAAACCCGAATGAACCGAACACAT
1 CCCATATCATGAGAACAAACCCGAATGAACCGAACACAT
1553282 CCCATATCATGAGAACAAACCCGAATGAACCGAACACAT
1 CCCATATCATGAGAACAAACCCGAATGAACCGAACACAT
1553321 C
1 C
1553322 GAGAAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.43, C:0.32, G:0.13, T:0.13
Consensus pattern (39 bp):
CCCATATCATGAGAACAAACCCGAATGAACCGAACACAT
Found at i:1556343 original size:18 final size:18
Alignment explanation
Indices: 1556320--1556365 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1556310 AACATTCACA
1556320 GTAATCTTATTCCCACCG
1 GTAATCTTATTCCCACCG
** *
1556338 GTAATCCCATTCCCACTG
1 GTAATCTTATTCCCACCG
*
1556356 ATAATCTTAT
1 GTAATCTTAT
1556366 ATTCCGTGAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.35
Consensus pattern (18 bp):
GTAATCTTATTCCCACCG
Found at i:1557668 original size:19 final size:19
Alignment explanation
Indices: 1557644--1557685 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1557634 TTAACTAAAC
1557644 AAACAAACA-AAATTAAATA
1 AAACAAA-AGAAATTAAATA
*
1557663 AAACAAAAGCAATTAAATA
1 AAACAAAAGAAATTAAATA
1557682 AAAC
1 AAAC
1557686 TTAGGCTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.14
Consensus pattern (19 bp):
AAACAAAAGAAATTAAATA
Found at i:1562842 original size:18 final size:18
Alignment explanation
Indices: 1562815--1562849 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1562805 TTCGAAGGGA
*
1562815 TTGAAATAAATGATAAGT
1 TTGAAATAAATAATAAGT
*
1562833 TTGAATTAAATAATAAG
1 TTGAAATAAATAATAAG
1562850 ACCCGACGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (18 bp):
TTGAAATAAATAATAAGT
Found at i:1564399 original size:31 final size:32
Alignment explanation
Indices: 1564364--1564431 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
1564354 TAGGCTTTGA
* *
1564364 GGCCCTGAGAT-CATTCTCAGGTAGGCCCTGT
1 GGCCCTAAGATGCATTCTCAGGTAGGCCCCGT
** *
1564395 GGCCCTAAGATGTGTTCTTAGGTAGGCCCCGT
1 GGCCCTAAGATGCATTCTCAGGTAGGCCCCGT
1564427 GGCCC
1 GGCCC
1564432 CGAACTTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.15, C:0.29, G:0.31, T:0.25
Consensus pattern (32 bp):
GGCCCTAAGATGCATTCTCAGGTAGGCCCCGT
Found at i:1570604 original size:23 final size:23
Alignment explanation
Indices: 1570574--1570647 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
1570564 TCCAGTCACT
1570574 GAGTTAACTCGTTGACTTTGACC
1 GAGTTAACTCGTTGACTTTGACC
* * *
1570597 GAGTTAACCCATTGATCGTTGACC
1 GAGTTAACTCGTTGA-CTTTGACC
* *
1570621 -AGTCTGA-TCGTTGATTTTGACC
1 GAGT-TAACTCGTTGACTTTGACC
1570643 G-GTTA
1 GAGTTA
1570648 GACAATTGAT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
21 1 0.03
22 8 0.21
23 21 0.54
24 9 0.23
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (23 bp):
GAGTTAACTCGTTGACTTTGACC
Found at i:1574724 original size:19 final size:19
Alignment explanation
Indices: 1574684--1574726 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1574674 ATCTCACATG
** *
1574684 AAATTTATAAATCTTCATA
1 AAATTTATAAATCTAAAAA
1574703 AAATTTATAAATCTAAAAA
1 AAATTTATAAATCTAAAAA
1574722 AAATT
1 AAATT
1574727 ACTTGATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTTATAAATCTAAAAA
Found at i:1580222 original size:19 final size:20
Alignment explanation
Indices: 1580198--1580247 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
1580188 CTTTTATCAT
1580198 TTTATTTTA-ATCTCTCTTC
1 TTTATTTTATATCTCTCTTC
*
1580217 TTTATTTTCTATTTTCTCTCTTC
1 TTTA-TTT-TA-TATCTCTCTTC
1580240 TTTATTTT
1 TTTATTTT
1580248 TGGACGGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 4 0.15
20 3 0.12
21 3 0.12
22 3 0.12
23 13 0.50
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATTTTATATCTCTCTTC
Found at i:1581632 original size:13 final size:13
Alignment explanation
Indices: 1581614--1581638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1581604 ACCCGACCAA
1581614 GGACTATCAGGAG
1 GGACTATCAGGAG
1581627 GGACTATCAGGA
1 GGACTATCAGGA
1581639 CCATCAACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (13 bp):
GGACTATCAGGAG
Found at i:1584980 original size:65 final size:64
Alignment explanation
Indices: 1584887--1585016 Score: 199
Period size: 65 Copynumber: 2.0 Consensus size: 64
1584877 AATAACTAGA
* * *
1584887 TTCTTCTATAGATAATTCTGGACATAATATTAAATATTAAAAATAT-CATCTAACAAATATTTTT
1 TTCTTCTATAGATAATTCTAGACATAATATTAAATA-TAAAAAAATCCACCTAA-AAATATTTTT
1584951 T
64 T
*
1584952 TTCTTCTATAGATAATTCTAGATATAATATTAAATATAAAAAAATCCACCTAAAAATATTTTTT
1 TTCTTCTATAGATAATTCTAGACATAATATTAAATATAAAAAAATCCACCTAAAAATATTTTTT
1585016 T
1 T
1585017 CAAAGTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
64 20 0.33
65 40 0.67
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (64 bp):
TTCTTCTATAGATAATTCTAGACATAATATTAAATATAAAAAAATCCACCTAAAAATATTTTTT
Found at i:1587277 original size:21 final size:21
Alignment explanation
Indices: 1587251--1587303 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1587241 GTTTCCAGAT
1587251 TCGCAACGCGAACATCAACTA
1 TCGCAACGCGAACATCAACTA
* *
1587272 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCAACTA
*
1587293 TCGCAATGCGA
1 TCGCAACGCGA
1587304 TTTTCCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCAACTA
Found at i:1587341 original size:21 final size:21
Alignment explanation
Indices: 1587315--1587566 Score: 227
Period size: 21 Copynumber: 12.1 Consensus size: 21
1587305 TTTCCAAATT
1587315 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1587336 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
1587357 CGTTGCGATAGTCCAAATTCG
1 CGTTGCGATAGTCCAAGTTCG
1587378 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
1587397 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1587418 CGTTGCGATAGTCGAAGTTCA
1 CGTTGCGATAGTCCAAGTTCG
* *
1587439 CGTTGTGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
1587460 CGTTACGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1587481 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
1587502 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1587523 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
1587544 CGTTGCGATAGTCGAAGTCCG
1 CGTTGCGATAGTCCAAGTTCG
1587565 CG
1 CG
1587567 ATTTATTCCA
Statistics
Matches: 190, Mismatches: 23, Indels: 36
0.76 0.09 0.14
Matches are distributed among these distances:
19 54 0.28
21 100 0.53
23 36 0.19
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:1587470 original size:42 final size:42
Alignment explanation
Indices: 1587378--1587593 Score: 279
Period size: 42 Copynumber: 5.3 Consensus size: 42
1587368 TCCAAATTCG
* * *
1587378 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
* *
1587416 CGCGTTGCGATAGTCGAAGTTCACGTTGTGATTTATTCCAAGTT
1 --CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
*
1587460 CGTTACGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1587502 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
*
1587544 CGTTGCGATAGTCGAAG-TC-C---GCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
*
1587581 CATTGCGATAGTC
1 CGTTGCGATAGTC
1587594 CAAAATCGCA
Statistics
Matches: 162, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
37 28 0.17
40 19 0.12
41 2 0.01
42 104 0.64
44 9 0.06
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
Found at i:1587697 original size:6 final size:6
Alignment explanation
Indices: 1587686--1587722 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1587676 GACACGTATT
1587686 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1587723 TCCGAGACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1588503 original size:21 final size:21
Alignment explanation
Indices: 1588479--1588592 Score: 92
Period size: 21 Copynumber: 5.4 Consensus size: 21
1588469 ATTTTGAACT
1588479 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
1588500 ATCGCAACACGAACTTAGACT--
1 ATCGC-A-ACGAATTTGGAATAA
*
1588521 ATCGCAACGAATTTGTAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
1588542 ATCGCAACGCAAACTTAGACT--
1 ATCGCAACG--AATTTGGAATAA
*
1588563 ATCGCAACAAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
1588584 ATCGCAACG
1 ATCGCAACG
1588593 CGATAGTCGA
Statistics
Matches: 69, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
19 16 0.23
20 1 0.01
21 35 0.51
22 1 0.01
23 16 0.23
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:1588592 original size:42 final size:42
Alignment explanation
Indices: 1588476--1588593 Score: 200
Period size: 42 Copynumber: 2.8 Consensus size: 42
1588466 GCGATTTTGA
* *
1588476 ACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTAG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTAG
*
1588518 ACTATCGCAACGAATTTGTAATAAATCGCAACGCAAACTTAG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTAG
*
1588560 ACTATCGCAACAAATTTGGAATAAATCGCAACGC
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGC
1588594 GATAGTCGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (42 bp):
ACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTAG
Found at i:1593070 original size:19 final size:20
Alignment explanation
Indices: 1593043--1593128 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 20
1593033 CATAAAACCA
*
1593043 ATCACTTCATATAATTAAAC
1 ATCAGTTCATATAATTAAAC
1593063 A-CAGTTCATATAATT-AAC
1 ATCAGTTCATATAATTAAAC
** *
1593081 ATTCA-TTCAGCTAATAAAACC
1 A-TCAGTTCATATAATTAAA-C
*
1593102 AATCACTTCATATAATTAAAC
1 -ATCAGTTCATATAATTAAAC
1593123 A-CAGTT
1 ATCAGTT
1593129 TAGTAGACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.08
19 25 0.48
20 6 0.12
21 5 0.10
22 12 0.23
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (20 bp):
ATCAGTTCATATAATTAAAC
Found at i:1600466 original size:30 final size:30
Alignment explanation
Indices: 1600432--1600497 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
1600422 ATAATTATTT
*
1600432 TAATCGGTAT-TTTTTTCAA-ATATTACAAAA
1 TAATCAGTATATTTTTT-AACAT-TTACAAAA
*
1600462 TAATCATTATATTTTTTAAGCATTTACAAAA
1 TAATCAGTATATTTTTTAA-CATTTACAAAA
1600493 TAATC
1 TAATC
1600498 TTCATTCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 10 0.32
31 19 0.61
32 2 0.06
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.44
Consensus pattern (30 bp):
TAATCAGTATATTTTTTAACATTTACAAAA
Found at i:1604404 original size:18 final size:18
Alignment explanation
Indices: 1604381--1604419 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1604371 ACCATAAACA
*
1604381 GAATAAA-TGAAATCAAAT
1 GAATAAAGTG-AATAAAAT
1604399 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
1604417 GAA
1 GAA
1604420 AAGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.21
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:1604567 original size:33 final size:31
Alignment explanation
Indices: 1604524--1604591 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
1604514 ACTATATACC
1604524 ATATAGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
1604556 ATATGAGTTTTCCAAAATATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATATTTTTAAAAATAT
1604588 ATAT
1 ATAT
1604592 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:1604681 original size:35 final size:34
Alignment explanation
Indices: 1604637--1604716 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 34
1604627 TATACATTAT
*
1604637 ATTTTCAAAATGATTTCAAAAATATATGTTATATA
1 ATTTTCAAAATGATTTCAAAAAT-TATATTATATA
* * * *
1604672 ATTTTCAAAATGTTTTTAAAACTTATATTGTATA
1 ATTTTCAAAATGATTTCAAAAATTATATTATATA
1604706 AGTTTTCAAAA
1 A-TTTTCAAAA
1604717 AACGTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 10 0.26
35 29 0.74
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (34 bp):
ATTTTCAAAATGATTTCAAAAATTATATTATATA
Found at i:1604724 original size:108 final size:109
Alignment explanation
Indices: 1604525--1604725 Score: 261
Period size: 108 Copynumber: 1.9 Consensus size: 109
1604515 CTATATACCA
* *
1604525 TATAGTTTTCAAAAATGATTTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAACTATAT
1 TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATATTTTTAAAACTATAT
*
1604590 ATTATATAAAATTTTCAAAAATGTTTTTATTTTAAACTATACAT
66 ATTATATAAAATTTTCAAAAACGTTTTTATTTTAAACTATACAT
*
1604634 TATA-TTTTC-AAAATGATTTCAAAAATATATGTTATAT-AATTTT-CAAAATGTTTTTAAAACT
1 TATAGTTTTCAAAAATGATTT-AAAAA-ATA--TTATATGAATTTTCCAAAATATTTTTAAAACT
* *
1604695 -TATATTGTAT-AAGTTTTCAAAAAACGTTTTT
62 ATATATTATATAAAATTTTC-AAAAACGTTTTT
1604726 TAAAAAAACT
Statistics
Matches: 81, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
107 17 0.21
108 29 0.36
109 24 0.30
110 5 0.06
111 6 0.07
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (109 bp):
TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATATTTTTAAAACTATAT
ATTATATAAAATTTTCAAAAACGTTTTTATTTTAAACTATACAT
Found at i:1604735 original size:108 final size:109
Alignment explanation
Indices: 1604511--1604753 Score: 250
Period size: 108 Copynumber: 2.2 Consensus size: 109
1604501 AAATGTTTTC
* * *
1604511 AAAACTATATACCATATA-GTTTTCAAAAATGATTTTAAAAATATTATATGAGTTTTCCAAAATA
1 AAAACTATAT--CATATATATTTTC-AAAATGATTTAAAAAATATTATATGAATTTTCCAAAATA
* **
1604575 TTTTTAAAACTATATATTATATAAAATTTTCAAAAATGTTTTTATTT
63 TTTTTAAAACTATATATTATATAAAATTTTCAAAAACGTTTTTATAA
*
1604622 TAAACTATA-CAT-TATATTTTCAAAATGATTTCAAAAATATATGTTATAT-AATTTT-CAAAAT
1 AAAACTATATCATATATATTTTCAAAATGATTT-AAAAA-ATA--TTATATGAATTTTCCAAAAT
* * *
1604683 GTTTTTAAAACT-TATATTGTAT-AAGTTTTCAAAAAACGTTTTT-TAAA
62 ATTTTTAAAACTATATATTATATAAAATTTTC-AAAAACGTTTTTAT-AA
*
1604730 AAAACTATATTATATATATTTTCA
1 AAAACTATATCATATATATTTTCA
1604754 GAAACCATTT
Statistics
Matches: 111, Mismatches: 12, Indels: 19
0.78 0.08 0.13
Matches are distributed among these distances:
107 20 0.18
108 40 0.36
109 22 0.20
110 15 0.14
111 14 0.13
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (109 bp):
AAAACTATATCATATATATTTTCAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATATTT
TTAAAACTATATATTATATAAAATTTTCAAAAACGTTTTTATAA
Found at i:1604765 original size:40 final size:41
Alignment explanation
Indices: 1604689--1604766 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1604679 AAATGTTTTT
* *
1604689 AAAACTTATATTGTATAAGTTTTCAAAAAACGTTTTTTAAA
1 AAAACTTATATTATATAAGTTTTCAAAAAACATTTTTTAAA
* *
1604730 AAAAC-TATATTATATATA-TTTTCAGAAACCATTTTTT
1 AAAACTTATATTATATA-AGTTTTCAAAAAACATTTTTT
1604767 GTAAACTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 26 0.81
41 6 0.19
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (41 bp):
AAAACTTATATTATATAAGTTTTCAAAAAACATTTTTTAAA
Found at i:1606642 original size:106 final size:106
Alignment explanation
Indices: 1605754--1606639 Score: 1558
Period size: 106 Copynumber: 8.4 Consensus size: 106
1605744 TATTGTTCCA
* * * * * *
1605754 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTTTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
* *
1605819 CAGTC-ATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
66 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1605860 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
1605925 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1605966 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1606031 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1606072 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
1606137 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1606178 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1606243 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1606284 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
1606349 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1606390 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1606455 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1606496 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
1606561 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1606602 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1606640 AAAGGCTGTA
Statistics
Matches: 754, Mismatches: 25, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
105 1 0.00
106 753 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1611481 original size:18 final size:18
Alignment explanation
Indices: 1611458--1611495 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1611448 CCATAAACAT
*
1611458 AATAAA-TGAAATCAAATG
1 AATAAAGTG-AATAAAATG
1611476 AATAAAGTGAATAAAATG
1 AATAAAGTGAATAAAATG
1611494 AA
1 AA
1611496 AAGAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.63, C:0.03, G:0.13, T:0.21
Consensus pattern (18 bp):
AATAAAGTGAATAAAATG
Found at i:1611643 original size:33 final size:31
Alignment explanation
Indices: 1611600--1611667 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
1611590 ACTATATACC
1611600 ATATAGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
1611632 ATATGAGTTTTCCAAAATATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATATTTTTAAAAATAT
1611664 ATAT
1 ATAT
1611668 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:1611693 original size:38 final size:36
Alignment explanation
Indices: 1611544--1611874 Score: 192
Period size: 40 Copynumber: 9.1 Consensus size: 36
1611534 ATATATCCCA
* *
1611544 AAAAATATTTTTTAAACTATATA-T-TAT-A-TTT-
1 AAAAATGTTTTTAAAACTATATATTATATAATTTTC
* ** *
1611575 AAAAATGTTTTCAAAACTATATACCATATAGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATATAATTTTC
* *
1611611 AAAAATGATTTT-AAA--A-ATATTATATGAGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATAT-AATTTTC
* *
1611644 CAAAATATTTTTAAAACTATATATTATATAAAATTTTC
1 AAAAATGTTTTTAAAACTATATATTATAT--AATTTTC
*
1611682 AAAAATGTTTTTATTTTAAACTATACA-T-TAT-ATTTTC
1 AAAAATGTTTTTA----AAACTATATATTATATAATTTTC
* * * *
1611719 -AAAATGATTTCAAAAATATATGTTATATAATTTTC
1 AAAAATGTTTTTAAAACTATATATTATATAATTTTC
1611754 -AAAATGTTTTTAAAACTTATATATTGTATATAAGTTTTC
1 AAAAATGTTTTTAAAAC-TATATA-T-TATATAA-TTTTC
* **
1611793 AAAAAACGTTTTTTAAAAAAACTATATTATATATATTTTC
1 -AAAAATG-TTTTTAAAACTA-TATATTATATA-ATTTTC
* *
1611833 AGAAACCAT-TTTTTGTAAACTATATGTTATAT--TTTTC
1 A-AAA--ATGTTTTT-AAAACTATATATTATATAATTTTC
1611870 AAAAA
1 AAAAA
1611875 CACTTTCAAA
Statistics
Matches: 235, Mismatches: 34, Indels: 59
0.72 0.10 0.18
Matches are distributed among these distances:
31 20 0.09
32 14 0.06
33 21 0.09
34 7 0.03
35 25 0.11
36 29 0.12
37 22 0.09
38 24 0.10
39 6 0.03
40 31 0.13
41 13 0.06
42 23 0.10
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (36 bp):
AAAAATGTTTTTAAAACTATATATTATATAATTTTC
Found at i:1611757 original size:35 final size:36
Alignment explanation
Indices: 1611713--1611796 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
1611703 TATACATTAT
1611713 ATTTTCAAAATGATTTCAAAA-ATATA-TGTTATATA
1 ATTTTCAAAATGATTTCAAAATATATATTG-TATATA
* *
1611748 ATTTTCAAAATGTTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGATTTCAAAA--TATATATTGTATATA
1611786 AGTTTTCAAAA
1 A-TTTTCAAAA
1611797 AACGTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 19 0.45
38 12 0.29
39 11 0.26
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (36 bp):
ATTTTCAAAATGATTTCAAAATATATATTGTATATA
Found at i:1622024 original size:2 final size:2
Alignment explanation
Indices: 1622017--1622061 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1622007 GGCTTGGATT
1622017 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1622059 GA G
1 GA G
1622062 GACATGAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1625648 original size:75 final size:75
Alignment explanation
Indices: 1625525--1625677 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
1625515 GTTGATTGAC
1625525 TCAACAAAATCTACTTATCAATTATAAAATTTAGATCACACTATAAACTTTTTGAACTAACTAAA
1 TCAACAAAATCTACTTATCAATTATAAAATTTAGATCACACTATAAACTTTTTGAACTAACTAAA
1625590 TAGAATTCTA
66 TAGAATTCTA
1625600 TCAACAAAATCTACTTATCAATTATAAAATTTAGATCACACTATAAACTTTTTGAACTAACTAAA
1 TCAACAAAATCTACTTATCAATTATAAAATTTAGATCACACTATAAACTTTTTGAACTAACTAAA
1625665 TAGAATTCTA
66 TAGAATTCTA
1625675 TCA
1 TCA
1625678 TATTCGCTGG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (75 bp):
TCAACAAAATCTACTTATCAATTATAAAATTTAGATCACACTATAAACTTTTTGAACTAACTAAA
TAGAATTCTA
Found at i:1629261 original size:30 final size:29
Alignment explanation
Indices: 1629227--1629319 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 29
1629217 GTGAGCCACC
1629227 TTTCAAATGTTAGAAAATAATTATTGAACT
1 TTTCAAATGTTA-AAAATAATTATTGAACT
* * * *
1629257 TTTCAAATGATTAAAAATAGTCACTGAAAT
1 TTTCAAATG-TTAAAAATAATTATTGAACT
*
1629287 TTATTAAATAGTTATAAAATAATCT-TTGAACT
1 TT-TCAAAT-GTTA-AAAATAAT-TATTGAACT
1629319 T
1 T
1629320 ATTAAACTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
30 24 0.49
31 11 0.22
32 14 0.29
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTCAAATGTTAAAAATAATTATTGAACT
Found at i:1629840 original size:2 final size:2
Alignment explanation
Indices: 1629835--1629859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1629825 CGTATCAAAT
1629835 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 T
1629860 GAATTATCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1630843 original size:15 final size:16
Alignment explanation
Indices: 1630823--1630855 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1630813 TATGTTCATA
1630823 TAAAAT-AATATATTT
1 TAAAATCAATATATTT
1630838 TAAAATCGAATATATTT
1 TAAAATC-AATATATTT
1630855 T
1 T
1630856 TGTATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
TAAAATCAATATATTT
Found at i:1640771 original size:27 final size:27
Alignment explanation
Indices: 1640741--1640884 Score: 243
Period size: 27 Copynumber: 5.3 Consensus size: 27
1640731 AAAACAGTGT
1640741 TGAATGATTCAGCATAAAAGTACATTC
1 TGAATGATTCAGCATAAAAGTACATTC
1640768 TGAATGATTCAGCATAAAAGTACATTC
1 TGAATGATTCAGCATAAAAGTACATTC
1640795 TGAATGATTCAGCATAAAAGTACATTC
1 TGAATGATTCAGCATAAAAGTACATTC
* *
1640822 TGAATGATTCAACATAAAAGTACATTA
1 TGAATGATTCAGCATAAAAGTACATTC
** *
1640849 TGAATGATTCAATATAAAAGTACATTT
1 TGAATGATTCAGCATAAAAGTACATTC
1640876 TGAATGATT
1 TGAATGATT
1640885 AAGACCCATT
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 113 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (27 bp):
TGAATGATTCAGCATAAAAGTACATTC
Found at i:1645169 original size:15 final size:15
Alignment explanation
Indices: 1645149--1645181 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1645139 AGGAAATCTG
1645149 TCTACCTATTTTAAT
1 TCTACCTATTTTAAT
1645164 TCTACCTATTTTAAT
1 TCTACCTATTTTAAT
1645179 TCT
1 TCT
1645182 TTCCCCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTACCTATTTTAAT
Found at i:1646500 original size:14 final size:15
Alignment explanation
Indices: 1646483--1646523 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
1646473 ACTGCTTACA
1646483 ACATAACACTTAA-T
1 ACATAACACTTAATT
1646497 ACATAACAC-TAATT
1 ACATAACACTTAATT
1646511 ACATAACACTTAA
1 ACATAACACTTAA
1646524 ACCAAAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.12
14 19 0.76
15 3 0.12
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (15 bp):
ACATAACACTTAATT
Found at i:1651211 original size:315 final size:309
Alignment explanation
Indices: 1650625--1651248 Score: 1088
Period size: 315 Copynumber: 2.0 Consensus size: 309
1650615 GCTCCTCAAC
1650625 CTCCTCGATAGGCACTTAGAGAGGATCTTATATAATCCACCAACTAAGCTAATAGGCCTATAGTC
1 CTCCTCGATAGGCACTTAGAGAGGATCTTATATAATCCACCAACTAAGCTAATAGGCCTATAGTC
*
1650690 ATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTGATGCCATGAT
66 ATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTAATGCCATGAT
*
1650755 CCCAATCTTTCCCCAAATAGAAGTTATGGAAGAACTTTATAATCTCTCCTTTAAGTACATGCCAA
131 CCCAATCTTTCCCCAAATAGAAGTTATGGAAGAACTTTATAATCTCTCCTTCAAGTACATGCCAA
*
1650820 TATCTTTTGAAAAGACCCAAATTAAAACCATCTGGCACGGAGCTTTATTGCTATTGCCACACTTT
196 TATCTTTTGAAAAGACCCAAATTAAAACCATCTGGCACAGAGCTTTATTGCTATTGCCACACTTT
*
1650885 AAAGAATCCCATATTTCCTCCTCTGTGAATTCTTTCTCCAAACTCAAACTCTG
261 AAAGAATCCCATA-TT--TCCTCTAT-AATTCTTTCTCCAAACTCAAACTCTG
1650938 CTCCTCGATAGGGGCACTTAGAGAGGATCTTATATAATCCACCAACTAAGCTAATAGGCCTATAG
1 CTCCTCGATA--GGCACTTAGAGAGGATCTTATATAATCCACCAACTAAGCTAATAGGCCTATAG
*
1651003 TTATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTAATGCCATG
64 TCATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTAATGCCATG
1651068 ATCCCAATCTTTCCCCAAATAGAAGTTATGGAAGAACTTTATAATCTCTCCTTCAAGTACATGCC
129 ATCCCAATCTTTCCCCAAATAGAAGTTATGGAAGAACTTTATAATCTCTCCTTCAAGTACATGCC
* * * *
1651133 AATATCTTTTGAAAA-ATCCCAAATTAAAACCATCTGGCCCATAGCTTTATTGCTATTTCCAGAC
194 AATATCTTTTGAAAAGA-CCCAAATTAAAACCATCTGGCACAGAGCTTTATTGCTATTGCCACAC
*
1651197 TTTAAAGTATCCCATATTTCCTCTATAATTCTTTCTCCAAACTCAAACTCTG
258 TTTAAAGAATCCCATATTTCCTCTATAATTCTTTCTCCAAACTCAAACTCTG
1651249 TTGAACTGAA
Statistics
Matches: 298, Mismatches: 10, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
311 26 0.09
312 7 0.02
313 10 0.03
314 3 0.01
315 252 0.85
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (309 bp):
CTCCTCGATAGGCACTTAGAGAGGATCTTATATAATCCACCAACTAAGCTAATAGGCCTATAGTC
ATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTAATGCCATGAT
CCCAATCTTTCCCCAAATAGAAGTTATGGAAGAACTTTATAATCTCTCCTTCAAGTACATGCCAA
TATCTTTTGAAAAGACCCAAATTAAAACCATCTGGCACAGAGCTTTATTGCTATTGCCACACTTT
AAAGAATCCCATATTTCCTCTATAATTCTTTCTCCAAACTCAAACTCTG
Found at i:1660246 original size:14 final size:14
Alignment explanation
Indices: 1660220--1660263 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
1660210 GATCATTAGT
1660220 TTAT-TTATG-ATG
1 TTATATTATGAATG
1660232 TTATATTATGAATG
1 TTATATTATGAATG
1660246 TTATATTATGAATG
1 TTATATTATGAATG
1660260 TTAT
1 TTAT
1660264 TTCGGGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.13
13 5 0.17
14 21 0.70
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (14 bp):
TTATATTATGAATG
Found at i:1661611 original size:28 final size:28
Alignment explanation
Indices: 1661579--1661635 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1661569 CAATAATGTA
1661579 TATATTGATGCTATAATTAATGCCACCC
1 TATATTGATGCTATAATTAATGCCACCC
1661607 TATATTGATGCTATAATTAATGCCACCC
1 TATATTGATGCTATAATTAATGCCACCC
1661635 T
1 T
1661636 CAAAATTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (28 bp):
TATATTGATGCTATAATTAATGCCACCC
Found at i:1661884 original size:14 final size:14
Alignment explanation
Indices: 1661867--1661927 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 14
1661857 CTATTATTTA
1661867 AAATATATTTATAT
1 AAATATATTTATAT
1661881 AAATATATATTTATATTT
1 -AA-ATATATTTATA--T
* ** *
1661899 AAATGTATAAATAA
1 AAATATATTTATAT
1661913 AAATATATTTATAT
1 AAATATATTTATAT
1661927 A
1 A
1661928 TTTAAATGTA
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
14 11 0.31
15 2 0.06
16 19 0.54
17 2 0.06
18 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
AAATATATTTATAT
Found at i:1661890 original size:16 final size:15
Alignment explanation
Indices: 1661860--1661959 Score: 69
Period size: 14 Copynumber: 6.5 Consensus size: 15
1661850 GTATAAACTA
*
1661860 TTATTTAAAATATAT
1 TTATATAAAATATAT
1661875 TTATATAAATATATAT
1 TTATATAAA-ATATAT
* *
1661891 TTATATTTAAATGTAT
1 TTATA-TAAAATATAT
**
1661907 AAATA-AAAATATAT
1 TTATATAAAATATAT
*
1661921 TTATATATTTAAATGTAT
1 TTATATA---AAATATAT
**
1661939 AAATA-AAAATATAT
1 TTATATAAAATATAT
1661953 TTATATA
1 TTATATA
1661960 TTTAAATGTA
Statistics
Matches: 63, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
14 20 0.32
15 10 0.16
16 19 0.30
17 4 0.06
18 10 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TTATATAAAATATAT
Found at i:1661988 original size:32 final size:32
Alignment explanation
Indices: 1661881--1661970 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
1661871 ATATTTATAT
1661881 AAATATATATT-TATATTTAAATGTATAAATAA
1 AAATATAT-TTATATATTTAAATGTATAAATAA
1661913 AAATATATTTATATATTTAAATGTATAAATAA
1 AAATATATTTATATATTTAAATGTATAAATAA
1661945 AAATATATTTATATATTTAAATGTAT
1 AAATATATTTATATATTTAAATGTAT
1661971 GAATCATTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
31 2 0.04
32 55 0.96
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (32 bp):
AAATATATTTATATATTTAAATGTATAAATAA
Found at i:1662138 original size:15 final size:15
Alignment explanation
Indices: 1662118--1662153 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1662108 AATATAAATC
1662118 TTAAATTTAATTTTA
1 TTAAATTTAATTTTA
1662133 TTAAATTTAATTTTA
1 TTAAATTTAATTTTA
*
1662148 TGAAAT
1 TTAAAT
1662154 CTATCCCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTAAATTTAATTTTA
Found at i:1662138 original size:28 final size:28
Alignment explanation
Indices: 1662050--1662132 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1662040 TTAAGATTAT
*
1662050 ATATATAATCATTAAATTATAAATGTT-AAAA
1 ATATA-AAT-ATTAAATT-T-AATTTTAAAAA
*
1662081 ATATAAATATTAAATTTAGTTTTAAAAA
1 ATATAAATATTAAATTTAATTTTAAAAA
*
1662109 ATATAAATCTTAAATTTAATTTTA
1 ATATAAATATTAAATTTAATTTTA
1662133 TTAAATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.09
28 27 0.57
29 8 0.17
30 3 0.06
31 5 0.11
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
ATATAAATATTAAATTTAATTTTAAAAA
Found at i:1667692 original size:14 final size:14
Alignment explanation
Indices: 1667669--1667706 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1667659 TCTGTCTATA
* *
1667669 TGCAGAGATTTTTT
1 TGCAGGGATTTATT
1667683 TGCAGGGATTTATT
1 TGCAGGGATTTATT
1667697 TGCAGGGATT
1 TGCAGGGATT
1667707 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.29, T:0.42
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:1667939 original size:3 final size:3
Alignment explanation
Indices: 1667931--1667955 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1667921 GAATTGGGTT
1667931 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
1667956 ATTTATGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1668673 original size:13 final size:13
Alignment explanation
Indices: 1668655--1668680 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1668645 TTTGAACCAA
1668655 ATATTATAAAAAT
1 ATATTATAAAAAT
1668668 ATATTATAAAAAT
1 ATATTATAAAAAT
1668681 GATCATTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATTATAAAAAT
Found at i:1669310 original size:12 final size:12
Alignment explanation
Indices: 1669293--1669318 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1669283 CAATTATGCT
1669293 AAAAATAATAAA
1 AAAAATAATAAA
1669305 AAAAATAATAAA
1 AAAAATAATAAA
1669317 AA
1 AA
1669319 TATTTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAATAATAAA
Found at i:1671401 original size:22 final size:22
Alignment explanation
Indices: 1671360--1671426 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1671350 CTCGTATAAA
1671360 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1671383 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1671405 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1671427 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1673151 original size:21 final size:20
Alignment explanation
Indices: 1673127--1673170 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1673117 TCTTGTTCGT
* *
1673127 TTGAAGGGGTATCGGTTCCCC
1 TTGAA-GGGTACCGATTCCCC
*
1673148 TTGAATGGTACCGATTCCCC
1 TTGAAGGGTACCGATTCCCC
1673168 TTG
1 TTG
1673171 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:1679685 original size:2 final size:2
Alignment explanation
Indices: 1679678--1679706 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1679668 TCCGACACAA
1679678 AT AT 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 A
1679707 CTCATTTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1684155 original size:37 final size:37
Alignment explanation
Indices: 1684105--1684178 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1684095 AACTCAATCC
*
1684105 GATTCAATCGAATCTAAACTCAAACTCAAATTGCCAA
1 GATTCAATCGAATCTAAACTCAAACTCAAAATGCCAA
* *
1684142 GATTCAATTGAATCTAATCTCAAACTCAAAATGCCAA
1 GATTCAATCGAATCTAAACTCAAACTCAAAATGCCAA
1684179 CAATCTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (37 bp):
GATTCAATCGAATCTAAACTCAAACTCAAAATGCCAA
Found at i:1686632 original size:127 final size:127
Alignment explanation
Indices: 1686402--1686650 Score: 462
Period size: 127 Copynumber: 2.0 Consensus size: 127
1686392 AGGTGCAAAT
* *
1686402 AGTTATTTTCATAAAGTAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGTGAGTTTT
1 AGTTATTTTCATAAAGCAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGAGAGTTTT
1686467 CTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGTAGAAA
66 CTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGTAGAAA
1686529 AGTTATTTTCATAAAGCAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGAGAGTTTT
1 AGTTATTTTCATAAAGCAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGAGAGTTTT
* *
1686594 CTTGATGTTCAAAGTGATGAACTCACTGATATTGAACTAACTAGCAACTCAATCAGT
66 CTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGT
1686651 GCCACTGCTC
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 118 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (127 bp):
AGTTATTTTCATAAAGCAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGAGAGTTTT
CTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGTAGAAA
Found at i:1695848 original size:51 final size:51
Alignment explanation
Indices: 1695768--1695864 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
1695758 GACTAATGAA
* * * *
1695768 TAAAAATAATGTTTTGATTCTATCATAATTCCTAATAAGATAATAATAAAC
1 TAAAAATAATGTTTTAACTCAATCATAATTCCTAATAAAATAATAATAAAC
*
1695819 TAAAAATAATGTTTTAACTCAATCTTAATTCCTAATAAAATAATAA
1 TAAAAATAATGTTTTAACTCAATCATAATTCCTAATAAAATAATAA
1695865 ATCTAATACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.37
Consensus pattern (51 bp):
TAAAAATAATGTTTTAACTCAATCATAATTCCTAATAAAATAATAATAAAC
Found at i:1707354 original size:21 final size:21
Alignment explanation
Indices: 1707330--1707371 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1707320 TCAGCACCAC
1707330 AAGCGCTCAACGGAACACCTT
1 AAGCGCTCAACGGAACACCTT
*
1707351 AAGCGCTCCACGGAACACCTT
1 AAGCGCTCAACGGAACACCTT
1707372 CAGATTCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.36, G:0.19, T:0.14
Consensus pattern (21 bp):
AAGCGCTCAACGGAACACCTT
Found at i:1709912 original size:29 final size:30
Alignment explanation
Indices: 1709871--1709927 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
1709861 GATAAAACGA
*
1709871 AAAGAACGATCAAATGATCA-ATAAAAATCG
1 AAAGAACGATCAAAAGA-CAGATAAAAATCG
*
1709901 AAAGTACG-TCAAAAGACAGATAAAAAT
1 AAAGAACGATCAAAAGACAGATAAAAAT
1709928 GTGTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 15 0.62
30 7 0.29
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.16
Consensus pattern (30 bp):
AAAGAACGATCAAAAGACAGATAAAAATCG
Found at i:1711613 original size:2 final size:2
Alignment explanation
Indices: 1711606--1711640 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1711596 ATATTTTATC
1711606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1711641 TTGAAAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1712851 original size:24 final size:24
Alignment explanation
Indices: 1712824--1712929 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
1712814 AAACGGAGAT
*
1712824 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
1712848 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1712872 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
1712896 ATCAGATGTC-AAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1712919 ATCAGAAATCA
1 ATCAGAAATCA
1712930 GATAAAATAT
Statistics
Matches: 61, Mismatches: 20, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
23 18 0.30
24 43 0.70
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1715415 original size:18 final size:18
Alignment explanation
Indices: 1715392--1715479 Score: 114
Period size: 18 Copynumber: 5.2 Consensus size: 18
1715382 TCCGGTCAAC
1715392 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1715410 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1715428 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
* *
1715441 GGTAAACGGGTCAGGTCG
1 GGTCAACGGGTCGGGTCG
*
1715459 GGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCGGGTCG
1715477 GGT
1 GGT
1715480 TGTGACCGGT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
13 12 0.19
18 50 0.81
ACGTcount: A:0.15, C:0.20, G:0.48, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1715440 original size:31 final size:31
Alignment explanation
Indices: 1715403--1715475 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
1715393 GTCAACGGGT
*
1715403 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCAACGGGTCAGGTCGGGTCAA
*
1715434 CGGGTCGGGTAAACGGGTCAGGTCGGGTCAA
1 CGGGTCGGGTCAACGGGTCAGGTCGGGTCAA
*
1715465 CGGGTCAGGTC
1 CGGGTCGGGTC
1715476 GGGTTGTGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCAGGTCGGGTCAA
Found at i:1715475 original size:13 final size:13
Alignment explanation
Indices: 1715421--1715457 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1715411 GTCAACGGGT
1715421 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
1715434 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
*
1715447 CGGGTCAGGTC
1 CGGGTCGGGTC
1715458 GGGTCAACGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1718872 original size:23 final size:22
Alignment explanation
Indices: 1718840--1718882 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1718830 GCATCAAATA
*
1718840 TCTCGGTCCGGTGAGTCTTTATT
1 TCTCGCTCCGGT-AGTCTTTATT
*
1718863 TCTCGCTCCGGTAGTGTTTA
1 TCTCGCTCCGGTAGTCTTTA
1718883 GGTGCACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.09, C:0.23, G:0.26, T:0.42
Consensus pattern (22 bp):
TCTCGCTCCGGTAGTCTTTATT
Found at i:1720412 original size:12 final size:12
Alignment explanation
Indices: 1720395--1720422 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1720385 GTCATTAAAT
1720395 TTTATTTTTTAA
1 TTTATTTTTTAA
1720407 TTTATTTTTTAA
1 TTTATTTTTTAA
1720419 TTTA
1 TTTA
1720423 CTCTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTTTTTAA
Found at i:1743051 original size:75 final size:75
Alignment explanation
Indices: 1742924--1743128 Score: 329
Period size: 75 Copynumber: 2.7 Consensus size: 75
1742914 AGGAACAAAG
* *
1742924 GAAATCATTTCGGAAGTTGACTCCGACAATGCAAGTAATACGTACATACATACATCCACACATAC
1 GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAATACATACATACATACATCCACACATAC
*
1742989 ATATACGTAT
66 ATATACATAT
* * *
1742999 GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAAAACATACATTCATACATCCACATATAC
1 GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAATACATACATACATACATCCACACATAC
1743064 ATATACATAT
66 ATATACATAT
* * *
1743074 GAAATCATTTCGGAAGTTGACTCCGACAATGTAATTAATACATCCACACATACAT
1 GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAATACATACATACATACAT
1743129 ATACGTATGT
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 119 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (75 bp):
GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAATACATACATACATACATCCACACATAC
ATATACATAT
Found at i:1744103 original size:21 final size:22
Alignment explanation
Indices: 1744079--1744131 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1744069 AATGTATAAA
1744079 ATTTAAACTTGTTATA-TATAT
1 ATTTAAACTTGTTATACTATAT
* * *
1744100 ATTTGAGCATGTTATACTATAT
1 ATTTAAACTTGTTATACTATAT
1744122 A-TTAAA-TTGT
1 ATTTAAACTTGT
1744132 ATCAAATTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
20 3 0.12
21 16 0.64
22 6 0.24
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTAAACTTGTTATACTATAT
Found at i:1747648 original size:18 final size:18
Alignment explanation
Indices: 1747621--1747660 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1747611 TCTCTCTCTC
* *
1747621 TGTATATATATATATATA
1 TGTATATATATACATACA
*
1747639 TGTATGTATATACATACA
1 TGTATATATATACATACA
1747657 TGTA
1 TGTA
1747661 AGCCAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (18 bp):
TGTATATATATACATACA
Found at i:1748315 original size:34 final size:35
Alignment explanation
Indices: 1748277--1748351 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 35
1748267 AAAACAGTCC
* *
1748277 TCAATTTCATTCTAAACCC-AATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1748311 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1748346 TCAATT
1 TCAATT
1748352 AAATTCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 19 0.50
35 19 0.50
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
Found at i:1750625 original size:20 final size:20
Alignment explanation
Indices: 1750602--1750647 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1750592 TAAAAAAGAT
1750602 TAAAAACATGTAAAAAAACA
1 TAAAAACATGTAAAAAAACA
* * *
1750622 TAAAAACTTGTTATAAAACA
1 TAAAAACATGTAAAAAAACA
1750642 TAAAAA
1 TAAAAA
1750648 TACATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.65, C:0.09, G:0.04, T:0.22
Consensus pattern (20 bp):
TAAAAACATGTAAAAAAACA
Found at i:1750657 original size:22 final size:20
Alignment explanation
Indices: 1750602--1750660 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1750592 TAAAAAAGAT
* * *
1750602 TAAAAACATGTAAAAAAACA
1 TAAAAACATATTATAAAACA
* *
1750622 TAAAAACTTGTTATAAAACA
1 TAAAAACATATTATAAAACA
1750642 TAAAAATACATATTATAAA
1 T-AAAA-ACATATTATAAA
1750661 GACAGATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 18 0.56
21 4 0.12
22 10 0.31
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.25
Consensus pattern (20 bp):
TAAAAACATATTATAAAACA
Found at i:1751720 original size:37 final size:36
Alignment explanation
Indices: 1751634--1751721 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 36
1751624 TATTAACAAG
* *
1751634 TTGAAAAATATTTATATATATATATATATTTTAAAAA
1 TTGAAAAATA-TAAAATATATATATATATTTTAAAAA
* * *
1751671 TT--AAATTCATAAAATATATATATTTTTTTTACAAAA
1 TTGAAAAAT-ATAAAATATATATATATATTTTA-AAAA
1751707 TTGAAAAATATAAAA
1 TTGAAAAATATAAAA
1751722 AGGTTTAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
35 22 0.54
36 7 0.17
37 8 0.20
38 4 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (36 bp):
TTGAAAAATATAAAATATATATATATATTTTAAAAA
Found at i:1754314 original size:38 final size:38
Alignment explanation
Indices: 1754263--1754340 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
1754253 AGTGACTTCG
1754263 ATGGTAGAGGAGATTGTTATTCTTCATAGAGGATCTGA
1 ATGGTAGAGGAGATTGTTATTCTTCATAGAGGATCTGA
1754301 ATGGTAGAGGAGATTGTTATTCTTCATAGAGGATCTGA
1 ATGGTAGAGGAGATTGTTATTCTTCATAGAGGATCTGA
1754339 AT
1 AT
1754341 TTGAGTAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.29, C:0.08, G:0.28, T:0.35
Consensus pattern (38 bp):
ATGGTAGAGGAGATTGTTATTCTTCATAGAGGATCTGA
Found at i:1756297 original size:9 final size:8
Alignment explanation
Indices: 1756274--1756299 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1756264 TTTATTCTCT
1756274 TTTAAAAA
1 TTTAAAAA
1756282 TTTAAAAA
1 TTTAAAAA
1756290 TTTAAAAA
1 TTTAAAAA
1756298 TT
1 TT
1756300 CACTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTTAAAAA
Found at i:1757347 original size:134 final size:134
Alignment explanation
Indices: 1757180--1757428 Score: 408
Period size: 134 Copynumber: 1.9 Consensus size: 134
1757170 AAAATAAGGG
* * *
1757180 TTTTTCATCCTAAAATGAAATGTTGGAAGCTAAAATGCTAAAGAATAAAAGATTAAGTGTCAAAA
1 TTTTTCACCCTAAAATAAAATGTTGGAAGCTAAAATGCTAAAGAATAAAAGAATAAGTGTCAAAA
* *
1757245 CGACTATTTAATCAAATGTTAGAAATATTTCCCTCCTAAAATGAGACATAATGTTCTAAAATAGG
66 CAACTATTTAATCAAATGTTAGAAATATTTCCCCCCTAAAATGAGACATAATGTTCTAAAATAGG
1757310 GGTT
131 GGTT
* * *
1757314 TTTTTCACCCTAAAATAAAATGTTGGAATCTAAAATGCTATATAATAAAAGAATAAGTGTCAAAA
1 TTTTTCACCCTAAAATAAAATGTTGGAAGCTAAAATGCTAAAGAATAAAAGAATAAGTGTCAAAA
* *
1757379 TAACTATTTAATCAAATGTTATAAATATTTCCCCCCTAAAATGAGACATA
66 CAACTATTTAATCAAATGTTAGAAATATTTCCCCCCTAAAATGAGACATA
1757429 GAAAGCAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
134 105 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (134 bp):
TTTTTCACCCTAAAATAAAATGTTGGAAGCTAAAATGCTAAAGAATAAAAGAATAAGTGTCAAAA
CAACTATTTAATCAAATGTTAGAAATATTTCCCCCCTAAAATGAGACATAATGTTCTAAAATAGG
GGTT
Found at i:1758225 original size:10 final size:10
Alignment explanation
Indices: 1758195--1758229 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
1758185 TCTGCGCCTT
1758195 AAAATTTTAA
1 AAAATTTTAA
1758205 AAAATGCTTTAA
1 AAAAT--TTTAA
1758217 AAAATTTTAA
1 AAAATTTTAA
1758227 AAA
1 AAA
1758230 TAAAATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:1759533 original size:21 final size:20
Alignment explanation
Indices: 1759492--1759551 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
1759482 GGGTTTAATT
* *
1759492 TTTTAAGATTTAAGTTGTAGA
1 TTTTAAAATTTAAATT-TAGA
1759513 TTTTAAAATTTAGAATTTAGA
1 TTTTAAAATTTA-AATTTAGA
* *
1759534 TATTAAAATTAAAATTTA
1 TTTTAAAATTTAAATTTA
1759552 AAATAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.18
21 25 0.74
22 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTTAAAATTTAAATTTAGA
Done.