Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 129 of 316
Found at i:41075478 original size:49 final size:49
Alignment explanation
Indices: 41075409--41075537 Score: 145
Period size: 49 Copynumber: 2.6 Consensus size: 49
41075399 ATCAAAGTCG
* * * * *
41075409 ATGCCATGTCCTAGACAGGTCGTACACTGACTTTCATATATCGAG-G-CTG
1 ATGCCATGTCCCAGATAGGTCTTACACTGACTCTCATATATCG-GTGTC-A
* * * *
41075458 ATGTCGTGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCGGTGTCA
1 ATGCCATGTCCCAGATAGGTCTTACACTGACTCTCATATATCGGTGTCA
41075507 ATGCCATGTCCCAGATAGGTCTTACACTGAC
1 ATGCCATGTCCCAGATAGGTCTTACACTGAC
41075538 ACACAATAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.02
49 64 0.97
50 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGATAGGTCTTACACTGACTCTCATATATCGGTGTCA
Found at i:41075621 original size:48 final size:46
Alignment explanation
Indices: 41075555--41075675 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 46
41075545 AAGCTGACGC
* * ** *
41075555 CATGTCCCAAACAAGTCTTACACTAGCTTGTATATCTCGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGC-CCT-TATCTCAAGGCTGATG
* * * *
41075603 CATGTCCTAGACATGTCTTACACTGGCCCTTGTCTCAATGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCCCTTATCTCAAGGCTGATG
41075649 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
41075676 ACACATATCA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
46 38 0.61
47 1 0.02
48 23 0.37
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCCCTTATCTCAAGGCTGATG
Found at i:41079244 original size:29 final size:29
Alignment explanation
Indices: 41079191--41079461 Score: 165
Period size: 29 Copynumber: 9.4 Consensus size: 29
41079181 AAGGCGTATC
* *
41079191 GACGATCATCGATCAATGAAAAGGGATGGAT
1 GACGACCATCGA-CTATGAAAAGGGATGG-T
** *
41079222 -TTGACCATCGACTATGAAAAGGGATAGT
1 GACGACCATCGACTATGAAAAGGGATGGT
*** ** *
41079250 TTTGATTAT--ATTATGAAAAGGGATGGT
1 GACGACCATCGACTATGAAAAGGGATGGT
* **
41079277 GACAACCATCGTA-TATGAAAAGGGATAAT
1 GACGACCATCG-ACTATGAAAAGGGATGGT
*** * * *
41079306 TTTGACTATCAACTATGAAAAGGGATAGT
1 GACGACCATCGACTATGAAAAGGGATGGT
** * * * * * *
41079335 TTCGACTATCAAATATCAAAATGGATGAT
1 GACGACCATCGACTATGAAAAGGGATGGT
* *
41079364 GACGACCGTCAACTATG-AAAGGGATGGT
1 GACGACCATCGACTATGAAAAGGGATGGT
*
41079392 GACGACCATCGATTAATGAAAAGGGATGGT
1 GACGACCATCGACT-ATGAAAAGGGATGGT
* *
41079422 GACAACCATCGAATATGAAAAGGGATGGT
1 GACGACCATCGACTATGAAAAGGGATGGT
*
41079451 TACGACCATCG
1 GACGACCATCG
41079462 TTAGCACACT
Statistics
Matches: 188, Mismatches: 45, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
27 19 0.10
28 22 0.12
29 115 0.61
30 32 0.17
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (29 bp):
GACGACCATCGACTATGAAAAGGGATGGT
Found at i:41079417 original size:30 final size:29
Alignment explanation
Indices: 41079261--41079461 Score: 174
Period size: 29 Copynumber: 6.9 Consensus size: 29
41079251 TTGATTATAT
* *
41079261 TATGAAAAGGGATGGTGACAACCATCGTA
1 TATGAAAAGGGATGGTGACGACCATCGAA
** *** *
41079290 TATGAAAAGGGATAATTTTGACTATC-AA
1 TATGAAAAGGGATGGTGACGACCATCGAA
* ** * *
41079318 CTATGAAAAGGGATAGTTTCGACTATCAAA
1 -TATGAAAAGGGATGGTGACGACCATCGAA
* * * *
41079348 TATCAAAATGGATGATGACGACCGTC-AA
1 TATGAAAAGGGATGGTGACGACCATCGAA
*
41079376 CTATG-AAAGGGATGGTGACGACCATCGAT
1 -TATGAAAAGGGATGGTGACGACCATCGAA
*
41079405 TAATGAAAAGGGATGGTGACAACCATCGAA
1 T-ATGAAAAGGGATGGTGACGACCATCGAA
*
41079435 TATGAAAAGGGATGGTTACGACCATCG
1 TATGAAAAGGGATGGTGACGACCATCG
41079462 TTAGCACACT
Statistics
Matches: 139, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
28 22 0.16
29 92 0.66
30 25 0.18
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCGAA
Found at i:41089533 original size:29 final size:29
Alignment explanation
Indices: 41089491--41089758 Score: 214
Period size: 29 Copynumber: 9.2 Consensus size: 29
41089481 AGATGGATTT
* * * *
41089491 GACCATTGACTATGAAAATGGATAGTTTC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* * **
41089520 GACTATCGATTATGAAAAGGGATGGCAAC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* * * * *
41089549 GACCATCAACTATGAAAACGAATGGTGAT
1 GACCATCGACTATGAAAAGGGATGGTTAC
* * * **
41089578 GACCATCAACAATGAAAAGGAATGGTGCC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* *
41089607 GACCATCGTA-TATGAAAAGGGATAGTTTC
1 GACCATCG-ACTATGAAAAGGGATGGTTAC
* * * * *
41089636 AACTATCGACTATGAAAAGGAATAGTTTC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* * * * *
41089665 GACTATCAAATATGAAAAGGGATAGTGAC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* *
41089694 GACCATCGATTAATGAAAAGGGATGGTGAC
1 GACCATCGACT-ATGAAAAGGGATGGTTAC
*
41089724 GACCATCGAATATGAAAAGGGATGGTTAC
1 GACCATCGACTATGAAAAGGGATGGTTAC
41089753 GACCAT
1 GACCAT
41089759 TGTTAGCACA
Statistics
Matches: 195, Mismatches: 41, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
28 1 0.01
29 166 0.85
30 28 0.14
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (29 bp):
GACCATCGACTATGAAAAGGGATGGTTAC
Found at i:41091625 original size:52 final size:49
Alignment explanation
Indices: 41091456--41091682 Score: 276
Period size: 49 Copynumber: 4.5 Consensus size: 49
41091446 ACTAGTGACT
*
41091456 CAAGTGTGGTACTATATGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
*
41091505 CAATTGTGGTACTATGTGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
**
41091554 CAAGCATGGTACTATGTGAAGGCCACTTGGTGAAGAA-AGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTT--TG-AGAAGAGATAGC-TTGGTCA
* * * * *
41091606 CAAGTGTGGTATTATGTGAAGGCCACTTTGTGAAGAAGGTAGCTTTGACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGCTTGGTC-A
* * * *
41091657 AAAGGGTGGTAATATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
41091683 CGGGTACCCG
Statistics
Matches: 155, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
49 75 0.48
50 6 0.04
51 38 0.25
52 36 0.23
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (49 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
Found at i:41091634 original size:101 final size:99
Alignment explanation
Indices: 41091462--41091650 Score: 283
Period size: 101 Copynumber: 1.9 Consensus size: 99
41091452 GACTCAAGTG
*
41091462 TGGTACTATATGAAGGCCACTTTGAGAAGAGATAGCTTGGTCACAATTGTGGTACTATGTGAAGG
1 TGGTACTATATGAAGGCCACTTTGAGAAGAGATAGCTTGGTCACAAGTGTGGTACTATGTGAAGG
41091527 CCACTTTGAGAAG-AGATAGCTTGGTCACAAGCA
66 CCACTTTGAGAAGAAGATAGCTTGGTCACAAGCA
* *
41091560 TGGTACTATGTGAAGGCCACTTGGTGAAGAA-AGATAGCTTTGGTCACAAGTGTGGTATTATGTG
1 TGGTACTATATGAAGGCCACTT--TG-AGAAGAGATAGC-TTGGTCACAAGTGTGGTACTATGTG
* *
41091624 AAGGCCACTTTGTGAAGAAGGTAGCTT
62 AAGGCCACTTTGAGAAGAAGATAGCTT
41091651 TGACTAAAAG
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
98 21 0.26
100 9 0.11
101 43 0.53
102 8 0.10
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (99 bp):
TGGTACTATATGAAGGCCACTTTGAGAAGAGATAGCTTGGTCACAAGTGTGGTACTATGTGAAGG
CCACTTTGAGAAGAAGATAGCTTGGTCACAAGCA
Found at i:41096728 original size:9 final size:10
Alignment explanation
Indices: 41096702--41096727 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41096692 AAAAGTATTG
41096702 TTTTTTTAAA
1 TTTTTTTAAA
41096712 TTTTTTTAAA
1 TTTTTTTAAA
41096722 TTTTTT
1 TTTTTT
41096728 ATCAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:41100121 original size:26 final size:24
Alignment explanation
Indices: 41100040--41100122 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
41100030 AGCTGATGGA
* *
41100040 CAGTAAGCTCTAATGAGCTGAAA-
1 CAGTAAGCTCTTACGAGCTGAAAT
* * * *
41100063 CGGTAAACTCTGACGATCTGAAAAT
1 CAGTAAGCTCTTACGAGCTG-AAAT
41100088 -AGTAAGCTCTTACGAGCTGATATAT
1 CAGTAAGCTCTTACGAGCTGA-A-AT
41100113 CAGTAAGCTC
1 CAGTAAGCTC
41100123 ACACAAGCTG
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
23 16 0.35
24 19 0.41
25 2 0.04
26 9 0.20
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (24 bp):
CAGTAAGCTCTTACGAGCTGAAAT
Found at i:41108664 original size:16 final size:16
Alignment explanation
Indices: 41108643--41108689 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
41108633 CCTAATTTTT
41108643 TTATTTAAATTAAATA
1 TTATTTAAATTAAATA
**
41108659 TTATTTTTATATAAATA
1 TTATTTAAAT-TAAATA
41108676 TT-TTTATAATTAAA
1 TTATTTA-AATTAAA
41108690 ATATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTAAATTAAATA
Found at i:41108691 original size:17 final size:17
Alignment explanation
Indices: 41108646--41108693 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 17
41108636 AATTTTTTTA
41108646 TTTA-AATTAAATATTATT
1 TTTATAATTAAA-A-TATT
41108664 TTTAT-A-T-AAATATT
1 TTTATAATTAAAATATT
41108678 TTTATAATTAAAATAT
1 TTTATAATTAAAATAT
41108694 ATAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 3 0.12
17 7 0.27
18 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTATAATTAAAATATT
Found at i:41112208 original size:37 final size:36
Alignment explanation
Indices: 41112167--41112241 Score: 132
Period size: 37 Copynumber: 2.1 Consensus size: 36
41112157 GAACTTGAAA
41112167 AATTTTCGTCCCATAAGTCTGTGTACGATGATTTTAT
1 AATTTTCGTCCCATAAGTCTGTGTACGATGA-TTTAT
*
41112204 AATTTTCGTCCCATAAGTCTGTGTACGGTGATTTAT
1 AATTTTCGTCCCATAAGTCTGTGTACGATGATTTAT
41112240 AA
1 AA
41112242 AATCATCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 7 0.19
37 30 0.81
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (36 bp):
AATTTTCGTCCCATAAGTCTGTGTACGATGATTTAT
Found at i:41116143 original size:5 final size:5
Alignment explanation
Indices: 41116133--41116159 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41116123 AAGAAAATAT
41116133 TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TA
41116160 AAATAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:41117132 original size:16 final size:15
Alignment explanation
Indices: 41117081--41117133 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
41117071 GTTATATACT
41117081 CATGAATTGAGTATGG
1 CATGAATTGAGTAT-G
* * *
41117097 TATGAAATGATGTATT
1 CATGAATTGA-GTATG
41117113 CATGAATTGAGTACTG
1 CATGAATTGAGTA-TG
41117129 CATGA
1 CATGA
41117134 CTGATGCCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 22 0.76
17 4 0.14
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (15 bp):
CATGAATTGAGTATG
Found at i:41124323 original size:5 final size:5
Alignment explanation
Indices: 41124313--41124344 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
41124303 ATGAAAATAT
41124313 TATTA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TA
41124345 ATTAAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:41124580 original size:13 final size:13
Alignment explanation
Indices: 41124562--41124603 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
41124552 AAACAAGGGG
41124562 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
41124575 AAAGAAAGAAAGAA
1 AAAGAAAG-AAGAA
* *
41124589 AAAAAAAGGAGAA
1 AAAGAAAGAAGAA
41124602 AA
1 AA
41124604 TTTAGGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:41124602 original size:17 final size:17
Alignment explanation
Indices: 41124561--41124593 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41124551 GAAACAAGGG
41124561 GAAAGAAAGAAGAAAAA
1 GAAAGAAAGAAGAAAAA
41124578 GAAAGAAAGAA-AAAAA
1 GAAAGAAAGAAGAAAAA
41124594 AAGGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAGAAAAA
Found at i:41132769 original size:42 final size:42
Alignment explanation
Indices: 41132710--41132906 Score: 216
Period size: 42 Copynumber: 4.7 Consensus size: 42
41132700 TCGAAATCTT
* * * *
41132710 AACAGAATCTTATAAGAGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTG
* * * * *
41132752 AATAGAAGCTCATAAGAGCTGAAA-AAAAACTCGTATGAGTTA
1 AACAGAAGCTCATAAGAGCT-AAACAGAAACTCATAAGAGTTG
*
41132794 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTG
* ** *
41132836 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATATCAGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTG
* * * *
41132878 AACAGAAGTTCGTAAGAGTTAAACGGAAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAA
41132907 GAAAAACACG
Statistics
Matches: 130, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
41 2 0.02
42 125 0.96
43 3 0.02
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTG
Found at i:41132851 original size:84 final size:84
Alignment explanation
Indices: 41132710--41132906 Score: 268
Period size: 84 Copynumber: 2.3 Consensus size: 84
41132700 TCGAAATCTT
* * * *
41132710 AACAGAATCTTATAAGAGCTAAACAGAAACCCATAAGGGTTGAATAGAAGCTCATAAGAGCTGAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAGAAGCTCATAAGAGCTGAA
* *
41132775 AAAAAACTCGTATGAGTTA
66 AAAAAACTCATATCAGTTA
* *
41132794 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGTTGAACAGAAGCTCATAAGAGCTGAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAGAAGCTCATAAGAGCTGAA
* *
41132859 CAGAAACTCATATCAGTTA
66 AAAAAACTCATATCAGTTA
* * * *
41132878 AACAGAAGTTCGTAAGAGTTAAACGGAAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAA
41132907 GAAAAACACG
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 98 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (84 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAGAAGCTCATAAGAGCTGAA
AAAAAACTCATATCAGTTA
Found at i:41132881 original size:21 final size:21
Alignment explanation
Indices: 41132710--41132884 Score: 161
Period size: 21 Copynumber: 8.3 Consensus size: 21
41132700 TCGAAATCTT
* * * *
41132710 AACAGAATCTTATAAGAGCTA
1 AACAGAAACTCATAAGAGTTG
* *
41132731 AACAGAAACCCATAAGGGTTG
1 AACAGAAACTCATAAGAGTTG
* * *
41132752 AATAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGTTG
* * * * *
41132773 AAAAAAAACTCGTATGAGTTA
1 AACAGAAACTCATAAGAGTTG
* *
41132794 AACAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGTTG
41132815 AACAGAAACTCATAAGAGTTG
1 AACAGAAACTCATAAGAGTTG
* *
41132836 AACAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGTTG
** *
41132857 AACAGAAACTCATATCAGTTA
1 AACAGAAACTCATAAGAGTTG
41132878 AACAGAA
1 AACAGAA
41132885 GTTCGTAAGA
Statistics
Matches: 120, Mismatches: 34, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 120 1.00
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.18
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGTTG
Found at i:41139001 original size:21 final size:21
Alignment explanation
Indices: 41138925--41139003 Score: 63
Period size: 21 Copynumber: 3.9 Consensus size: 21
41138915 GTAAATCGTT
41138925 AACAGAAGCTTG-AA-AGTTG
1 AACAGAAGCTTGTAAGAGTTG
* * * *
41138944 AACAGAAGCTCGTGAGAGCTA
1 AACAGAAGCTTGTAAGAGTTG
* * * * *
41138965 AATAGAAACCTATAAGGGTTG
1 AACAGAAGCTTGTAAGAGTTG
41138986 AACAGAAGCTTGTAAGAG
1 AACAGAAGCTTGTAAGAG
41139004 CTAAAAAAAT
Statistics
Matches: 40, Mismatches: 18, Indels: 2
0.67 0.30 0.03
Matches are distributed among these distances:
19 11 0.28
20 1 0.03
21 28 0.70
ACGTcount: A:0.42, C:0.13, G:0.27, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTTGTAAGAGTTG
Found at i:41139052 original size:21 final size:21
Alignment explanation
Indices: 41138942--41139128 Score: 71
Period size: 21 Copynumber: 9.0 Consensus size: 21
41138932 GCTTGAAAGT
* *
41138942 TGAACAGAAGCTCGTGAGAGC
1 TGAACAGAAGCTCATAAGAGC
* * * * *
41138963 TAAATAGAAAC-CTATAAGGGT
1 TGAACAGAAGCTC-ATAAGAGC
**
41138984 TGAACAGAAGCTTGTAAGAGC
1 TGAACAGAAGCTCATAAGAGC
** * *
41139005 T-AA-A-AAAATCATATGAGT
1 TGAACAGAAGCTCATAAGAGC
* *
41139023 TAAATAGAAGCTCATAAGAGC
1 TGAACAGAAGCTCATAAGAGC
* **
41139044 TGAACAGAAACTCATAAGATT
1 TGAACAGAAGCTCATAAGAGC
* *
41139065 TGAACAGAAGCTTGA-AAAAGC
1 TGAACAGAAGC-TCATAAGAGC
* * *
41139086 TGAAC-GAAAACTCATATGAGT
1 TGAACAG-AAGCTCATAAGAGC
* * *
41139107 TAAACAAAAGCTCGTAAGAGC
1 TGAACAGAAGCTCATAAGAGC
41139128 T
1 T
41139129 AAACGAAAAG
Statistics
Matches: 112, Mismatches: 45, Indels: 18
0.64 0.26 0.10
Matches are distributed among these distances:
18 9 0.08
19 3 0.03
20 7 0.06
21 91 0.81
22 2 0.02
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (21 bp):
TGAACAGAAGCTCATAAGAGC
Found at i:41139137 original size:42 final size:42
Alignment explanation
Indices: 41138939--41139137 Score: 183
Period size: 42 Copynumber: 4.8 Consensus size: 42
41138929 GAAGCTTGAA
* * *
41138939 AGTTGAACAGAAGCTCGTGAGAGCTAAATAGAAACCT-ATAAG
1 AGTTGAACAGAAGCTCGTAAGAGCTAAA-CGAAAACTCATAAG
* * *
41138981 GGTTGAACAGAAGCTTGTAAGAGCTAAA--AAAA-TCATATG
1 AGTTGAACAGAAGCTCGTAAGAGCTAAACGAAAACTCATAAG
* * * *
41139020 AGTTAAATAGAAGCTCATAAGAGCTGAAC-AGAAACTCATAAG
1 AGTTGAACAGAAGCTCGTAAGAGCTAAACGA-AAACTCATAAG
* * * * * *
41139062 ATTTGAACAGAAGCTTGAAAAAGCTGAACGAAAACTCATATG
1 AGTTGAACAGAAGCTCGTAAGAGCTAAACGAAAACTCATAAG
* *
41139104 AGTTAAACAAAAGCTCGTAAGAGCTAAACGAAAA
1 AGTTGAACAGAAGCTCGTAAGAGCTAAACGAAAA
41139138 GTAAAACACG
Statistics
Matches: 125, Mismatches: 27, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.01
39 29 0.23
40 1 0.01
41 3 0.02
42 90 0.72
43 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.20
Consensus pattern (42 bp):
AGTTGAACAGAAGCTCGTAAGAGCTAAACGAAAACTCATAAG
Found at i:41140865 original size:53 final size:53
Alignment explanation
Indices: 41140775--41140982 Score: 276
Period size: 53 Copynumber: 3.9 Consensus size: 53
41140765 TCCTTAGATT
*
41140775 TTCCCATATGATGCCATAACCCACCAATTATGATCTTACACGATATGGTCTTC
1 TTCCCATATGATGCCATAACCCACCAATTACGATCTTACACGATATGGTCTTC
* * *
41140828 TTCCTATATGATGCCATAACCCA-CAAGTTACGGTCTTACACGTTATGGTCTTC
1 TTCCCATATGATGCCATAACCCACCAA-TTACGATCTTACACGATATGGTCTTC
* * * * *
41140881 TTCCCATATAATGTCATAACCCACCAATTACGGTCTTACACAATATGGTCTTT
1 TTCCCATATGATGCCATAACCCACCAATTACGATCTTACACGATATGGTCTTC
* * * *
41140934 TTTCCATATTAT-CCACAACCCACCAGTTACGATCTTACACGATATGGTC
1 TTCCCATATGATGCCATAACCCACCAATTACGATCTTACACGATATGGTC
41140983 CTTTAATGTT
Statistics
Matches: 136, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
52 35 0.26
53 98 0.72
54 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (53 bp):
TTCCCATATGATGCCATAACCCACCAATTACGATCTTACACGATATGGTCTTC
Found at i:41141933 original size:17 final size:16
Alignment explanation
Indices: 41141913--41141976 Score: 53
Period size: 17 Copynumber: 4.0 Consensus size: 16
41141903 TATATATTTA
41141913 TAATAAATATATAAAAT
1 TAATAAATAT-TAAAAT
*
41141930 TAATAATTATTAAAA-
1 TAATAAATATTAAAAT
* *
41141945 T-ATAAAAATTAAATT
1 TAATAAATATTAAAAT
41141960 TAATGATAATA-TAAAAT
1 TAAT-A-AATATTAAAAT
41141977 ATAGAATGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
14 10 0.27
15 2 0.05
16 7 0.19
17 15 0.41
18 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAATAAATATTAAAAT
Found at i:41142152 original size:32 final size:32
Alignment explanation
Indices: 41142116--41142181 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
41142106 AGTTTCTCTC
41142116 TTTTTTATGATTTGGGAATGTAGGTTTTACTT
1 TTTTTTATGATTTGGGAATGTAGGTTTTACTT
* * *
41142148 TTTTTTATGATTTGGTAATTTATGTTTTACTT
1 TTTTTTATGATTTGGGAATGTAGGTTTTACTT
41142180 TT
1 TT
41142182 AAATTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.18, C:0.03, G:0.17, T:0.62
Consensus pattern (32 bp):
TTTTTTATGATTTGGGAATGTAGGTTTTACTT
Found at i:41144430 original size:17 final size:19
Alignment explanation
Indices: 41144388--41144431 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41144378 ACGAAATTTT
*
41144388 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
41144407 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
41144425 AA-TATTA
1 AATTATTA
41144432 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:41153582 original size:15 final size:13
Alignment explanation
Indices: 41153562--41153606 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 13
41153552 GTTCTTGTTG
41153562 TTTTTACTTTCTTTA
1 TTTTTAC-TT-TTTA
41153577 TTTTTACTTTTTA
1 TTTTTACTTTTTA
41153590 TTTTTAGCATTTTTA
1 TTTTTA-C-TTTTTA
41153605 TT
1 TT
41153607 GTCATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.36
14 3 0.11
15 15 0.54
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTACTTTTTA
Found at i:41157403 original size:30 final size:30
Alignment explanation
Indices: 41157369--41157429 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41157359 TCCTTAACTC
41157369 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
41157399 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
41157429 A
1 A
41157430 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:41160199 original size:25 final size:25
Alignment explanation
Indices: 41160165--41160212 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
41160155 TAAACAAGTT
41160165 AGATAGATATCACTCTTAATTTGTA
1 AGATAGATATCACTCTTAATTTGTA
*
41160190 AGATAGATATGACTCTTAATTTG
1 AGATAGATATCACTCTTAATTTG
41160213 AGTGTGAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (25 bp):
AGATAGATATCACTCTTAATTTGTA
Found at i:41163159 original size:16 final size:17
Alignment explanation
Indices: 41163129--41163161 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
41163119 TTCATAAGTA
41163129 TATATCAATTATTTCAT
1 TATATCAATTATTTCAT
41163146 TATATCAA-TATTTCAT
1 TATATCAATTATTTCAT
41163162 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATCAATTATTTCAT
Found at i:41163508 original size:46 final size:46
Alignment explanation
Indices: 41163448--41163715 Score: 288
Period size: 46 Copynumber: 5.8 Consensus size: 46
41163438 TTTGACATGA
* * * ** *
41163448 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTTAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
* ** *
41163494 TGCCATGGTATCTTTCGACCATGGTCTTGTTCATTTCATGTTATAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
* ** *
41163540 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
* * * * * *
41163585 TGCCATTGTATCTTTCAACCATGGTCTTACACATTTTATATTCTAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
* *
41163631 TGCCATGGTATCTTTCAACCATGGTCTTA-TACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACT-CATTTCATGTTATGT
* * *
41163677 TGCCATGGTGTCGTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
41163716 ATCATGTTTT
Statistics
Matches: 184, Mismatches: 35, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
45 38 0.21
46 146 0.79
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
Found at i:41163607 original size:91 final size:92
Alignment explanation
Indices: 41163492--41163717 Score: 319
Period size: 91 Copynumber: 2.5 Consensus size: 92
41163482 TTTTTGTTAG
* *** *
41163492 GTTGCCATGGTATCTTTCGACCATGGTCTTGTTCATTTCATGTTATATTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATATTGCCATGGTATCTTTCA
* * *
41163557 ACCATGGTCTTATTCA-TTCCCGTCAT
66 ACCATGGTCTTATACATTTCACATCAT
* * *
41163583 GTTGCCATTGTATCTTTCAACCATGGTCTTACACATTTTATATTCTATTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATATTGCCATGGTATCTTTCA
*
41163648 ACCATGGTCTTATACATTTCATATCAT
66 ACCATGGTCTTATACATTTCACATCAT
* *
41163675 GTTGCCATGGTGTCGTTCAACCATGGTCTTACACATTTCATAT
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
41163718 CATGTTTTCA
Statistics
Matches: 118, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
91 72 0.61
92 46 0.39
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (92 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATATTGCCATGGTATCTTTCA
ACCATGGTCTTATACATTTCACATCAT
Found at i:41163680 original size:137 final size:137
Alignment explanation
Indices: 41163443--41163705 Score: 364
Period size: 137 Copynumber: 1.9 Consensus size: 137
41163433 TTATCTTTGA
* * * * * *
41163443 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTTAGGTTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTTTATATTAGATTGCCATGGTATCTT
* * * * * *
41163508 TCGACCATGGTCTTGTTCATTTCATGTTATATTGCCATGGTATCTTTCAACCATGGTCTTATTCA
66 TCAACCATGGTCTTATACATTTCATATCATATTGCCATGGTATCGTTCAACCATGGTCTTATTCA
41163573 TTCCCGT
131 TTCCCGT
* * **
41163580 CATGTTGCCATTGTATCTTTCAACCATGGTCTTACACATTTTATATTCTATTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTTTATATTAGATTGCCATGGTATCTT
* *
41163645 TCAACCATGGTCTTATACATTTCATATCATGTTGCCATGGTGTCGTTCAACCATGGTCTTA
66 TCAACCATGGTCTTATACATTTCATATCATATTGCCATGGTATCGTTCAACCATGGTCTTA
41163706 CACATTTCAT
Statistics
Matches: 108, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
137 108 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.43
Consensus pattern (137 bp):
CATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTTTATATTAGATTGCCATGGTATCTT
TCAACCATGGTCTTATACATTTCATATCATATTGCCATGGTATCGTTCAACCATGGTCTTATTCA
TTCCCGT
Found at i:41175382 original size:18 final size:18
Alignment explanation
Indices: 41175340--41175382 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
41175330 GCCCATTCCG
* *
41175340 AAGTATATATATATACAT
1 AAGTATGTATATATACAC
41175358 ATA-TATGTATATATACAC
1 A-AGTATGTATATATACAC
41175376 AAGTATG
1 AAGTATG
41175383 CCCATTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATATACAC
Found at i:41175889 original size:56 final size:56
Alignment explanation
Indices: 41175827--41176060 Score: 332
Period size: 56 Copynumber: 4.2 Consensus size: 56
41175817 GAGATTGGCG
* * *
41175827 CTAAGTGTGCGGGTTTAAAT-TGTGCAGCACTAAGTGTGCGA-ATTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGAATATGT--AGCACTAAGTGTGCGAGTTTGACTATGTAGCA
*
41175883 CTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCA
*
41175939 CTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCA
* * * *
41175995 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCA
41176050 CTGAA-TGTGCG
1 CT-AAGTGTGCG
41176061 GACTTATTAT
Statistics
Matches: 167, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
55 36 0.22
56 128 0.77
57 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCA
Found at i:41175909 original size:28 final size:28
Alignment explanation
Indices: 41175852--41176060 Score: 343
Period size: 28 Copynumber: 7.5 Consensus size: 28
41175842 TAAATTGTGC
*
41175852 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
41175879 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
41175907 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
41175935 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
41175963 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
41175991 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
41176019 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
41176046 AGCACTGAA-TGTGCG
1 AGCACT-AAGTGTGCG
41176061 GACTTATTAT
Statistics
Matches: 177, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
27 38 0.21
28 139 0.79
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:41182730 original size:7 final size:7
Alignment explanation
Indices: 41182718--41182743 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41182708 TATATATGCA
41182718 AATGTCG
1 AATGTCG
41182725 AATGTCG
1 AATGTCG
41182732 AATGTCG
1 AATGTCG
41182739 AATGT
1 AATGT
41182744 ATACAAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (7 bp):
AATGTCG
Found at i:41200405 original size:48 final size:48
Alignment explanation
Indices: 41200339--41200478 Score: 219
Period size: 48 Copynumber: 2.9 Consensus size: 48
41200329 GTTATGTGTA
* * *
41200339 ATCCCATGTAAGATCATGTTTGGGACATGGCATTGGCATCGATATGTG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTG
41200387 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTG
* * *
41200435 ATCCCATGTAAGACCATATCT-GGATATGGCATTGGCATCTATAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATAT
41200479 CAGACATCGT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
47 21 0.24
48 65 0.76
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (48 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTG
Found at i:41201600 original size:30 final size:30
Alignment explanation
Indices: 41201560--41201618 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
41201550 TAAGCACAGG
* *
41201560 GGCGTATGTCTAAACCGTGTGTGACACACA
1 GGCGTATGTCTAAACCATGTGTCACACACA
* *
41201590 GGCGTGTGTCTAGACCATGTGTCACACAC
1 GGCGTATGTCTAAACCATGTGTCACACAC
41201619 GGTCTGTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (30 bp):
GGCGTATGTCTAAACCATGTGTCACACACA
Found at i:41204170 original size:20 final size:20
Alignment explanation
Indices: 41204140--41204184 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
41204130 CTGTTTTGTT
41204140 ATGGG-CCAACTATATTAAA
1 ATGGGCCCAACTATATTAAA
* *
41204159 ATGGGCCCAACTATGTTAAT
1 ATGGGCCCAACTATATTAAA
41204179 ATGGGC
1 ATGGGC
41204185 AAGGCCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTATATTAAA
Found at i:41204250 original size:60 final size:60
Alignment explanation
Indices: 41204175--41204289 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
41204165 CCAACTATGT
* *
41204175 TAATATGGGCAAGGCCTAATATA-TCTCA-ACTTGTAATAGGGCTATGGCCCAGATTGATAC
1 TAATATAGGCAAGGCCCAATATACTCTCATA-TTGTAA-AGGGCTATGGCCCAGATTGATAC
* * * * *
41204235 TAATATAGGCTAGGCCCAGTATACTCTGATATTGTAAGGGGCTATGGCCTAGATT
1 TAATATAGGCAAGGCCCAATATACTCTCATATTGTAAAGGGCTATGGCCCAGATT
41204290 AATATTGATG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 35 0.76
61 10 0.22
62 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (60 bp):
TAATATAGGCAAGGCCCAATATACTCTCATATTGTAAAGGGCTATGGCCCAGATTGATAC
Found at i:41209997 original size:16 final size:16
Alignment explanation
Indices: 41209973--41210006 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41209963 GCAATGTAGC
*
41209973 TATGATATGAATGATA
1 TATGATATGAAAGATA
*
41209989 TATGCTATGAAAGATA
1 TATGATATGAAAGATA
41210005 TA
1 TA
41210007 CATATTTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (16 bp):
TATGATATGAAAGATA
Found at i:41211464 original size:21 final size:22
Alignment explanation
Indices: 41211422--41211469 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
41211412 TTAATTGATG
*
41211422 TTTATGTCATTATTGTTATTTTA
1 TTTATGT-ATTATAGTTATTTTA
* *
41211445 TTTATGT-TTATAGTTTTTTTT
1 TTTATGTATTATAGTTATTTTA
41211466 TTTA
1 TTTA
41211470 GACAATTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 15 0.68
23 7 0.32
ACGTcount: A:0.19, C:0.02, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTATGTATTATAGTTATTTTA
Found at i:41212659 original size:20 final size:20
Alignment explanation
Indices: 41212634--41212684 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
41212624 CTTAATAAAG
*
41212634 ACACATACACATACATGCAC
1 ACACATACACATACACGCAC
* *
41212654 ACACATACACGTGCACGCAC
1 ACACATACACATACACGCAC
*
41212674 ACACACACACA
1 ACACATACACA
41212685 CAGAGACACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.39, G:0.08, T:0.10
Consensus pattern (20 bp):
ACACATACACATACACGCAC
Found at i:41228370 original size:17 final size:17
Alignment explanation
Indices: 41228348--41228382 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41228338 AACTTTTTTA
41228348 TATTTTTAATAAA-ATTT
1 TATTTTTAA-AAAGATTT
41228365 TATTTTTAAAAAGATTT
1 TATTTTTAAAAAGATTT
41228382 T
1 T
41228383 TCATAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TATTTTTAAAAAGATTT
Found at i:41228966 original size:42 final size:43
Alignment explanation
Indices: 41228915--41229016 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 43
41228905 ATTTAATATA
41228915 AATATTATTTTTAAATTTTATTAAATA-TAAAAAT-AAAATATTTT
1 AATA-TATTTTTAAA-TTTATTAAA-AGTAAAAATAAAAATATTTT
41228959 AA-ATA-TTTT-AA--TA-TAAAAGTAAAAATAAAAATATTTT
1 AATATATTTTTAAATTTATTAAAAGTAAAAATAAAAATATTTT
*
41228996 AATATATATTTAAATATTATT
1 AATATATTTTTAAAT-TTATT
41229017 CTTTTGATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 18
0.72 0.01 0.27
Matches are distributed among these distances:
35 1 0.02
36 11 0.23
37 14 0.29
38 3 0.06
39 3 0.06
40 4 0.08
41 4 0.08
42 2 0.04
43 3 0.06
44 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (43 bp):
AATATATTTTTAAATTTATTAAAAGTAAAAATAAAAATATTTT
Found at i:41229046 original size:20 final size:21
Alignment explanation
Indices: 41229007--41229051 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
41228997 ATATATATTT
*
41229007 AAATATTATTCTTTTGATATA
1 AAATATTATTCTTTTAATATA
*
41229028 AAATATTATTC-TTTAATATT
1 AAATATTATTCTTTTAATATA
41229048 AAAT
1 AAAT
41229052 TGATGTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATATTATTCTTTTAATATA
Found at i:41229050 original size:21 final size:22
Alignment explanation
Indices: 41229001--41229050 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
41228991 ATTTTAATAT
* *
41229001 ATATTTAAATATTATTCTTTTG
1 ATATTAAAATATTATTCTTTTA
41229023 ATA-TAAAATATTATTC-TTTA
1 ATATTAAAATATTATTCTTTTA
41229043 ATATTAAA
1 ATATTAAA
41229051 TTGATGTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 16 0.64
22 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTAAAATATTATTCTTTTA
Found at i:41230594 original size:44 final size:44
Alignment explanation
Indices: 41230546--41230634 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
41230536 TGAAATAAAG
** *
41230546 TAGAAATTGTGATAATTATGCA-TTTTAAATAAATTTTAATTTAA
1 TAGAAATTGTGATAATTAAACATTTTTAAAT-AATTATAATTTAA
*
41230590 TAGAAGTTGTGATAATTAAACATTTTTAAATAATTATAATTTAA
1 TAGAAATTGTGATAATTAAACATTTTTAAATAATTATAATTTAA
41230634 T
1 T
41230635 TTATACTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 32 0.80
45 8 0.20
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (44 bp):
TAGAAATTGTGATAATTAAACATTTTTAAATAATTATAATTTAA
Found at i:41241513 original size:15 final size:15
Alignment explanation
Indices: 41241493--41241524 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41241483 CATTTCACTG
41241493 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
41241508 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
41241523 TT
1 TT
41241525 TGCATGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:41243154 original size:37 final size:36
Alignment explanation
Indices: 41243103--41243215 Score: 101
Period size: 37 Copynumber: 3.1 Consensus size: 36
41243093 ATTCGAAAAA
*
41243103 TAAT-ATTATTTTAATAGTTTAATATTAAATTTAATT
1 TAATGATTATCTTAATAGTTTAATATT-AATTTAATT
* *
41243139 TAAT-ACTTGTCTTAATAGTATT-TTATTAATTTAATAT
1 TAATGA-TTATCTTAATAGT-TTAATATTAATTTAAT-T
*
41243176 TAAAGTGATTATCTTAATAG-TAAAT-TTAATTTAATT
1 T-AA-TGATTATCTTAATAGTTTAATATTAATTTAATT
41243212 TAAT
1 TAAT
41243216 TTAATGTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
34 1 0.02
35 2 0.03
36 15 0.23
37 28 0.44
38 5 0.08
39 12 0.19
40 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (36 bp):
TAATGATTATCTTAATAGTTTAATATTAATTTAATT
Found at i:41245599 original size:47 final size:47
Alignment explanation
Indices: 41245530--41245631 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 47
41245520 ACCAACACAC
* * * **
41245530 CAGTACGACACTCAGTGCCTCATTGGCTT-TGCCGAAGTAAACAGTAA
1 CAGTACGACACTCAGTACCTCATCGGATTAAACCGAAGT-AACAGTAA
* *
41245577 CAGTACGATACTTAGTACCTCATCGGATTAAACCGAAGTAACAGTAA
1 CAGTACGACACTCAGTACCTCATCGGATTAAACCGAAGTAACAGTAA
41245624 CAGTACGA
1 CAGTACGA
41245632 AACACAAGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 40 0.85
48 7 0.15
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (47 bp):
CAGTACGACACTCAGTACCTCATCGGATTAAACCGAAGTAACAGTAA
Found at i:41246581 original size:27 final size:27
Alignment explanation
Indices: 41246551--41246605 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
41246541 CGTTTGAATG
* *
41246551 ACTTCTGTT-GTTCTTTTTGTTTCTTTT
1 ACTTCTGTTCTTTC-TTTAGTTTCTTTT
*
41246578 ACTTCTTTTCTTTCTTTAGTTTCTTTT
1 ACTTCTGTTCTTTCTTTAGTTTCTTTT
41246605 A
1 A
41246606 TTTACTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.07, C:0.16, G:0.07, T:0.69
Consensus pattern (27 bp):
ACTTCTGTTCTTTCTTTAGTTTCTTTT
Found at i:41247018 original size:3 final size:3
Alignment explanation
Indices: 41247010--41247042 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
41247000 TTAATTTATT
*
41247010 TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
41247043 TAATCTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:41251994 original size:67 final size:66
Alignment explanation
Indices: 41251881--41252010 Score: 233
Period size: 67 Copynumber: 2.0 Consensus size: 66
41251871 AGATAAAGTA
41251881 AGACCAGAAGGTAATCTTGTCACGCACCCGTTCGATAGTTCCATATTAACCAATGAGGTCGGAAG
1 AGACCAGAAGGTAATCTTGTCACGCACCCGTTCGATAGTTCCATATTAACCAATGAGGT-GGAAG
41251946 AT
65 AT
* *
41251948 AGACCAGAAGGTAATCTTGTCATGCACCCGTTCGATAGTTCTATATTAACCAATGAGGTGGAA
1 AGACCAGAAGGTAATCTTGTCACGCACCCGTTCGATAGTTCCATATTAACCAATGAGGTGGAA
41252011 AATAAGCTAG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 4 0.07
67 57 0.93
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (66 bp):
AGACCAGAAGGTAATCTTGTCACGCACCCGTTCGATAGTTCCATATTAACCAATGAGGTGGAAGA
T
Found at i:41252650 original size:25 final size:25
Alignment explanation
Indices: 41252616--41252681 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
41252606 CCCATTTCAC
*
41252616 AGCTCATGTGAGCATTTACAGTCAT
1 AGCTCGTGTGAGCATTTACAGTCAT
*
41252641 AGCTCGTGTGAGCATTTACTGTCAT
1 AGCTCGTGTGAGCATTTACAGTCAT
*
41252666 AGCTTGTGTGAGCATT
1 AGCTCGTGTGAGCATT
41252682 GTTCCCGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (25 bp):
AGCTCGTGTGAGCATTTACAGTCAT
Found at i:41252771 original size:26 final size:27
Alignment explanation
Indices: 41252741--41252791 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
41252731 GAGTAAATGG
*
41252741 AAATGGTAATAT-GAAATGGATATACA
1 AAATGGTAATATGGAAATAGATATACA
* *
41252767 AAATGTTTATATGGAAATAGATATA
1 AAATGGTAATATGGAAATAGATATA
41252792 TGAAACGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (27 bp):
AAATGGTAATATGGAAATAGATATACA
Found at i:41252796 original size:13 final size:13
Alignment explanation
Indices: 41252773--41252849 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
41252763 TACAAAATGT
41252773 TTATATGGAAATAG
1 TTATAT-GAAATAG
* **
41252787 ATATATGAAACGG
1 TTATATGAAATAG
* *
41252800 TTATATGAAGTAT
1 TTATATGAAATAG
* *
41252813 TTATACGAAATAT
1 TTATATGAAATAG
*
41252826 TTATAAGAATATAG
1 TTATATGAA-ATAG
*
41252840 ATATATGAAA
1 TTATATGAAA
41252850 AATGACATTT
Statistics
Matches: 48, Mismatches: 14, Indels: 3
0.74 0.22 0.05
Matches are distributed among these distances:
13 33 0.69
14 15 0.31
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.35
Consensus pattern (13 bp):
TTATATGAAATAG
Found at i:41252876 original size:13 final size:13
Alignment explanation
Indices: 41252858--41252882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41252848 AAAATGACAT
41252858 TTGAAATGAATAC
1 TTGAAATGAATAC
41252871 TTGAAATGAATA
1 TTGAAATGAATA
41252883 TGTCAAATGT
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:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAAATGAATAC
Found at i:41256979 original size:40 final size:40
Alignment explanation
Indices: 41256924--41257221 Score: 442
Period size: 40 Copynumber: 7.5 Consensus size: 40
41256914 CGGATGATAA
* *
41256924 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
41256964 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
41257004 CCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
41257044 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
41257084 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41257124 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
41257164 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
41257204 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41257222 TACTTGGTTG
Statistics
Matches: 237, Mismatches: 17, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
39 18 0.08
40 217 0.92
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41257133 original size:120 final size:120
Alignment explanation
Indices: 41256920--41257221 Score: 520
Period size: 120 Copynumber: 2.5 Consensus size: 120
41256910 TATTCGGATG
41256920 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA
*
41256985 TTTGTGCGAGTTACTATATCCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTTGTACGAGTTACTATATCCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
41257040 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA
*
41257105 TTTGTACGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTTGTACGAGTTACTATATCCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
41257160 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT-AGCT-ATGTCC-GGCTAAATCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-CTAAT-TCCGGGCTAAGTCCCGAAGG
41257222 TACTTGGTTG
Statistics
Matches: 175, Mismatches: 5, Indels: 5
0.95 0.03 0.03
Matches are distributed among these distances:
119 18 0.10
120 157 0.90
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (120 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCA
TTTGTACGAGTTACTATATCCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:41259343 original size:3 final size:3
Alignment explanation
Indices: 41259335--41259362 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41259325 TTTTATTTAT
41259335 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41259363 AAGTGTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41260746 original size:18 final size:18
Alignment explanation
Indices: 41260704--41260747 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
41260694 ATTTTCATTC
41260704 TTTTATTACTATTGTTGT
1 TTTTATTACTATTGTTGT
** * *
41260722 TGCTATTTCTCTTGTTGT
1 TTTTATTACTATTGTTGT
41260740 TTTTATTA
1 TTTTATTA
41260748 TTTATATTAT
Statistics
Matches: 19, Mismatches: 7, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.14, C:0.09, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTATTACTATTGTTGT
Found at i:41260760 original size:21 final size:21
Alignment explanation
Indices: 41260736--41260812 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
41260726 ATTTCTCTTG
*
41260736 TTGTTTTTATTATTTATATTA
1 TTGTTTTTATTATTTATATCA
** *
41260757 TTGTTAGTATTA-TTAT-TCC
1 TTGTTTTTATTATTTATATCA
41260776 TTAGTTTATTATTATTT-TATCA
1 TT-GTTT-TTATTATTTATATCA
*
41260798 TTATTTTCTATTATT
1 TTGTTTT-TATTATT
41260813 GTTTTTATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
19 3 0.07
20 8 0.19
21 26 0.60
22 6 0.14
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.66
Consensus pattern (21 bp):
TTGTTTTTATTATTTATATCA
Found at i:41261108 original size:27 final size:26
Alignment explanation
Indices: 41261038--41261135 Score: 81
Period size: 27 Copynumber: 3.7 Consensus size: 26
41261028 ATTATTATCA
* * *
41261038 ATTTTAAATATTTTACATATATTATTT
1 ATTTTAAAT-TTTTATATGTAGTATTT
* * *
41261065 CTTTTAAATTATCATATGTAGTATTT
1 ATTTTAAATTTTTATATGTAGTATTT
*
41261091 ATTTTGAAATTTTTATATGTA-TCTTTGT
1 ATTTT-AAATTTTTATATGTAGT-ATT-T
*
41261119 ATTTTAAATTATTATAT
1 ATTTTAAATTTTTATAT
41261136 ATATACATAT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
26 17 0.30
27 34 0.60
28 6 0.11
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (26 bp):
ATTTTAAATTTTTATATGTAGTATTT
Found at i:41261385 original size:13 final size:12
Alignment explanation
Indices: 41261364--41261415 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 12
41261354 TTATACGCAA
41261364 TTTTAAATTATTC
1 TTTT-AATTATTC
*
41261377 TTTTGAATTATTA
1 TTTT-AATTATTC
41261390 TTTTAAGTTATTC
1 TTTTAA-TTATTC
41261403 TATTTATATTATT
1 T-TTTA-ATTATT
41261416 TTCTTATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 2 0.06
13 21 0.64
14 9 0.27
15 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (12 bp):
TTTTAATTATTC
Found at i:41262059 original size:127 final size:127
Alignment explanation
Indices: 41261835--41262191 Score: 407
Period size: 127 Copynumber: 2.8 Consensus size: 127
41261825 AAAAGGTGAA
** * * *
41261835 GTTTGATGTTTAGAAATTCGAGGGCTTGTGCCCTAATGTGTTGGGTTTCGATCTTTCGTTTGTTT
1 GTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGTTGGGTTTCGATCTTTCATTTGTCT
* * * *
41261900 AAATAATCAAATTTCCCTTTAAAATTTTGTCCGCGTTT-TCTAAACCTTAAAACAAAGGCAAT
66 AAATAATCAAATTTCCCTTTAAAACTTCGTCCGCATTTAT-TAAACCTTAAAACAAAAGCAAT
*
41261962 GTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGCTGGGTTTCGATCTTTCATTTGTCT
1 GTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGTTGGGTTTCGATCTTTCATTTGTCT
* * * * *
41262027 AAATAATCAGATTTCCCTTTTACACTTCGTCCGCATTTATTAAACTTTAAAACAAAAGCGAT
66 AAATAATCAAATTTCCCTTTAAAACTTCGTCCGCATTTATTAAACCTTAAAACAAAAGCAAT
* * * * * ** *
41262089 GATTGATGTTTGGCAATTC-AGGAAATCGTACCCTAATGTGTTGGGTTTCAAT-TTCTTGTTTAT
1 GTTTGATGTTTAGAAATTCGAGG-AATCGTGCCCTAATGTGTTGGGTTTCGATCTT-TCATTTGT
* ** *
41262152 CCAAATAATCAAACATCCCTTTAAAA-TTCCGTCCACATTT
64 CTAAATAATCAAATTTCCCTTTAAAACTT-CGTCCGCATTT
41262192 TTCTTCAAAA
Statistics
Matches: 195, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
126 7 0.04
127 187 0.96
128 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (127 bp):
GTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGTTGGGTTTCGATCTTTCATTTGTCT
AAATAATCAAATTTCCCTTTAAAACTTCGTCCGCATTTATTAAACCTTAAAACAAAAGCAAT
Found at i:41266534 original size:4 final size:4
Alignment explanation
Indices: 41266527--41266560 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
41266517 GCAGTAAAAA
*
41266527 AAAG AAAG AAAG AAAG AAAG AAA- AGAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
41266561 AAAACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 25 0.93
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:41266544 original size:12 final size:11
Alignment explanation
Indices: 41266524--41266563 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
41266514 AATGCAGTAA
41266524 AAAAAAGAAAG
1 AAAAAAGAAAG
41266535 AAAGAAAGAAAG
1 AAA-AAAGAAAG
*
41266547 AAAAGAGAAAG
1 AAAAAAGAAAG
41266558 AAAAAA
1 AAAAAA
41266564 ACAAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:41266569 original size:19 final size:19
Alignment explanation
Indices: 41266533--41266569 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41266523 AAAAAAAGAA
* *
41266533 AGAAAGAAAGAAAGAAAAG
1 AGAAAGAAAAAAACAAAAG
41266552 AGAAAGAAAAAAACAAAA
1 AGAAAGAAAAAAACAAAA
41266570 ACAACAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (19 bp):
AGAAAGAAAAAAACAAAAG
Found at i:41268244 original size:64 final size:64
Alignment explanation
Indices: 41268143--41268263 Score: 215
Period size: 64 Copynumber: 1.9 Consensus size: 64
41268133 TATATCATTC
* *
41268143 AGTTAGGAGCATTTGATTTATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCACATCT
1 AGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGACATAAGCATCACATCT
*
41268207 AGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGGCATAAGCAT
1 AGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGACATAAGCAT
41268264 AGATACATGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (64 bp):
AGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGACATAAGCATCACATCT
Found at i:41268689 original size:44 final size:44
Alignment explanation
Indices: 41268641--41268809 Score: 187
Period size: 44 Copynumber: 3.8 Consensus size: 44
41268631 AGCTATAAAC
** *
41268641 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-ATTTCAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAA-T
* * * *
41268685 CTTATTTCTCTGAAGTTGTAGTGGAGCAGACTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAAT
* * *
41268729 CTTATCTCCCCGAAGTTGCAGTGGGGCAGACTGAAGATAGTAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-TCAAT
* * * *
41268774 CTTATTTCCCTAAAGTTGCAGTGGAACAGATTGAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
41268810 CTAAATTACA
Statistics
Matches: 103, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
44 65 0.63
45 38 0.37
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAAT
Found at i:41270609 original size:3 final size:3
Alignment explanation
Indices: 41270367--41270591 Score: 81
Period size: 3 Copynumber: 75.3 Consensus size: 3
41270357 TAATATTTGC
* *
41270367 TAT TAT TAT TAT TAT TAT TAT TAT T-T TCAT TCT T-T TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* * ** * * * *
41270411 TGT TGT TGC TAT T-T CTCT TGT TGT TTT TAT TAT TAT T-T ATAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * * * *
41270456 TGT TAG TAT TAT TAT TCCT TAG T-T TAT TAT TAT TAT T-T TAT CAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
41270500 TAT TTT CTAT TAT TGT TAT TAT CAA TA- CAC TAT TAT TAT TCT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
41270545 TAAT GTAT TAT TAT TTT TGAC T-T TAT TTT TAT TA- TAT TAT TAC TAT
1 T-AT -TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41270591 T
1 T
41270592 GCTATCATCA
Statistics
Matches: 165, Mismatches: 40, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
2 13 0.08
3 138 0.84
4 13 0.08
5 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:41270846 original size:28 final size:28
Alignment explanation
Indices: 41270787--41270849 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
41270777 TATGTAGTAT
* * * *
41270787 TTATTTTGAAATTTTTATATGTATCTTT
1 TTATTTTGAAATTATTATATATATCATA
41270815 TTATTTT-AAATTATTATATATATACATA
1 TTATTTTGAAATTATTATATATAT-CATA
41270843 TTATTTT
1 TTATTTT
41270850 TTAAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (28 bp):
TTATTTTGAAATTATTATATATATCATA
Found at i:41271083 original size:13 final size:12
Alignment explanation
Indices: 41271062--41271113 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 12
41271052 TTATACGCAA
41271062 TTTTAAATTATTC
1 TTTT-AATTATTC
*
41271075 TTTTGAATTATTA
1 TTTT-AATTATTC
41271088 TTTTAAGTTATTC
1 TTTTAA-TTATTC
41271101 TATTTATATTATT
1 T-TTTA-ATTATT
41271114 TTCTTATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 2 0.06
13 21 0.64
14 9 0.27
15 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (12 bp):
TTTTAATTATTC
Found at i:41271717 original size:127 final size:127
Alignment explanation
Indices: 41271523--41271888 Score: 450
Period size: 127 Copynumber: 2.9 Consensus size: 127
41271513 TTTGTAAGAA
* * * *
41271523 AAAGGTGAAGTTTGATGTTTAGAAATTCGAGGGACCGTGCCCTAATGTGTTGGGTTTCGATCTTT
1 AAAGGCGATGTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGTTGGGTTTCGATCTTT
* * *
41271588 CGTTTGTTTAAATAATCAAATTTCCCTTTAAAATTTTGTCCGCGTTT-TCTAAACCTTAAAAC
66 CGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGTCCGCATTTAT-TAAACCTTAAAAC
*
41271650 AAAGGCGATGTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGCTGGGTTTCGATCTTT
1 AAAGGCGATGTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGTTGGGTTTCGATCTTT
* * * * * *
41271715 CGTTTGTCTAAATACTCAGATTTCCCTTTTAAACTTCGTTCGCATTTATTAAACTTTAAAAC
66 CGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGTCCGCATTTATTAAACCTTAAAAC
* * * * *
41271777 AAAAGCGATGATTGATGTTTGGCAATTC-AGGAAATTGTGCCCTAATGTGTTGGGTTTCGAT-TT
1 AAAGGCGATGTTTGATGTTTAGAAATTCGAGG-AATCGTGCCCTAATGTGTTGGGTTTCGATCTT
* * * ** * *
41271840 CTTGTTTATCCAAATAATCAAACATCCCTTTAAAATTCCGTCCACATTT
65 -TCGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGTCCGCATTT
41271889 TTCTTCAAAA
Statistics
Matches: 204, Mismatches: 32, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
126 5 0.02
127 198 0.97
128 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (127 bp):
AAAGGCGATGTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGTTGGGTTTCGATCTTT
CGTTTGTCTAAATAATCAAATTTCCCTTTAAAATTTCGTCCGCATTTATTAAACCTTAAAAC
Found at i:41273362 original size:33 final size:31
Alignment explanation
Indices: 41273323--41273409 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 31
41273313 TTAACCCATA
*
41273323 AATTGGTACTTAAACTATATTCTCTTTCTTTCAT
1 AATTGGTACTTAAACTATATT-T-TTT-TGTCAT
* *
41273357 -CTTGGTACTTAAAATA-ATTTTTTTGTCAT
1 AATTGGTACTTAAACTATATTTTTTTGTCAT
*
41273386 AAGTGGTACTTAAACTATATTTTT
1 AATTGGTACTTAAACTATATTTTT
41273410 CCGAAGTTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.11
30 16 0.36
31 7 0.16
32 3 0.07
33 14 0.31
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (31 bp):
AATTGGTACTTAAACTATATTTTTTTGTCAT
Found at i:41274164 original size:21 final size:20
Alignment explanation
Indices: 41274127--41274176 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
41274117 CCGACACTAT
*
41274127 AAAAGAAGAAGAAAGGAAGA
1 AAAAGAAAAAGAAAGGAAGA
* *
41274147 AAAAGCAAAAAGAGAGGAAAA
1 AAAAG-AAAAAGAAAGGAAGA
41274168 TAAAAGAAA
1 -AAAAGAAA
41274177 GGGAGAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 5 0.20
21 15 0.60
22 5 0.20
ACGTcount: A:0.72, C:0.02, G:0.24, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAGAAAGGAAGA
Found at i:41277578 original size:19 final size:19
Alignment explanation
Indices: 41277541--41277578 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41277531 CAAGTATCGA
*
41277541 TTTGGGTATCAATACATTT
1 TTTGGGTATCAATAAATTT
*
41277560 TTTGGGTATCGATAAATTT
1 TTTGGGTATCAATAAATTT
41277579 CTTCAAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.47
Consensus pattern (19 bp):
TTTGGGTATCAATAAATTT
Found at i:41280713 original size:18 final size:18
Alignment explanation
Indices: 41280690--41280753 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
41280680 CCTTCGTGAT
41280690 CTGAAGCCCGAAGTTTAG
1 CTGAAGCCCGAAGTTTAG
** * *
41280708 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT--TTAG
*
41280729 CGGAAGCCCGAAGTTTAG
1 CTGAAGCCCGAAGTTTAG
41280747 CTGAAGC
1 CTGAAGC
41280754 ACATAAGTGC
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
18 15 0.45
19 5 0.15
20 5 0.15
21 8 0.24
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.19
Consensus pattern (18 bp):
CTGAAGCCCGAAGTTTAG
Found at i:41280746 original size:39 final size:40
Alignment explanation
Indices: 41280692--41280948 Score: 384
Period size: 39 Copynumber: 6.6 Consensus size: 40
41280682 TTCGTGATCT
** *
41280692 GAAGCCCGAAGTTTAG-CTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAGACTGAAGCACAGAAGTGCTAAACG
** *
41280731 GAAGCCCGAAGTTTAG-CTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAGACTGAAGCACAGAAGTGCTAAACG
*
41280770 GAAGCCCGGAGGCTA-ACTGAAGCACAGAAGTGCTAAACG
1 GAAGCCCGAAGGCTAGACTGAAGCACAGAAGTGCTAAACG
41280809 GAAGCCCGAAGGCT-GACTGAAGCACAGAAGTGCTAAACG
1 GAAGCCCGAAGGCTAGACTGAAGCACAGAAGTGCTAAACG
*
41280848 GAAGCCCGAAGGC-CGACTGAAGCACAGAAGTGCTAAACG
1 GAAGCCCGAAGGCTAGACTGAAGCACAGAAGTGCTAAACG
*
41280887 GAAGCCCGAAGGCT-GACTGAAGCATAGAAGTGCTAAACG
1 GAAGCCCGAAGGCTAGACTGAAGCACAGAAGTGCTAAACG
41280926 GAAGCCCGAAGGCTA-ACTGAAGC
1 GAAGCCCGAAGGCTAGACTGAAGC
41280949 TCACCAGAGC
Statistics
Matches: 207, Mismatches: 6, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
39 207 1.00
ACGTcount: A:0.36, C:0.23, G:0.29, T:0.12
Consensus pattern (40 bp):
GAAGCCCGAAGGCTAGACTGAAGCACAGAAGTGCTAAACG
Found at i:41291006 original size:17 final size:16
Alignment explanation
Indices: 41290983--41291030 Score: 78
Period size: 17 Copynumber: 2.9 Consensus size: 16
41290973 AAATTTTTTA
41290983 AAAATTAAAAAATATT
1 AAAATTAAAAAATATT
41290999 AAATATTAAAAATATATT
1 AAA-ATTAAAAA-ATATT
41291017 AAAATTAAAAAATA
1 AAAATTAAAAAATA
41291031 ATTCTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.20
17 16 0.53
18 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTAAAAAATATT
Found at i:41291863 original size:54 final size:54
Alignment explanation
Indices: 41291805--41291908 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
41291795 GGCATAGGTT
* * *
41291805 TATGATTCTTTTTTGTATTAAAGTA-TATGATAGGTTTAGATTTATTTGTTGAAA
1 TATGATTATTATTTGTATCAAAG-AGTATGATAGGTTTAGATTTATTTGTTGAAA
* * *
41291859 TATGATTATTATTTGTATCAAAGAGTATGGTAGGTTTGGATTTTTTTGTT
1 TATGATTATTATTTGTATCAAAGAGTATGATAGGTTTAGATTTATTTGTT
41291909 ATTGTCTATC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.02
54 42 0.98
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.52
Consensus pattern (54 bp):
TATGATTATTATTTGTATCAAAGAGTATGATAGGTTTAGATTTATTTGTTGAAA
Found at i:41292095 original size:128 final size:128
Alignment explanation
Indices: 41291816--41292349 Score: 732
Period size: 128 Copynumber: 4.2 Consensus size: 128
41291806 ATGATTCTTT
* **
41291816 TTTGTATTAAAGTATATGATAGGTTT-AGATTTATTTGTTGAAATATGATTATTATTTGTATCAA
1 TTTGTATTAAAGTGTATGGCAGGTTTGA-ATTTATTTGTTGAAATATGATTATTATTTGTATCAA
* * * * * *
41291880 AGAGTATGGTAGGTTTGGATTTTTTTG-TTATTGTCTATCACGTGCATCACATAAATGGATTTG
65 AGAGTATGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGCATCACATAAATGGATTTG
* *
41291943 TTTGTGTTAAAGTGTATGGCAGGTTTGAATTTATTTGTTAAAATATGATTATTATTTGTATCAAA
1 TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTATTATTTGTATCAAA
* * *
41292008 GAGTAAGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGTATCAAATAAATGGATTTG
66 GAGTATGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGCATCACATAAATGGATTTG
* *
41292071 TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTTTTTTTTGTATCAAA
1 TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTATTATTTGTATCAAA
* ** ** *
41292136 GAGTATGGCATGTTCGGATTTCTTTGGCTATTGTCTGTCATGTACATCACATAAATGGATTTG
66 GAGTATGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGCATCACATAAATGGATTTG
** *
41292199 TTTGTATTAAAGTGTATGATAGGTTTGAATTTATTTGTTGAAATATGATTATTGTTTGTATCAAA
1 TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTATTATTTGTATCAAA
* * * *
41292264 GAGTATGACAAGTTTAGATTTCTTT-AGTTATTGTCTGTCATGTGTATCACATAAATAGATTTA
66 GAGTATGGCAAGTTTAGATTTCTTTGA-TTATTGTCTGTCATGTGCATCACATAAATGGATTTG
**
41292327 TTCATATTATAAAGTGTATGGCA
1 TTTGTA-T-TAAAGTGTATGGCA
41292350 TGTGCGTAAT
Statistics
Matches: 357, Mismatches: 45, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
127 79 0.22
128 265 0.74
129 1 0.00
130 12 0.03
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (128 bp):
TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTATTATTTGTATCAAA
GAGTATGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGCATCACATAAATGGATTTG
Found at i:41296274 original size:22 final size:22
Alignment explanation
Indices: 41296249--41296293 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41296239 TTTAATAAAG
41296249 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
41296271 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
41296293 A
1 A
41296294 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:41300047 original size:22 final size:22
Alignment explanation
Indices: 41300022--41300066 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41300012 TTTAATAAAG
41300022 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
41300044 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
41300066 A
1 A
41300067 CATGATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:41302729 original size:161 final size:161
Alignment explanation
Indices: 41302552--41302861 Score: 494
Period size: 161 Copynumber: 1.9 Consensus size: 161
41302542 TGATATTAAT
* * *
41302552 AAATTAAAAAAATTCATGTTAGTATTTTAATCAAAATAAAATATTTAAATTGATTAATGACATTG
1 AAATTAAAAAAATTCATGTTAGCATTTTAATCAAAATAAAATATTTAAATTAATTAATGACATTA
* *
41302617 TAAAAAATTAATGTATAAAGAATAAAATTTAAATTAAATATAAGATAAGGACTAAAACTGAATTG
66 TAAAAAATTAATGTATAAAAAATAAAATTTAAATTAAATATAAGATAAGGACTAAAACTAAATTG
* * *
41302682 TAACGATTGCTTTATAATCTTAAGAAAATGC
131 TAACCATTACTGTATAATCTTAAGAAAATGC
* *
41302713 AAATTTAAAAAATTCATGTTAGCATTTTAATTAAAATAAAATATTTAAATTAATTAATGACATTA
1 AAATTAAAAAAATTCATGTTAGCATTTTAATCAAAATAAAATATTTAAATTAATTAATGACATTA
* * * *
41302778 TAAAAAATTAATGTATAAAAAATAAATTTTAAGTTGAATATAAGATAAGGACTAAAACTAAATTT
66 TAAAAAATTAATGTATAAAAAATAAAATTTAAATTAAATATAAGATAAGGACTAAAACTAAATTG
41302843 TAACCATTACTGTATAATC
131 TAACCATTACTGTATAATC
41302862 CTAACAAGAT
Statistics
Matches: 135, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
161 135 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (161 bp):
AAATTAAAAAAATTCATGTTAGCATTTTAATCAAAATAAAATATTTAAATTAATTAATGACATTA
TAAAAAATTAATGTATAAAAAATAAAATTTAAATTAAATATAAGATAAGGACTAAAACTAAATTG
TAACCATTACTGTATAATCTTAAGAAAATGC
Found at i:41319591 original size:20 final size:20
Alignment explanation
Indices: 41319566--41319605 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41319556 CTGTTTTTAC
41319566 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
41319586 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
41319606 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:41319610 original size:16 final size:18
Alignment explanation
Indices: 41319561--41319605 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
41319551 AAAAGCTGTT
* *
41319561 TTTACATATATTAATAAA
1 TTTATATATTTTAATAAA
41319579 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
41319599 TTTATAT
1 TTTATAT
41319606 TTTAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:41325009 original size:171 final size:170
Alignment explanation
Indices: 41324805--41325138 Score: 446
Period size: 171 Copynumber: 1.9 Consensus size: 170
41324795 AGATTTAAGT
* *
41324805 GAAACGAAACAACAGCCCTGAGAAGAGAAGATATGCGACAGACA-CTAAGG-AAAACGAAAA-TA
1 GAAACGAAACAACAGCCCTAAGAAGAGAAGATATGCGA-A-A-AGCTAAGGAAAAAAGAAAATTA
*
41324867 AAAGATGACCAACAGAAGAAGTAGAAGGAAAAAAGTTACCTAGATGAAGAAGAAGGAAGATGAAG
63 AAAGATGAACAACAGAAGAAGTAGAAGG---AAAG-TACCTAGATGAAGAAGAAGGAAGATGAAG
* * *
41324932 TAC-G-GCTA-GGAAAGATTGGTGAGAGTTGGAAAATGTTACAGAGC
124 AACAGCGCAAGGGAAAGATTAGTGAGAGTTGGAAAATGTTACAGAGC
*
41324976 GAAACGAAACAGCAGCCCTAAGAAGAGAAGATATGCGAAAAGCTAAGGAAAAAAGAAAATTAAAA
1 GAAACGAAACAACAGCCCTAAGAAGAGAAGATATGCGAAAAGCTAAGGAAAAAAGAAAATTAAAA
* * * *
41325041 GATGAAGAACAGAAGAAGTAGGAGGAAAGTACCTGGATGATGAAGAAGGAAGATGAAGAACAGCG
66 GATGAACAACAGAAGAAGTAGAAGGAAAGTACCTAGATGAAGAAGAAGGAAGATGAAGAACAGCG
41325106 CAAGGGGGAAAGATTAGTGAGAGTTGGAAAATG
131 CAA--GGGAAAGATTAGTGAGAGTTGGAAAATG
41325139 CCTTACAAAA
Statistics
Matches: 144, Mismatches: 11, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
167 29 0.20
168 6 0.04
169 10 0.07
170 10 0.07
171 63 0.44
172 26 0.18
ACGTcount: A:0.49, C:0.10, G:0.29, T:0.12
Consensus pattern (170 bp):
GAAACGAAACAACAGCCCTAAGAAGAGAAGATATGCGAAAAGCTAAGGAAAAAAGAAAATTAAAA
GATGAACAACAGAAGAAGTAGAAGGAAAGTACCTAGATGAAGAAGAAGGAAGATGAAGAACAGCG
CAAGGGAAAGATTAGTGAGAGTTGGAAAATGTTACAGAGC
Found at i:41335708 original size:34 final size:34
Alignment explanation
Indices: 41335665--41335740 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
41335655 TTACATACTG
41335665 TACTGAAATGGGCT-AAGGCCCAAACTGTCACTAA
1 TACTGAAATGGGCTCAA-GCCCAAACTGTCACTAA
* * **
41335699 TACTGAAATGGGCTCAAGCCCAGACTGTTACTGC
1 TACTGAAATGGGCTCAAGCCCAAACTGTCACTAA
41335733 TACTGAAA
1 TACTGAAA
41335741 GAGGGGCTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (34 bp):
TACTGAAATGGGCTCAAGCCCAAACTGTCACTAA
Found at i:41341002 original size:38 final size:38
Alignment explanation
Indices: 41340951--41341027 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
41340941 AGCTAGCCCA
41340951 AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
1 AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
41340989 AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
1 AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
41341027 A
1 A
41341028 CCATTTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (38 bp):
AGTACTAATTCATAATACTGTCAAATTTTTGAAAATTT
Found at i:41342369 original size:28 final size:28
Alignment explanation
Indices: 41342329--41342427 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
41342319 GTGTTTCTTG
41342329 TTTTTTAGATTTTATAATTTTGCCCCTA
1 TTTTTTAGATTTTATAATTTTGCCCCTA
* **
41342357 TTTTTTGGATTTTATAATTTTGCCTATA
1 TTTTTTAGATTTTATAATTTTGCCCCTA
* **
41342385 TTTTTTTAGATTTTATAGTTTTTTCCCTA
1 -TTTTTTAGATTTTATAATTTTGCCCCTA
41342414 TTTTTTAGATTTTA
1 TTTTTTAGATTTTA
41342428 CAAAATTTCC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 39 0.64
29 22 0.36
ACGTcount: A:0.20, C:0.09, G:0.08, T:0.63
Consensus pattern (28 bp):
TTTTTTAGATTTTATAATTTTGCCCCTA
Found at i:41342443 original size:28 final size:27
Alignment explanation
Indices: 41342329--41342445 Score: 101
Period size: 28 Copynumber: 4.1 Consensus size: 27
41342319 GTGTTTCTTG
* *
41342329 TTTTTTAGATTTTATAATTTTGCCCCTA
1 TTTTTTAGATTTTAAAATTTT-CCCTTA
* * *
41342357 TTTTTTGGATTTTATAATTTTGCCTATA
1 TTTTTTAGATTTTAAAATTTTCCCT-TA
**
41342385 TTTTTTTAGATTTTATAGTTTTTTCCC-TA
1 -TTTTTTAGATTTTA-A-AATTTTCCCTTA
*
41342414 TTTTTTAGATTTTACAAAATTTCCCTTA
1 TTTTTTAGATTTTA-AAATTTTCCCTTA
41342442 TTTT
1 TTTT
41342446 CCAAATTTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
27 8 0.11
28 43 0.60
29 15 0.21
31 6 0.08
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (27 bp):
TTTTTTAGATTTTAAAATTTTCCCTTA
Found at i:41342444 original size:57 final size:57
Alignment explanation
Indices: 41342329--41342445 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
41342319 GTGTTTCTTG
* * * *
41342329 TTTTTTAGATTTTATAATTTTGCCCCTATTTTTTGGATTTTATAATTTTGCCTATAT
1 TTTTTTAGATTTTATAATTTTGCCCCTATTTTTTAGATTTTAAAAATTTCCCTATAT
* **
41342386 TTTTTTAGATTTTATAGTTTTTTCCCTATTTTTTAGATTTTACAAAATTTCCCT-TAT
1 TTTTTTAGATTTTATAATTTTGCCCCTATTTTTTAGATTTTA-AAAATTTCCCTATAT
41342443 TTT
1 TTT
41342446 CCAAATTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
57 44 0.85
58 8 0.15
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (57 bp):
TTTTTTAGATTTTATAATTTTGCCCCTATTTTTTAGATTTTAAAAATTTCCCTATAT
Found at i:41343088 original size:89 final size:90
Alignment explanation
Indices: 41342976--41343190 Score: 335
Period size: 90 Copynumber: 2.4 Consensus size: 90
41342966 CCTGCAAATA
* *** *
41342976 TGTTGTGCATCTACAATGTAGTGGCAGATTTTATCTGTGATATTTTGCTGTGTACCCACAGCC-A
1 TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCTGCGATATTTTGCTGTGTACCCACAGCCTA
41343040 GTGACAGGTTTCATCTGC-GAATTTT
66 GTGACAGGTTTCATCT-CTGAATTTT
* * *
41343065 TGTTGTGTATTCACAGCCTAGTGGCAAATTTTATCTGCGATATTTTGCTGTGTACCCACAGCCTA
1 TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCTGCGATATTTTGCTGTGTACCCACAGCCTA
41343130 GTGACAGGTTTCATCTCTGAATTTT
66 GTGACAGGTTTCATCTCTGAATTTT
41343155 TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCT
1 TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCT
41343191 ATGAAACCAG
Statistics
Matches: 113, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
89 56 0.50
90 57 0.50
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (90 bp):
TGTTGTGCATCCACAGCCTAGTGGCAGATTTTATCTGCGATATTTTGCTGTGTACCCACAGCCTA
GTGACAGGTTTCATCTCTGAATTTT
Found at i:41343111 original size:45 final size:45
Alignment explanation
Indices: 41342994--41343190 Score: 213
Period size: 45 Copynumber: 4.4 Consensus size: 45
41342984 ATCTACAATG
*
41342994 TAGTGGCAGATTTTATCTGTG-ATATTTTGCTGTGTACCCACAGCC
1 TAGTGGCAGATTTTATCTGCGAAT-TTTTGCTGTGTACCCACAGCC
* * * * **
41343039 -AGTGACAGGTTTCATCTGCGAATTTTTGTTGTGTATTCACAGCC
1 TAGTGGCAGATTTTATCTGCGAATTTTTGCTGTGTACCCACAGCC
*
41343083 TAGTGGCAAATTTTATCTGCG-ATATTTTGCTGTGTACCCACAGCC
1 TAGTGGCAGATTTTATCTGCGAAT-TTTTGCTGTGTACCCACAGCC
* * * * * *
41343128 TAGTGACAGGTTTCATCT-CTGAATTTTTGTTGTGCATCCACAGCC
1 TAGTGGCAGATTTTATCTGC-GAATTTTTGCTGTGTACCCACAGCC
41343173 TAGTGGCAGATTTTATCT
1 TAGTGGCAGATTTTATCT
41343191 ATGAAACCAG
Statistics
Matches: 123, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
44 37 0.30
45 84 0.68
46 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (45 bp):
TAGTGGCAGATTTTATCTGCGAATTTTTGCTGTGTACCCACAGCC
Found at i:41343800 original size:20 final size:20
Alignment explanation
Indices: 41343775--41343815 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41343765 AACAAAGTAA
41343775 AAAAAAATCACTTTTCCGCT
1 AAAAAAATCACTTTTCCGCT
41343795 AAAAAAATCACTTTTCCGCT
1 AAAAAAATCACTTTTCCGCT
41343815 A
1 A
41343816 CTAGATTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAATCACTTTTCCGCT
Found at i:41346668 original size:48 final size:46
Alignment explanation
Indices: 41346461--41346668 Score: 163
Period size: 46 Copynumber: 4.4 Consensus size: 46
41346451 TGTCATATCT
* * ** * *
41346461 CAGACACGATCTTACACTAGCTTATATCTC-AAGTCGAAGCCATGTCC
1 CAGACATG-TCTTACACTAGCCTACGTCTCGAAGCCGATG-CATGTCC
* * * * * *
41346508 CAGACATGGTCTTACACT-GACTACCATCTTGTAGTCGACGCATGTCC
1 CAGACAT-GTCTTACACTAGCCTA-CGTCTCGAAGCCGATGCATGTCC
* * *
41346555 CAGACATGTCTTACACTGGCTTACGTCTCGAAGCCGATGTATGTCC
1 CAGACATGTCTTACACTAGCCTACGTCTCGAAGCCGATGCATGTCC
* *
41346601 CAGACATGTCTTACACTAGCACT-CGTCTC-AATTCCGATGCCATGTCG
1 CAGACATGTCTTACACTAGC-CTACGTCTCGAA-GCCGATG-CATGTCC
41346648 CAGACATGGTCTTACACTAGC
1 CAGACAT-GTCTTACACTAGC
41346669 TCTCACAAAT
Statistics
Matches: 133, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
45 2 0.02
46 61 0.46
47 49 0.37
48 21 0.16
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (46 bp):
CAGACATGTCTTACACTAGCCTACGTCTCGAAGCCGATGCATGTCC
Found at i:41350298 original size:29 final size:29
Alignment explanation
Indices: 41350237--41350352 Score: 144
Period size: 29 Copynumber: 4.0 Consensus size: 29
41350227 TACCTGTATC
* *
41350237 TGGCCCACCAGGCCC-AATCACATTTGTA
1 TGGCCCATCAGGCCCAAATCACATTTATA
* * * **
41350265 TGGCCCATTAGGCCTAATTTGCATTTATA
1 TGGCCCATCAGGCCCAAATCACATTTATA
*
41350294 TGGCCCATCAGACCCAAATCACATTTATA
1 TGGCCCATCAGGCCCAAATCACATTTATA
*
41350323 TGGCCCATCAGGCCCAAATCACATTCATA
1 TGGCCCATCAGGCCCAAATCACATTTATA
41350352 T
1 T
41350353 TCATGCTCGC
Statistics
Matches: 72, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
28 12 0.17
29 60 0.83
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
TGGCCCATCAGGCCCAAATCACATTTATA
Found at i:41350591 original size:24 final size:24
Alignment explanation
Indices: 41350564--41350614 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
41350554 GTAGCCAAAC
*
41350564 TTTCGACTTTTCGGCATTTCAGCT
1 TTTCGACTTTTCAGCATTTCAGCT
41350588 TTTCGACTTTTCAGCATTTCAGCT
1 TTTCGACTTTTCAGCATTTCAGCT
41350612 TTT
1 TTT
41350615 GCCGATCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.49
Consensus pattern (24 bp):
TTTCGACTTTTCAGCATTTCAGCT
Found at i:41351293 original size:4 final size:4
Alignment explanation
Indices: 41351284--41351308 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
41351274 ATATTTATAC
41351284 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
41351309 CACCTACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:41363577 original size:28 final size:28
Alignment explanation
Indices: 41363522--41363579 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
41363512 TACAGGGGTT
*
41363522 TTCACACGGCCTGTCACACGCCCGTGTCC
1 TTCACACGGCCTG-CACACACCCGTGTCC
*
41363551 TTCACACGGCCATG-ACACACTCGTGTCC
1 TTCACACGGCC-TGCACACACCCGTGTCC
41363579 T
1 T
41363580 AGCCCCTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 11 0.42
30 2 0.08
ACGTcount: A:0.17, C:0.41, G:0.19, T:0.22
Consensus pattern (28 bp):
TTCACACGGCCTGCACACACCCGTGTCC
Found at i:41364667 original size:46 final size:46
Alignment explanation
Indices: 41364584--41364700 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
41364574 AAGTTGAAGC
* *
41364584 CATGTCACAGACATGGTCTTACACTGACTATCATCTTGTA-GCCGACG
1 CATGTCCCAGACAT-GTCTTACACTGACTATCATCTTG-AGGCCGACA
* * *
41364631 CATGTCCCAGACATGTCTTACACTGGCT-TACGTCTTGAGGCCGATA
1 CATGTCCCAGACATGTCTTACACTGACTAT-CATCTTGAGGCCGACA
*
41364677 CATGTCCCAAACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
41364701 AGCACTCGTC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
45 2 0.03
46 47 0.76
47 13 0.21
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGACTATCATCTTGAGGCCGACA
Found at i:41367093 original size:46 final size:47
Alignment explanation
Indices: 41367035--41367166 Score: 164
Period size: 46 Copynumber: 2.8 Consensus size: 47
41367025 ATCTCGTAGT
* * *
41367035 CGATGCATGTCCCAAACATGTCTTATACTAGCTTA-T-GTCTTAAGGC
1 CGATGCATGTCCCAAACATGTCTTACACTAGC-TACTCATCTCAAGGC
* *
41367081 CGATGCATGTCCCAGACATGTCTTACACTAGC-ACTCATCTCAATGC
1 CGATGCATGTCCCAAACATGTCTTACACTAGCTACTCATCTCAAGGC
41367127 CGATGCCATGTCCCAAACATGGTCTTACACTAGCT-CTCAT
1 CGATG-CATGTCCCAAACAT-GTCTTACACTAGCTACTCAT
41367167 AATGTATCCA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 42 0.56
47 13 0.17
48 18 0.24
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.29
Consensus pattern (47 bp):
CGATGCATGTCCCAAACATGTCTTACACTAGCTACTCATCTCAAGGC
Found at i:41367131 original size:92 final size:94
Alignment explanation
Indices: 41366987--41367161 Score: 245
Period size: 92 Copynumber: 1.9 Consensus size: 94
41366977 GTATATCTGT
* *
41366987 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACATATCTCGTAGTCGATG-CATGTCCCAAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACATATCTCATAGCCGATGCCATGTCCCAAA
*
41367051 CAT-GTCTTATACTAGCTTATGTCTTAAG
66 CATGGTCTTACACTAGCTTATGTCTTAAG
41367079 GCCGATG-CATGTCCCAGACAT-GTCTTACACT-AGCACTCATCTCA-ATGCCGATGCCATGTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CA-T-ATCTCATA-GCCGATGCCATGTCC
41367140 CAAACATGGTCTTACACTAGCT
62 CAAACATGGTCTTACACTAGCT
41367162 CTCATAATGT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
89 1 0.01
90 12 0.16
91 16 0.22
92 18 0.24
93 14 0.19
94 13 0.18
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (94 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGACATATCTCATAGCCGATGCCATGTCCCAAA
CATGGTCTTACACTAGCTTATGTCTTAAG
Found at i:41367184 original size:47 final size:47
Alignment explanation
Indices: 41367037--41367208 Score: 158
Period size: 46 Copynumber: 3.7 Consensus size: 47
41367027 CTCGTAGTCG
* * * * *
41367037 ATGCATGTCCCAAACAT-GTCTTATACTAGCT-T-ATGTCTTAAGGCCG
1 ATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC--AATGCCA
* * *
41367083 ATGCATGTCCCAGACAT-GTCTTACACTAGCACTCATCTCAATGCCG
1 ATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCA
* **
41367129 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATAATGTAT-CCA
1 ATG-CATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATCAATGCCA
*
41367177 ATGCATGTCCCAGACATGG-CTTACTCTAGCTC
1 ATGCATGTCCCAGACATGGTCTTACACTAGCTC
41367209 ACACAAGTGA
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
46 49 0.45
47 29 0.27
48 27 0.25
49 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (47 bp):
ATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCA
Found at i:41374205 original size:28 final size:28
Alignment explanation
Indices: 41374164--41374243 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 28
41374154 CATACATGCT
* *
41374164 TATGGTCCACTAGGCCCAATCTCAT-TCA
1 TATGGCCCACTAGGCCCAATCACATCT-A
*
41374192 TATGGCCCATTAGGCCCAAATCACATCTA
1 TATGGCCCACTAGGCCC-AATCACATCTA
41374221 TATGGCCCACTAGGCCCAATCAC
1 TATGGCCCACTAGGCCCAATCAC
41374244 TTTTACAGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.46
29 24 0.52
30 1 0.02
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATCTA
Found at i:41374224 original size:29 final size:28
Alignment explanation
Indices: 41374164--41374243 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 28
41374154 CATACATGCT
* *
41374164 TATGGTCCACTAGGCCCAATCTCATTCA
1 TATGGCCCACTAGGCCCAATCACATTCA
*
41374192 TATGGCCCATTAGGCCCAAATCACA-TCTA
1 TATGGCCCACTAGGCCC-AATCACATTC-A
41374221 TATGGCCCACTAGGCCCAATCAC
1 TATGGCCCACTAGGCCCAATCAC
41374244 TTTTACAGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 23 0.50
29 23 0.50
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATTCA
Found at i:41377196 original size:21 final size:21
Alignment explanation
Indices: 41377166--41377212 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
41377156 ACACCAACTA
41377166 AATTAAAAGAACTTAAAAT-AC
1 AATTAAAAGAAC-TAAAATCAC
* *
41377187 AATTATAAGAACTCAAATCAC
1 AATTAAAAGAACTAAAATCAC
41377208 AATTA
1 AATTA
41377213 CAATAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (21 bp):
AATTAAAAGAACTAAAATCAC
Found at i:41379786 original size:40 final size:41
Alignment explanation
Indices: 41379707--41379791 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 41
41379697 TGAATCCATG
41379707 AAAAGGTTGAAAAGGAAGTTATCTGAAAAGGATAGCAAATA
1 AAAAGGTTGAAAAGGAAGTTATCTGAAAAGGATAGCAAATA
* * *
41379748 AAAAGGTTGAAAAGGATG-TAT-TCGAAAAGGATATCAAATG
1 AAAAGGTTGAAAAGGAAGTTATCT-GAAAAGGATAGCAAATA
41379788 AAAA
1 AAAA
41379792 TGCTGTAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 1 0.03
40 22 0.55
41 17 0.43
ACGTcount: A:0.52, C:0.05, G:0.24, T:0.20
Consensus pattern (41 bp):
AAAAGGTTGAAAAGGAAGTTATCTGAAAAGGATAGCAAATA
Found at i:41379802 original size:40 final size:41
Alignment explanation
Indices: 41379704--41379834 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 41
41379694 TTTTGAATCC
* * *
41379704 ATGAAAAGGTTGAAAAGGA-AGTTATCTGAAAAGGATAGCAA
1 ATGAAAAGGCTGAAAAGGATAG-TATCCGAAAAGGATAACAA
* * * *
41379745 ATAAAAAGGTTGAAAAGGAT-GTATTCGAAAAGGATATCAA
1 ATGAAAAGGCTGAAAAGGATAGTATCCGAAAAGGATAACAA
* * * * *
41379785 ATGAAAATGCTGTAAAGGATATTATCCAAAAAGGGTAACAA
1 ATGAAAAGGCTGAAAAGGATAGTATCCGAAAAGGATAACAA
41379826 ATGAAAAGG
1 ATGAAAAGG
41379835 GTGTGTTTGA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
40 32 0.43
41 42 0.57
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.21
Consensus pattern (41 bp):
ATGAAAAGGCTGAAAAGGATAGTATCCGAAAAGGATAACAA
Found at i:41387130 original size:13 final size:14
Alignment explanation
Indices: 41387109--41387137 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41387099 TGAAAAATGG
41387109 ATTAGAAAATATTT
1 ATTAGAAAATATTT
41387123 ATTA-AAAATATTT
1 ATTAGAAAATATTT
41387136 AT
1 AT
41387138 GAAGTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:41388216 original size:15 final size:15
Alignment explanation
Indices: 41388172--41388218 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
41388162 GAATTTATCA
41388172 AATTTATATTGATTG
1 AATTTATATTGATTG
* * * *
41388187 AAATCATTTTAATTG
1 AATTTATATTGATTG
41388202 AATTTATATTGATTG
1 AATTTATATTGATTG
41388217 AA
1 AA
41388219 ATATAATATA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (15 bp):
AATTTATATTGATTG
Found at i:41393430 original size:55 final size:56
Alignment explanation
Indices: 41393356--41393478 Score: 142
Period size: 55 Copynumber: 2.2 Consensus size: 56
41393346 GTTAATTTAA
* * *
41393356 CAGGTTCGACCA-TGATTCTTCCACATGGGCGTGTCGAACGCCCATGCAGTTTTGG
1 CAGGCTCGACCACTGATTCTTCCACACGGGCATGTCGAACGCCCATGCAGTTTTGG
* * ** **
41393411 CAGGCTCGACCACTG-TTCTTCCACACGGGCATGTCGCATGCCTGTGTTGTTTTGG
1 CAGGCTCGACCACTGATTCTTCCACACGGGCATGTCGAACGCCCATGCAGTTTTGG
*
41393466 CAGGCTCAACCAC
1 CAGGCTCGACCAC
41393479 GGCCATATCG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 55 0.96
56 2 0.04
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.27
Consensus pattern (56 bp):
CAGGCTCGACCACTGATTCTTCCACACGGGCATGTCGAACGCCCATGCAGTTTTGG
Found at i:41403748 original size:16 final size:16
Alignment explanation
Indices: 41403720--41403758 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
41403710 GTTGGGAAGC
*
41403720 ATGTTATTGAATGCTTA
1 ATGTTAATGAATG-TTA
41403737 AT-TTAATGAATGTTA
1 ATGTTAATGAATGTTA
41403752 ATGTTAA
1 ATGTTAA
41403759 GTTTAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 13 0.65
17 2 0.10
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (16 bp):
ATGTTAATGAATGTTA
Found at i:41405177 original size:25 final size:25
Alignment explanation
Indices: 41405149--41405230 Score: 130
Period size: 25 Copynumber: 3.3 Consensus size: 25
41405139 GAAGTTATCC
41405149 AAAAAGGATAA-AAATGAAAAGGTT
1 AAAAAGGATAACAAATGAAAAGGTT
*
41405173 AAAAAGGATAACAAATGAAAGGGTT
1 AAAAAGGATAACAAATGAAAAGGTT
*
41405198 AAAAAGGATAACAAATTAAAAGGTT
1 AAAAAGGATAACAAATGAAAAGGTT
*
41405223 GAAAAGGA
1 AAAAAGGA
41405231 AGTATCTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 11 0.21
25 42 0.79
ACGTcount: A:0.60, C:0.02, G:0.22, T:0.16
Consensus pattern (25 bp):
AAAAAGGATAACAAATGAAAAGGTT
Found at i:41405244 original size:40 final size:40
Alignment explanation
Indices: 41405199--41405339 Score: 183
Period size: 40 Copynumber: 3.5 Consensus size: 40
41405189 GAAAGGGTTA
* *
41405199 AAAAGGATAACAAATTAAAAGGTTGAAAAGGAAGTATCTG
1 AAAAGGATAACAAATGAAAAGGTTGAAAAGGAAGTAACTG
* * * *
41405239 AAAAGGATAACAGATGAAAAGGTTGAAAAGGATGTACCCG
1 AAAAGGATAACAAATGAAAAGGTTGAAAAGGAAGTAACTG
* * *
41405279 AAAAGGATATCAAATGAAAATGTTGAAAAGGATATTAACTG
1 AAAAGGATAACAAATGAAAAGGTTGAAAAGGA-AGTAACTG
*
41405320 AAAAGGGTAACAAATGAAAA
1 AAAAGGATAACAAATGAAAA
41405340 TGATGTGTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 64 0.74
41 22 0.26
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.18
Consensus pattern (40 bp):
AAAAGGATAACAAATGAAAAGGTTGAAAAGGAAGTAACTG
Found at i:41405493 original size:21 final size:21
Alignment explanation
Indices: 41405469--41405508 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41405459 ATATATTGAG
* *
41405469 ATATTATGCATGATATGTTAC
1 ATATTATGAATAATATGTTAC
41405490 ATATTATGAATAATATGTT
1 ATATTATGAATAATATGTT
41405509 CTTATATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
ATATTATGAATAATATGTTAC
Done.