Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 77 of 82
Found at i:28868189 original size:12 final size:13
Alignment explanation
Indices: 28868172--28868200 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28868162 CCATCACTTT
28868172 AAAAAAGAAAAA-
1 AAAAAAGAAAAAG
28868184 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
28868197 AAAA
1 AAAA
28868201 TCCATAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:28878516 original size:16 final size:16
Alignment explanation
Indices: 28878495--28878529 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28878485 GGACAGAGGG
* *
28878495 GAGAGGGGAGAGGGGA
1 GAGAGGAGAGAGGAGA
28878511 GAGAGGAGAGAGGAGA
1 GAGAGGAGAGAGGAGA
28878527 GAG
1 GAG
28878530 TAGAGAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (16 bp):
GAGAGGAGAGAGGAGA
Found at i:28878528 original size:7 final size:7
Alignment explanation
Indices: 28878489--28878536 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
28878479 AGGAAAGGAC
*
28878489 AGAGGGG
1 AGAGAGG
*
28878496 AGAGGGG
1 AGAGAGG
*
28878503 AGAGGGG
1 AGAGAGG
28878510 AGAGAGG
1 AGAGAGG
28878517 AGAGAGG
1 AGAGAGG
*
28878524 AGAGAGT
1 AGAGAGG
28878531 AGAGAG
1 AGAGAG
28878537 AAGTGTGAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (7 bp):
AGAGAGG
Found at i:28879596 original size:2 final size:2
Alignment explanation
Indices: 28879584--28879667 Score: 72
Period size: 2 Copynumber: 44.0 Consensus size: 2
28879574 TTCTTTTCCC
*
28879584 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT -T CGT -T CT -T
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT
* * *
28879624 TT TT CT -T CT -T NCC CT CT CT -T CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28879664 CT CT
1 CT CT
28879668 TTCGTCTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 16
0.77 0.06 0.18
Matches are distributed among these distances:
1 6 0.09
2 62 0.90
3 1 0.01
ACGTcount: A:0.00, C:0.43, G:0.01, T:0.55
Consensus pattern (2 bp):
CT
Found at i:28879650 original size:52 final size:52
Alignment explanation
Indices: 28879574--28879679 Score: 171
Period size: 52 Copynumber: 2.0 Consensus size: 52
28879564 AAGTGAACCC
28879574 TTCTTTTCCCCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTC-TTCGTTCTTTT
1 TTCTTTTCCCCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTTTCG-TCTTTT
*
28879626 TTCTTCTTNCCCTCTC-TTCTCTCTCTCTCTCTCTCTCTCTCTTTCGTCTTTT
1 TTCTT-TTCCCCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTTTCGTCTTTT
28879678 TT
1 TT
28879680 TCTCTTTGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
52 38 0.75
53 13 0.25
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.58
Consensus pattern (52 bp):
TTCTTTTCCCCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTTTCGTCTTTT
Found at i:28884530 original size:13 final size:13
Alignment explanation
Indices: 28884491--28884532 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
28884481 TTTATATATT
28884491 AATAATTTTTAAA
1 AATAATTTTTAAA
*
28884504 TAT-ATTTTTAAAA
1 AATAATTTTT-AAA
*
28884517 AATAATATTTAAA
1 AATAATTTTTAAA
28884530 AAT
1 AAT
28884533 TATCAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 6 0.25
13 13 0.54
14 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATAATTTTTAAA
Found at i:28885562 original size:27 final size:27
Alignment explanation
Indices: 28885452--28885581 Score: 136
Period size: 27 Copynumber: 4.8 Consensus size: 27
28885442 CCAAACGCAT
* *
28885452 AAGCACCCAAGGGTGTTTCAAACGTGG
1 AAGCACCCAAGGGTGTTTCAAGCATGG
* * *
28885479 AAGCACCCAGGGGTGTTTCAAACGTGG
1 AAGCACCCAAGGGTGTTTCAAGCATGG
* *
28885506 AAGCACCCAGGGGTG-TTCTAAGCATAG
1 AAGCACCCAAGGGTGTTTC-AAGCATGG
* *
28885533 AAGCGCCCAAGGGTGTTTCAAGTATGG
1 AAGCACCCAAGGGTGTTTCAAGCATGG
** *
28885560 AAGTGCCCAAGGGCGTTTCAAG
1 AAGCACCCAAGGGTGTTTCAAG
28885582 GGCAGAAGCG
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
26 3 0.03
27 85 0.93
28 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.32, T:0.19
Consensus pattern (27 bp):
AAGCACCCAAGGGTGTTTCAAGCATGG
Found at i:28885589 original size:27 final size:27
Alignment explanation
Indices: 28885531--28885595 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
28885521 TTCTAAGCAT
* * *
28885531 AGAAGCGCCCAAGGGTGTTTCAAGTAT
1 AGAAGCGCCCAAGGGCGTTTCAAGGAC
* * *
28885558 GGAAGTGCCCAAGGGCGTTTCAAGGGC
1 AGAAGCGCCCAAGGGCGTTTCAAGGAC
28885585 AGAAGCGCCCA
1 AGAAGCGCCCA
28885596 TGGTGTTCTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGAAGCGCCCAAGGGCGTTTCAAGGAC
Found at i:28885640 original size:27 final size:27
Alignment explanation
Indices: 28885606--28885681 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 27
28885596 TGGTGTTCTA
* *
28885606 GTGTTCCAAGCGTGGAAGCGCCCAGGG
1 GTGTTCCAAGCGCGGAAGCGCCTAGGG
* * ** * *
28885633 GTATTCCAAACGCATAAACGCCTAGAG
1 GTGTTCCAAGCGCGGAAGCGCCTAGGG
**
28885660 GTGTTCCAAGTACGGAAGCGCC
1 GTGTTCCAAGCGCGGAAGCGCC
28885682 CAAGGGCATT
Statistics
Matches: 34, Mismatches: 15, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.17
Consensus pattern (27 bp):
GTGTTCCAAGCGCGGAAGCGCCTAGGG
Found at i:28885663 original size:115 final size:115
Alignment explanation
Indices: 28885491--28885730 Score: 297
Period size: 115 Copynumber: 2.1 Consensus size: 115
28885481 GCACCCAGGG
* * * * *
28885491 GTGTTTCAAACGTGGAAGCACCCAGGGGTGTTCTAAGCATAGAAGCGCCCAAGGGTGTTTCAAGT
1 GTGTTCCAAGCGTGGAAGCACCCAGGGGTATTCAAAGCATAGAAGCGCCCAAGGGTGTTCCAAGT
* * * * * *
28885556 ATGGAAGTGCCCAAGGGCGTTTCAAGGGCAGAAGCGCCCATGGTGTTCTA
66 ACGGAAGCGCCCAAGGGCATTCCAAGCGCAGAAGCGCCCAAGGTGTTCTA
* *
28885606 GTGTTCCAAGCGTGGAAGCGCCCAGGGGTATTCCAAACGCATA-AA-CG-CCTAGAGGTGTTCCA
1 GTGTTCCAAGCGTGGAAGCACCCAGGGGTATT-CAAA-GCATAGAAGCGCCCAAG-GGTGTTCCA
* *
28885668 AGTACGGAAGCGCCCAAGGGCATTCCAAGCGTAGAAGTGCCCAAGGTGTTCTA
63 AGTACGGAAGCGCCCAAGGGCATTCCAAGCGCAGAAGCGCCCAAGGTGTTCTA
28885721 GTGTTCCAAG
1 GTGTTCCAAG
28885731 AATGGAGGTG
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
114 4 0.04
115 93 0.87
116 5 0.05
117 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (115 bp):
GTGTTCCAAGCGTGGAAGCACCCAGGGGTATTCAAAGCATAGAAGCGCCCAAGGGTGTTCCAAGT
ACGGAAGCGCCCAAGGGCATTCCAAGCGCAGAAGCGCCCAAGGTGTTCTA
Found at i:28885755 original size:115 final size:115
Alignment explanation
Indices: 28885544--28885759 Score: 288
Period size: 115 Copynumber: 1.9 Consensus size: 115
28885534 AGCGCCCAAG
* * * * * * *
28885544 GGTGTTTCAAGTATGGAAGTGCCCAAGGGCGTTTCAAGGGCAGAAGCGCCCATGGTGTTCTAGTG
1 GGTGTTCCAAGTACGGAAGCGCCCAAGGGCATTCCAAGCGCAGAAGCGCCCAAGGTGTTCTAGTG
** *
28885609 TTCCAAGCGTGGAAGCGCCCAGGGGTATTCCAAACGCATAAACGCCTAGA
66 TTCCAAGAATGGAAGCGCCCAGGGATATTCCAAACGCATAAACGCCTAGA
* *
28885659 GGTGTTCCAAGTACGGAAGCGCCCAAGGGCATTCCAAGCGTAGAAGTGCCCAAGGTGTTCTAGTG
1 GGTGTTCCAAGTACGGAAGCGCCCAAGGGCATTCCAAGCGCAGAAGCGCCCAAGGTGTTCTAGTG
* * * *
28885724 TTCCAAGAATGGAGGTGCCTAGGGATGTTCCAAACG
66 TTCCAAGAATGGAAGCGCCCAGGGATATTCCAAACG
28885760 TGGAAGCGGC
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
115 85 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.21
Consensus pattern (115 bp):
GGTGTTCCAAGTACGGAAGCGCCCAAGGGCATTCCAAGCGCAGAAGCGCCCAAGGTGTTCTAGTG
TTCCAAGAATGGAAGCGCCCAGGGATATTCCAAACGCATAAACGCCTAGA
Found at i:28885778 original size:115 final size:115
Alignment explanation
Indices: 28885531--28885784 Score: 278
Period size: 115 Copynumber: 2.2 Consensus size: 115
28885521 TTCTAAGCAT
* * * * * * * *
28885531 AGAAGCGCCCAAGGGTGTTTCAAGTATGGAAGTGCCCAAGGGCGTTTCAAGGGCAGAAGCGCCCA
1 AGAAGCGGCCATGGGTGTTCCAAGTACGGAAGCGCCCAAGGGCATTCCAAGCGCAGAAGCGCCCA
* ** *
28885596 TGGTGTTCTAGTGTTCCAAGCGTGGAAGCGCCCAGGGGTATTCCAAACGC
66 AGGTGTTCTAGTGTTCCAAGAATGGAAGCGCCCAGGGATATTCCAAACGC
* * * *
28885646 ATAAAC-GCC-TAGAGGTGTTCCAAGTACGGAAGCGCCCAAGGGCATTCCAAGCGTAGAAGTGCC
1 AGAAGCGGCCAT-G-GGTGTTCCAAGTACGGAAGCGCCCAAGGGCATTCCAAGCGCAGAAGCGCC
* * * * *
28885709 CAAGGTGTTCTAGTGTTCCAAGAATGGAGGTGCCTAGGGATGTTCCAAACGT
64 CAAGGTGTTCTAGTGTTCCAAGAATGGAAGCGCCCAGGGATATTCCAAACGC
*
28885761 GGAAGCGGCCATGGGTGTTCCAAG
1 AGAAGCGGCCATGGGTGTTCCAAG
28885785 CGCAGAAGCG
Statistics
Matches: 111, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
114 3 0.03
115 103 0.93
116 4 0.04
117 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (115 bp):
AGAAGCGGCCATGGGTGTTCCAAGTACGGAAGCGCCCAAGGGCATTCCAAGCGCAGAAGCGCCCA
AGGTGTTCTAGTGTTCCAAGAATGGAAGCGCCCAGGGATATTCCAAACGC
Found at i:28885792 original size:27 final size:26
Alignment explanation
Indices: 28885740--28885956 Score: 150
Period size: 27 Copynumber: 8.1 Consensus size: 26
28885730 GAATGGAGGT
* **
28885740 GCCTAGGGATGTTCCAAACGTGGAAGC
1 GCCTAGGG-TGTTCCAAGCGCAGAAGC
28885767 GGCC-ATGGGTGTTCCAAGCGCAGAAGC
1 -GCCTA-GGGTGTTCCAAGCGCAGAAGC
* *
28885794 GCCTAGAGGTGTTTCAAGGGCAGAAGC
1 GCCTAG-GGTGTTCCAAGCGCAGAAGC
* * * * *
28885821 GCCTAGAGTATTCCAAGTGCGGAAGG
1 GCCTAGGGTGTTCCAAGCGCAGAAGC
***
28885847 GCCTAAGGGTGTTCCAAGCATGGAAGC
1 GCCT-AGGGTGTTCCAAGCGCAGAAGC
* *
28885874 GCCTAGGG-GCATTCCAAGCGCATAAAC
1 GCCTAGGGTG--TTCCAAGCGCAGAAGC
* * * *
28885901 GCCCAAAGGTGTTCCAAGCACAGAAGA
1 G-CCTAGGGTGTTCCAAGCGCAGAAGC
* * *
28885928 GCTTAGGGCGTTCCAAGCACAGAAGC
1 GCCTAGGGTGTTCCAAGCGCAGAAGC
28885954 GCC
1 GCC
28885957 CAAAGAGCGT
Statistics
Matches: 147, Mismatches: 34, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
25 1 0.01
26 48 0.33
27 86 0.59
28 11 0.07
29 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.32, T:0.16
Consensus pattern (26 bp):
GCCTAGGGTGTTCCAAGCGCAGAAGC
Found at i:28885819 original size:115 final size:113
Alignment explanation
Indices: 28885559--28885823 Score: 255
Period size: 115 Copynumber: 2.3 Consensus size: 113
28885549 TTCAAGTATG
* * **
28885559 GAAGTGCCCAAGGGCGTTTCAAGGGCAGAAGCGCCCATGGTGTTCTAGTGTTCCAAGCGTGGAAG
1 GAAGCGCCCAA-GG-GTTTCAAGGGCAGAAGCGCCCAAGGTGTTCTAGTGTTCCAAGAATGGAAG
* * * *
28885624 CGCCCAGGGGTATTCCAAACGCATAAACGCCTAGAGGTGTTCCAAGTACG
64 CGCCCAGGGATATTCCAAACGCAGAAACGCCTAGAGGTGTTCCAAGCACA
* * * * *
28885674 GAAGCGCCCAAGGGCATTCCAAGCGTAGAAGTGCCCAAGGTGTTCTAGTGTTCCAAGAATGGAGG
1 GAAGCGCCCAAGGG--TTTCAAGGGCAGAAGCGCCCAAGGTGTTCTAGTGTTCCAAGAATGGAAG
* * * ** * *
28885739 TGCCTAGGGATGTTCCAAACGTGGAAGCGGCC-ATG-GGTGTTCCAAGCGCA
64 CGCCCAGGGATATTCCAAACGCAGAAAC-GCCTA-GAGGTGTTCCAAGCACA
*
28885789 GAAGCGCCTAGAGGTGTTTCAAGGGCAGAAGCGCC
1 GAAGCGCCCA-AGG-GTTTCAAGGGCAGAAGCGCC
28885824 TAGAGTATTC
Statistics
Matches: 119, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
113 1 0.01
114 2 0.02
115 108 0.91
116 7 0.06
117 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.18
Consensus pattern (113 bp):
GAAGCGCCCAAGGGTTTCAAGGGCAGAAGCGCCCAAGGTGTTCTAGTGTTCCAAGAATGGAAGCG
CCCAGGGATATTCCAAACGCAGAAACGCCTAGAGGTGTTCCAAGCACA
Found at i:28885912 original size:54 final size:53
Alignment explanation
Indices: 28885854--28885980 Score: 146
Period size: 54 Copynumber: 2.4 Consensus size: 53
28885844 AGGGCCTAAG
** * * *
28885854 GGTGTTCCAAGCATGGAAGCGCCTAGGGGCATTCCAAGCGCATAAACGCCCAAA
1 GGTGTTCCAAGCACAGAAGAGCCTA-GGGCATTCCAAGCACAGAAACGCCCAAA
* * *
28885908 GGTGTTCCAAGCACAGAAGAGCTTAGGGCGTTCCAAGCACAGAAGCGCCCAAA
1 GGTGTTCCAAGCACAGAAGAGCCTAGGGCATTCCAAGCACAGAAACGCCCAAA
* *
28885961 GAGCGTTACAAGCACAGAAG
1 G-GTGTTCCAAGCACAGAAG
28885981 CACACTGAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
53 25 0.40
54 37 0.60
ACGTcount: A:0.32, C:0.26, G:0.28, T:0.13
Consensus pattern (53 bp):
GGTGTTCCAAGCACAGAAGAGCCTAGGGCATTCCAAGCACAGAAACGCCCAAA
Found at i:28892819 original size:17 final size:18
Alignment explanation
Indices: 28892785--28892833 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
28892775 TCAATTTTTT
*
28892785 TTATTTTA-AATAAATAA
1 TTATTTTATAATTAATAA
28892802 TT-TTTTATAATTAATAA
1 TTATTTTATAATTAATAA
28892819 TTATTTTAT-ATTAAT
1 TTATTTTATAATTAAT
28892834 CAAAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 5 0.17
17 18 0.62
18 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTTTATAATTAATAA
Found at i:28918493 original size:9 final size:8
Alignment explanation
Indices: 28918473--28918512 Score: 53
Period size: 9 Copynumber: 4.6 Consensus size: 8
28918463 GGTTAAAAAA
28918473 TTAATAATT
1 TTAATAA-T
28918482 TTAATTAAT
1 TTAA-TAAT
28918491 TTAATAAT
1 TTAATAAT
28918499 TTAATATAT
1 TTAATA-AT
28918508 TTAAT
1 TTAAT
28918513 TATATACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 10 0.34
9 16 0.55
10 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TTAATAAT
Found at i:28918501 original size:17 final size:18
Alignment explanation
Indices: 28918473--28918512 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
28918463 GGTTAAAAAA
28918473 TTAATAATTTTAAT-TAAT
1 TTAATAATTTTAATAT-AT
28918491 TTAATAA-TTTAATATAT
1 TTAATAATTTTAATATAT
28918508 TTAAT
1 TTAAT
28918513 TATATACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATAATTTTAATATAT
Found at i:28918650 original size:15 final size:17
Alignment explanation
Indices: 28918620--28918657 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
28918610 GAATGAAATT
28918620 ATAAAATAATTTTATTA
1 ATAAAATAATTTTATTA
28918637 ATAAAA-AA-TTTATTA
1 ATAAAATAATTTTATTA
28918652 ACTAAA
1 A-TAAA
28918658 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 6 0.30
17 6 0.30
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAATAATTTTATTA
Found at i:28925685 original size:99 final size:99
Alignment explanation
Indices: 28925502--28925686 Score: 252
Period size: 99 Copynumber: 1.9 Consensus size: 99
28925492 GAGGTTGAGA
* * *
28925502 TGGTGATGGTGCTCAAGCGAAATGTAAATATTAAGGTGGTAATGACAGCAGTCAAAGAGCGATGG
1 TGGTGATGGTGCTCAAGCGAAATGAAAATATTAAGGTGGTAATGACAGCACTCAAAGAGCGATAG
* *
28925567 TGTTATGAAAGATACCAGGGTGTTTTGATGGAGG
66 TGTTAAGAAAGATAACAGGGTGTTTTGATGGAGG
*
28925601 TGGTGATGGTGCTCAAGC-AAATTGAAAATATTATGGTGGTAATGACAGCACT-AGAAGA-CTGA
1 TGGTGATGGTGCTCAAGCGAAA-TGAAAATATTAAGGTGGTAATGACAGCACTCA-AAGAGC-GA
28925663 TAGTGTTAAGAAA-AGTAACAGGGT
63 TAGTGTTAAGAAAGA-TAACAGGGT
28925687 ATTATTGTGA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
98 6 0.08
99 70 0.92
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (99 bp):
TGGTGATGGTGCTCAAGCGAAATGAAAATATTAAGGTGGTAATGACAGCACTCAAAGAGCGATAG
TGTTAAGAAAGATAACAGGGTGTTTTGATGGAGG
Found at i:28936694 original size:14 final size:15
Alignment explanation
Indices: 28936677--28936705 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28936667 ATAGCGCATC
28936677 AAAT-ATAAACTTTT
1 AAATAATAAACTTTT
28936691 AAATAATAAACTTTT
1 AAATAATAAACTTTT
28936706 GTGTTGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATAATAAACTTTT
Found at i:28937474 original size:22 final size:21
Alignment explanation
Indices: 28937439--28937480 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
28937429 NNNNNNNNNN
*
28937439 AAATTTTTATTTTTAATAAAT
1 AAATTTTTAATTTTAATAAAT
28937460 AAATTCTTTAATTTTAATAAA
1 AAATT-TTTAATTTTAATAAA
28937481 GAGTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATTTTTAATTTTAATAAAT
Found at i:28941450 original size:9 final size:10
Alignment explanation
Indices: 28941431--28941463 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
28941421 GCCTATGGAG
28941431 AAAGAAAAAA
1 AAAGAAAAAA
28941441 AAAGAAAAAA
1 AAAGAAAAAA
28941451 AAAGAAAAAA
1 AAAGAAAAAA
28941461 AAA
1 AAA
28941464 TATTTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:28941598 original size:17 final size:16
Alignment explanation
Indices: 28941517--28941671 Score: 59
Period size: 16 Copynumber: 10.2 Consensus size: 16
28941507 ATATGATTAA
*
28941517 TATTAATATGATTAAAA
1 TATTAATAT-ATTAAAT
* *
28941534 TATTAAAATAGT-AAT
1 TATTAATATATTAAAT
* * *
28941549 GT-TTTATTTATTAACT
1 -TATTAATATATTAAAT
28941565 TATTAATATATTAAAT
1 TATTAATATATTAAAT
28941581 TATTAATGAGTA-TAAAT
1 TATTAAT-A-TATTAAAT
* *
28941598 TA--AA-AAATTAAAAA
1 TATTAATATATT-AAAT
*
28941612 TATTAATAT-TTTAA-
1 TATTAATATATTAAAT
*
28941626 TAATAATAATATTAAAT
1 TATTAAT-ATATTAAAT
*
28941643 TA-TAA-ACA--AAA-
1 TATTAATATATTAAAT
28941654 TATTAATA-ATTAAAT
1 TATTAATATATTAAAT
28941669 TAT
1 TAT
28941672 ACGAAAATAT
Statistics
Matches: 102, Mismatches: 18, Indels: 38
0.65 0.11 0.24
Matches are distributed among these distances:
11 2 0.02
12 8 0.08
13 3 0.03
14 16 0.16
15 18 0.18
16 34 0.33
17 19 0.19
18 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (16 bp):
TATTAATATATTAAAT
Found at i:28941660 original size:25 final size:24
Alignment explanation
Indices: 28941627--28941693 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 24
28941617 ATATTTTAAT
*
28941627 AATAATAATATTAAATTATAAAC-AA
1 AATATTAATATTAAATTAT--ACGAA
28941652 AATATTAATAATTAAATTATACGAA
1 AATATTAAT-ATTAAATTATACGAA
28941677 AATATTAATATTTAAAT
1 AATATTAATA-TTAAAT
28941694 GATTAATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
24 3 0.08
25 25 0.66
26 10 0.26
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (24 bp):
AATATTAATATTAAATTATACGAA
Found at i:28941925 original size:22 final size:22
Alignment explanation
Indices: 28941897--28941941 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
28941887 TCATATTAAA
* *
28941897 TTACGTAATATTTATTTTATTT
1 TTACGTAATAATTATTATATTT
28941919 TTACGTAATAATTATTATATTT
1 TTACGTAATAATTATTATATTT
28941941 T
1 T
28941942 ATTTTTATTT
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:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (22 bp):
TTACGTAATAATTATTATATTT
Found at i:28942146 original size:26 final size:26
Alignment explanation
Indices: 28942110--28942163 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
28942100 GTGACGGATT
28942110 TAGAACTTTGAATGAGGAGTAAAGGG
1 TAGAACTTTGAATGAGGAGTAAAGGG
*
28942136 TAGAATTTTGAATGAGGAGTAAAGGG
1 TAGAACTTTGAATGAGGAGTAAAGGG
28942162 TA
1 TA
28942164 ATTATAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.02, G:0.33, T:0.26
Consensus pattern (26 bp):
TAGAACTTTGAATGAGGAGTAAAGGG
Found at i:28946783 original size:12 final size:12
Alignment explanation
Indices: 28946766--28946790 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28946756 TTTAGAATAT
28946766 ATAATTATAAAA
1 ATAATTATAAAA
28946778 ATAATTATAAAA
1 ATAATTATAAAA
28946790 A
1 A
28946791 AATAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATTATAAAA
Found at i:28947014 original size:11 final size:11
Alignment explanation
Indices: 28946990--28947021 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
28946980 CACGATTAAG
28946990 TAAACGTG-TT
1 TAAACGTGTTT
28947000 TAAACGTGTTT
1 TAAACGTGTTT
28947011 TAAACGTGTTT
1 TAAACGTGTTT
28947022 CGTGTCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (11 bp):
TAAACGTGTTT
Found at i:28947037 original size:10 final size:10
Alignment explanation
Indices: 28946990--28947021 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
28946980 CACGATTAAG
28946990 TAAACGTGTT
1 TAAACGTGTT
28947000 TAAACGTGTTT
1 TAAACGTG-TT
28947011 TAAACGTGTT
1 TAAACGTGTT
28947021 T
1 T
28947022 CGTGTCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (10 bp):
TAAACGTGTT
Found at i:28968838 original size:20 final size:19
Alignment explanation
Indices: 28968802--28968840 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
28968792 AATATATATT
*
28968802 TTTTCTTTTTTTTTGCTTG
1 TTTTCTTTTTTTATGCTTG
*
28968821 TTTTGTTTTGTTTATGCTTG
1 TTTTCTTTT-TTTATGCTTG
28968841 GTACTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.03, C:0.08, G:0.15, T:0.74
Consensus pattern (19 bp):
TTTTCTTTTTTTATGCTTG
Found at i:28983265 original size:10 final size:10
Alignment explanation
Indices: 28983250--28983277 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
28983240 ACAAACTGTA
28983250 AAAACTGAAT
1 AAAACTGAAT
28983260 AAAACTGAAT
1 AAAACTGAAT
28983270 AAAACTGA
1 AAAACTGA
28983278 CACATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.18
Consensus pattern (10 bp):
AAAACTGAAT
Found at i:28988716 original size:2 final size:2
Alignment explanation
Indices: 28988703--28988750 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
28988693 TGAAGACCAA
*
28988703 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28988745 AT AT AT
1 AT AT AT
28988751 TCATCCAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28991377 original size:20 final size:20
Alignment explanation
Indices: 28991354--28991396 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28991344 TTGACTGTAC
*
28991354 TGACTTAATATTGAATCTAA
1 TGACATAATATTGAATCTAA
* *
28991374 TGACATAGTATTGAATTTAA
1 TGACATAATATTGAATCTAA
28991394 TGA
1 TGA
28991397 TGTGACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (20 bp):
TGACATAATATTGAATCTAA
Found at i:28996418 original size:2 final size:2
Alignment explanation
Indices: 28996378--28996402 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28996368 TCTTACATTT
28996378 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
28996403 TAAAATGATT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29002121 original size:2 final size:2
Alignment explanation
Indices: 29002116--29002151 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
29002106 TTTTTTTTTT
*
29002116 TA TA TA T- TT 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 TA T
29002152 TTATTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:29006943 original size:4 final size:4
Alignment explanation
Indices: 29006929--29006958 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
29006919 TGTCTAAGTT
29006929 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T
29006959 AATTAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:29007078 original size:10 final size:9
Alignment explanation
Indices: 29007041--29007083 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
29007031 TGAAATGTTC
*
29007041 TTTTTTACT
1 TTTTTTATT
*
29007050 TTATTTATT
1 TTTTTTATT
*
29007059 GTTTTTATT
1 TTTTTTATT
29007068 TTTTTTAATT
1 TTTTTT-ATT
29007078 TTTTTT
1 TTTTTT
29007084 CTCTCTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTATT
Found at i:29018302 original size:78 final size:78
Alignment explanation
Indices: 29018069--29018302 Score: 371
Period size: 78 Copynumber: 3.0 Consensus size: 78
29018059 GGTTTAGTAG
* * *
29018069 TTTTCCTGATTGCACAAATTGAAGTAGATAC-CAGTAGGAATTTCATTGATAAAGTGTAAAAGGT
1 TTTTCATGATTGCACAAATTGAAGCAGATACTGA-TAGGAATTTCATTGATAAAGTGTAAAAGGT
*
29018133 GATATGCTAGCATG
65 GATATGCTAGCATA
* *
29018147 TTTTCGTGATTGCACAAATTGAAGCAGATACTGATAGGAATTTAATTGATAAAGTGTAAAAGGTG
1 TTTTCATGATTGCACAAATTGAAGCAGATACTGATAGGAATTTCATTGATAAAGTGTAAAAGGTG
*
29018212 AAATGCTAGCATA
66 ATATGCTAGCATA
* *
29018225 TTTTCATGATTGCACAAATTGAAGCAGATACTGATAGGAATTTCATTGTTAAGGTGTAAAAGGTG
1 TTTTCATGATTGCACAAATTGAAGCAGATACTGATAGGAATTTCATTGATAAAGTGTAAAAGGTG
29018290 ATATGCTAGCATA
66 ATATGCTAGCATA
29018303 ACATATTAAA
Statistics
Matches: 144, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
78 143 0.99
79 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (78 bp):
TTTTCATGATTGCACAAATTGAAGCAGATACTGATAGGAATTTCATTGATAAAGTGTAAAAGGTG
ATATGCTAGCATA
Found at i:29018823 original size:40 final size:40
Alignment explanation
Indices: 29018768--29018852 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
29018758 GTATTAAACT
*
29018768 TTTTCAGCCCAACTCTACCATGCTTATCTGATTCTCCTGA
1 TTTTCAGCCCAACTCTACCATGCTTACCTGATTCTCCTGA
*
29018808 TTTTCAGCCCAACTCTACCATGCTTACCTGATTCTCCTGG
1 TTTTCAGCCCAACTCTACCATGCTTACCTGATTCTCCTGA
29018848 TTTTC
1 TTTTC
29018853 CCCAACAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.39
Consensus pattern (40 bp):
TTTTCAGCCCAACTCTACCATGCTTACCTGATTCTCCTGA
Found at i:29018880 original size:24 final size:24
Alignment explanation
Indices: 29018842--29018898 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
29018832 TACCTGATTC
29018842 TCCTGG-TTTTCCCCAACAGTTTA
1 TCCTGGTTTTTCCCCAACAGTTTA
29018865 TCCTGGTTTTTCCCCAACAGTTTA
1 TCCTGGTTTTTCCCCAACAGTTTA
29018889 TCCTGGTTTT
1 TCCTGGTTTT
29018899 GCTCCAACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 6 0.18
24 27 0.82
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.44
Consensus pattern (24 bp):
TCCTGGTTTTTCCCCAACAGTTTA
Found at i:29021541 original size:2 final size:2
Alignment explanation
Indices: 29021534--29021560 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29021524 TAAGGGGGAA
29021534 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
29021561 AAGGTTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29033918 original size:2 final size:2
Alignment explanation
Indices: 29033911--29033943 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29033901 TAAACATAAG
29033911 AT AT 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 AT AT A
29033944 GCTTCTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29036458 original size:21 final size:21
Alignment explanation
Indices: 29036434--29036473 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29036424 ATATAAATAG
*
29036434 TTATAT-TATATATATTAAATT
1 TTATATCTATA-ATAATAAATT
29036455 TTATATCTATAATAATAAA
1 TTATATCTATAATAATAAA
29036474 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATATCTATAATAATAAATT
Found at i:29036911 original size:2 final size:2
Alignment explanation
Indices: 29036904--29036946 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
29036894 AAATTAAGTG
29036904 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29036946 T
1 T
29036947 CTCGAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29067418 original size:37 final size:38
Alignment explanation
Indices: 29067358--29067430 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
29067348 AGACAAAATG
* * *
29067358 GAAGATGAAACTGTTATTAATACACA-TTCATCATATT
1 GAAGATGAAACAGTAACTAATACACATTTCATCATATT
* *
29067395 GAAGATGAAACAGTAACTGATACATATTTCATCATA
1 GAAGATGAAACAGTAACTAATACACATTTCATCATA
29067431 AGCTGGAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 21 0.70
38 9 0.30
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (38 bp):
GAAGATGAAACAGTAACTAATACACATTTCATCATATT
Found at i:29074686 original size:2 final size:2
Alignment explanation
Indices: 29074666--29074769 Score: 126
Period size: 2 Copynumber: 54.0 Consensus size: 2
29074656 ATTGTGTCCA
* *
29074666 AT AT -T AT AT AC AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
29074707 AT AT AT AT AT AT AT TT NT AT AA AA AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29074748 AT AT AT -T AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
29074770 TGTCTTAGCC
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
1 4 0.04
2 85 0.96
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29075270 original size:27 final size:27
Alignment explanation
Indices: 29075231--29075301 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
29075221 ATAAGGTGGC
*
29075231 TCATACACCGGTGGTTTCTTAGGAGGT
1 TCATAAACCGGTGGTTTCTTAGGAGGT
* * * *
29075258 TCATATACTGGTGGCTTCTTCGGAGGT
1 TCATAAACCGGTGGTTTCTTAGGAGGT
*
29075285 TCGTAAACCGGTGGTTT
1 TCATAAACCGGTGGTTT
29075302 GGGCTCTGGC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.17, C:0.18, G:0.30, T:0.35
Consensus pattern (27 bp):
TCATAAACCGGTGGTTTCTTAGGAGGT
Found at i:29075362 original size:30 final size:30
Alignment explanation
Indices: 29075326--29075400 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
29075316 CTTTCTTCGG
29075326 AGGTTCATAAACTGGTGGTTTTGGTGGCTT
1 AGGTTCATAAACTGGTGGTTTTGGTGGCTT
*
29075356 AGGTTCATATACTGGTGGTTTTGGTGGCTT
1 AGGTTCATAAACTGGTGGTTTTGGTGGCTT
*
29075386 AGGTTCATACACTGG
1 AGGTTCATAAACTGG
29075401 AGGCTTCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.17, C:0.12, G:0.32, T:0.39
Consensus pattern (30 bp):
AGGTTCATAAACTGGTGGTTTTGGTGGCTT
Found at i:29075415 original size:132 final size:132
Alignment explanation
Indices: 29075254--29075559 Score: 477
Period size: 132 Copynumber: 2.3 Consensus size: 132
29075244 GTTTCTTAGG
* * *
29075254 AGGTTCATATACTGGTGGCTTCTTCGGAGGTTCGTAAACCGGTGGTTTGGGCTCTGGCTTCTCTT
1 AGGTTCATATACTGGTGGCTTCTTTGGAGGCTCATAAACCGGTGGTTTGGGCTCTGGCTTCTCTT
* * * *
29075319 TCTTCGGAGGTTCATAAACTGGTGGTTTTGGTGGCTTAGGTTCATATACTGGTGGTTTTGGTGGC
66 TCTTCGGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGGC
29075384 TT
131 TT
* * * * *
29075386 AGGTTCATACACTGGAGGCTTCTTTGGAGGCTCATATACTGGTGGTTTGGGTTCTGGCTTCTCTT
1 AGGTTCATATACTGGTGGCTTCTTTGGAGGCTCATAAACCGGTGGTTTGGGCTCTGGCTTCTCTT
*
29075451 TCTTTGGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGGC
66 TCTTCGGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGGC
29075516 TT
131 TT
* *
29075518 AGGTTCATATACTGGTGGTTTCTTTGGAGGCTCATACACCGG
1 AGGTTCATATACTGGTGGCTTCTTTGGAGGCTCATAAACCGG
29075560 AGGCTTCTTT
Statistics
Matches: 156, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 156 1.00
ACGTcount: A:0.14, C:0.17, G:0.31, T:0.38
Consensus pattern (132 bp):
AGGTTCATATACTGGTGGCTTCTTTGGAGGCTCATAAACCGGTGGTTTGGGCTCTGGCTTCTCTT
TCTTCGGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGGC
TT
Found at i:29075497 original size:30 final size:30
Alignment explanation
Indices: 29075462--29075880 Score: 241
Period size: 30 Copynumber: 14.4 Consensus size: 30
29075452 CTTTGGAGGT
29075462 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
*
29075492 TCATAAACTGGTGGCTTTGGTGGCTTAGGT
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
* **
29075522 TCATATACTGGTGG-TTTCTTTGG---AGGC
1 TCATAAACTGGTGGCTTT-GGTGGCTTAGGC
* * * *
29075549 TCATACACCGGAGGCTTCT-TTGG---AGGC
1 TCATAAACTGGTGGCTT-TGGTGGCTTAGGC
*
29075576 TCATAAACTGGTGGCTTTGGTGGCTTAGGT
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
*
29075606 TCATAAA-------C--TGGTGGCTTAGGT
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
*
29075627 TCATATACTGGTGGCTTTGGTGGCTTAGGC
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
*
29075657 TCATAAACTGGTGGCTTTGGTGGCTTAGGT
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
* **
29075687 TCATAAACTGGCGG-TTTCTTTGG---AGGC
1 TCATAAACTGGTGGCTTT-GGTGGCTTAGGC
* * * *
29075714 TCATACACCGGAGGCTTCT-TTGG---AGGC
1 TCATAAACTGGTGGCTT-TGGTGGCTTAGGC
*
29075741 TCATATACTGGTGG-TTTGGGTTCTGGCTTTGGAGGC
1 TCATAAACTGGTGGCTTT-GG---TGGC-TT--AGGC
* **
29075777 TTAGGTTCATATACTGGTGG-TTTCTTTGG---AGGC
1 ------TCATAAACTGGTGGCTTT-GGTGGCTTAGGC
29075810 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
* *
29075840 TCATAAACTGGTGGCTTTGGAGGCTTAGGT
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
29075870 TCATAAACTGG
1 TCATAAACTGG
29075881 CGGTTTCTTT
Statistics
Matches: 313, Mismatches: 36, Indels: 80
0.73 0.08 0.19
Matches are distributed among these distances:
21 19 0.06
23 1 0.00
25 1 0.00
26 3 0.01
27 88 0.28
28 8 0.03
29 8 0.03
30 157 0.50
33 4 0.01
36 4 0.01
39 3 0.01
42 17 0.05
ACGTcount: A:0.17, C:0.16, G:0.32, T:0.35
Consensus pattern (30 bp):
TCATAAACTGGTGGCTTTGGTGGCTTAGGC
Found at i:29075594 original size:114 final size:114
Alignment explanation
Indices: 29075450--29075942 Score: 396
Period size: 114 Copynumber: 4.3 Consensus size: 114
29075440 TGGCTTCTCT
29075450 TTCTTTGGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGG
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGG
*
29075515 CTTAGGTTCATATACTGGTGGTTTCTTTGGAGGCTCATACACCGGAGGC
66 CTTAGGTTCATATACTGGTGGTTTCTTTGGAGGCTCATACACCGGTGGC
* *
29075564 TTCTTTGGAGGCTCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATAAA-------C--TGGTGG
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGG
** * *
29075620 CTTAGGTTCATATACTGGTGGCTTT-GGTGGCTTAGGCTCATAAACTGGTGGC
66 CTTAGGTTCATATACTGGTGG-TTTCTTTGG---AGGCTCATACACCGGTGGC
* * ** * * *
29075672 TT-TGGTGGCTTAGGTTCATAAACTGGCGG-TTTCTTTGG---AGGCTCATACACCGGAGGCTTC
1 TTCT-TTGG---AGGTTCATAAACTGGTGGCTTT-GGTGGCTTAGGCTCATAAACTGGTGGCTT-
* * * *
29075732 T-TTGG---AGGCTCATATACTGGTGGTTTGGGTTCTGGCTTTGGAGGCTTAGGTTCATATACTG
60 TGGTGGCTTAGGTTCATATAC---TGG--T-GGTT-T--CTTTGGAGGC------TCATACACCG
*
29075793 GTGGT
110 GTGGC
* *
29075798 TTCTTTGGAGGCTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGAGG
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGG
* * *
29075863 CTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCATACACCGGTGGT
66 CTTAGGTTCATATACTGGTGGTTTCTTTGGAGGCTCATACACCGGTGGC
*
29075912 TTCTTGGGAGGTTCATAAACTGGTGG-TTTGG
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTTGG
29075943 GTTCTGGCTT
Statistics
Matches: 298, Mismatches: 37, Indels: 89
0.70 0.09 0.21
Matches are distributed among these distances:
105 30 0.10
106 3 0.01
107 2 0.01
108 30 0.10
110 3 0.01
111 19 0.06
113 5 0.02
114 95 0.32
115 1 0.00
117 6 0.02
118 1 0.00
119 3 0.01
120 17 0.06
122 1 0.00
123 26 0.09
124 3 0.01
125 1 0.00
126 41 0.14
127 1 0.00
129 10 0.03
ACGTcount: A:0.17, C:0.16, G:0.32, T:0.35
Consensus pattern (114 bp):
TTCTTTGGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGG
CTTAGGTTCATATACTGGTGGTTTCTTTGGAGGCTCATACACCGGTGGC
Found at i:29075619 original size:21 final size:21
Alignment explanation
Indices: 29075593--29075643 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
29075583 CTGGTGGCTT
29075593 TGGTGGCTTAGGTTCATAAAC
1 TGGTGGCTTAGGTTCATAAAC
*
29075614 TGGTGGCTTAGGTTCATATAC
1 TGGTGGCTTAGGTTCATAAAC
29075635 TGGTGGCTT
1 TGGTGGCTT
29075644 TGGTGGCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.31, T:0.37
Consensus pattern (21 bp):
TGGTGGCTTAGGTTCATAAAC
Found at i:29075637 original size:51 final size:51
Alignment explanation
Indices: 29075576--29075673 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
29075566 CTTTGGAGGC
*
29075576 TCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATAAACTGGTGGCTTAGGT
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTAGGT
*
29075627 TCATATACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTT
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTT
29075674 TGGTGGCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (51 bp):
TCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGGCTTAGGT
Found at i:29075667 original size:165 final size:158
Alignment explanation
Indices: 29075330--29075864 Score: 675
Period size: 165 Copynumber: 3.4 Consensus size: 158
29075320 CTTCGGAGGT
* * * *
29075330 TCATAAACTGGTGGTTTTGGTGGCTTAGGTTCATATACTGGTGGTTT-TGGTGGCTTAGGTTCAT
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATAAACTGGTGGTTTCT-TTGG---AGGCTCAT
* *
29075394 ACACTGGAGGCTTCTTTGGAGGCTCATATACTGGTGGTTTGGGTTCTGGCTTCTCT--T-TCTTT
62 ACACCGGAGGCTTCTTTGGAGGCTCATATACTGGTGGTTTGGGTTCTGG-TTCTCTGGTGGC-TT
*
29075456 GGAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGC
125 --AGGTTCATATACTGGTGGCTTTGGTGGCTTAGGC
*
29075492 TCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATATACTGGTGGTTTCTTTGGAGGCTCATACAC
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATAAACTGGTGGTTTCTTTGGAGGCTCATACAC
* *
29075557 CGGAGGCTTCTTTGGAGGCTCATAAACTGGTGGCTTTGGTGGCTT-AGGTTCATAAACTGGTGGC
66 CGGAGGCTTCTTTGGAGGCTCATATACTGGTGG-TTT-G-GG-TTCTGGTTC-T---CTGGTGGC
29075621 TTAGGTTCATATACTGGTGGCTTTGGTGGCTTAGGC
123 TTAGGTTCATATACTGGTGGCTTTGGTGGCTTAGGC
*
29075657 TCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCATACAC
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATAAACTGGTGGTTTCTTTGGAGGCTCATACAC
* *
29075722 CGGAGGCTTCTTTGGAGGCTCATATACTGGTGGTTTGGGTTCTGG--CTTTGGAGGCTTAGGTTC
66 CGGAGGCTTCTTTGGAGGCTCATATACTGGTGGTTTGGGTTCTGGTTCTCTGGTGGCTTAGGTTC
**
29075785 ATATACTGGTGG-TTTCTTTGG---AGGC
131 ATATACTGGTGGCTTT-GGTGGCTTAGGC
*
29075810 TCATAAACTGGTGGCTTTGGTGGCTTAGGCTCATAAACTGGTGG---CTTTGGAGGCT
1 TCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATAAACTGGTGGTTTCTTTGGAGGCT
29075865 TAGGTTCATA
Statistics
Matches: 341, Mismatches: 18, Indels: 40
0.85 0.05 0.10
Matches are distributed among these distances:
150 11 0.03
153 46 0.13
155 3 0.01
156 29 0.09
159 43 0.13
160 4 0.01
161 6 0.02
162 58 0.17
163 4 0.01
164 3 0.01
165 130 0.38
167 3 0.01
168 1 0.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (158 bp):
TCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATAAACTGGTGGTTTCTTTGGAGGCTCATACAC
CGGAGGCTTCTTTGGAGGCTCATATACTGGTGGTTTGGGTTCTGGTTCTCTGGTGGCTTAGGTTC
ATATACTGGTGGCTTTGGTGGCTTAGGC
Found at i:29075853 original size:183 final size:177
Alignment explanation
Indices: 29075587--29075953 Score: 590
Period size: 183 Copynumber: 2.0 Consensus size: 177
29075577 CATAAACTGG
* * *
29075587 TGGCTTTGGTGGCTTAGGTTCATAAACTGGTGGCTTAGGTTCATATACTGGTGGCTTTGGTGGCT
1 TGGCTTTGGAGGCTTAGGTTCATAAACTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGGCT
*
29075652 TAGGCTCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCA
66 TAGGCTCATAAACTGGTGGCTTTGGAGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCA
* *
29075717 TACACCGGAGGCTTCTTTGGAGGCTCATATACTGGTGGTTTGGGTTC
131 TACACCGGAGGCTTCTTGGGAGGCTCATAAACTGGTGGTTTGGGTTC
*
29075764 TGGCTTTGGAGGCTTAGGTTCATATACTGGTGGTTTCTTTGGAGGCTCATAAACTGGTGGCTTTG
1 TGGCTTTGGAGGCTTAGGTTCATAAACTGGTGG---C-TT--AGGCTCATAAACTGGTGGCTTTG
29075829 GTGGCTTAGGCTCATAAACTGGTGGCTTTGGAGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGA
60 GTGGCTTAGGCTCATAAACTGGTGGCTTTGGAGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGA
* * *
29075894 GGCTCATACACCGGTGGTTTCTTGGGAGGTTCATAAACTGGTGGTTTGGGTTC
125 GGCTCATACACCGGAGGCTTCTTGGGAGGCTCATAAACTGGTGGTTTGGGTTC
29075947 TGGCTTT
1 TGGCTTT
29075954 TCCTTCTTTG
Statistics
Matches: 174, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
177 31 0.18
180 1 0.01
181 2 0.01
183 140 0.80
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (177 bp):
TGGCTTTGGAGGCTTAGGTTCATAAACTGGTGGCTTAGGCTCATAAACTGGTGGCTTTGGTGGCT
TAGGCTCATAAACTGGTGGCTTTGGAGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCA
TACACCGGAGGCTTCTTGGGAGGCTCATAAACTGGTGGTTTGGGTTC
Found at i:29075865 original size:96 final size:94
Alignment explanation
Indices: 29075669--29075944 Score: 288
Period size: 87 Copynumber: 3.0 Consensus size: 94
29075659 ATAAACTGGT
* * *
29075669 GGCTTTGGTGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCATACACCGGAGGCTTCTT
1 GGCTTTGGAGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCATAAACCGGAGGCTTCTG
* *
29075734 TGGAGGCTCATATACTGGTGGTTTGGGTTCT
66 TGGAGGCTCATAAACTGGTGGTTTGGG-T-A
* * * *
29075765 GGCTTTGGAGGCTTAGGTTCATATACTGGTGGTTTCTTTGGAGGCTCATAAACTGGTGGCTT-TG
1 GGCTTTGGAGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCATAAACCGGAGGCTTCT-
29075829 GTGGCTTAGGCTCATAAAC--------T-GGT-
65 GTGG---AGGCTCATAAACTGGTGGTTTGGGTA
* * *
29075852 GGCTTTGGAGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCATACACCGGTGGTTTCT-
1 GGCTTTGGAGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCATAAACCGGAGGCTTCTG
*
29075916 TGGGAGGTTCATAAACTGGTGGTTTGGGT
66 T-GGAGGCTCATAAACTGGTGGTTTGGGT
29075945 TCTGGCTTTT
Statistics
Matches: 151, Mismatches: 14, Indels: 33
0.76 0.07 0.17
Matches are distributed among these distances:
84 11 0.07
86 1 0.01
87 59 0.39
88 1 0.01
89 1 0.01
90 2 0.01
91 1 0.01
92 1 0.01
93 3 0.02
95 1 0.01
96 59 0.39
99 11 0.07
ACGTcount: A:0.16, C:0.16, G:0.33, T:0.35
Consensus pattern (94 bp):
GGCTTTGGAGGCTTAGGTTCATAAACTGGCGGTTTCTTTGGAGGCTCATAAACCGGAGGCTTCTG
TGGAGGCTCATAAACTGGTGGTTTGGGTA
Found at i:29075938 original size:27 final size:27
Alignment explanation
Indices: 29075783--29075940 Score: 129
Period size: 27 Copynumber: 5.6 Consensus size: 27
29075773 AGGCTTAGGT
* *
29075783 TCATATACTGGTGGTTTCTTTGGAGGC
1 TCATAAACTGGTGGTTTCTTGGGAGGC
** *
29075810 TCATAAACTGGTGGCTTTGGTGGCTTAGGC
1 TCATAAACTGGTGG-TTTCTTGG--GAGGC
* * *
29075840 TCATAAACTGGTGGCTT-TGGAGGCTTAGGT
1 TCATAAACTGGTGGTTTCTTG-GG---AGGC
* *
29075870 TCATAAACTGGCGGTTTCTTTGGAGGC
1 TCATAAACTGGTGGTTTCTTGGGAGGC
* * *
29075897 TCATACACCGGTGGTTTCTTGGGAGGT
1 TCATAAACTGGTGGTTTCTTGGGAGGC
29075924 TCATAAACTGGTGGTTT
1 TCATAAACTGGTGGTTT
29075941 GGGTTCTGGC
Statistics
Matches: 101, Mismatches: 22, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
27 53 0.52
28 6 0.06
29 3 0.03
30 38 0.38
31 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (27 bp):
TCATAAACTGGTGGTTTCTTGGGAGGC
Found at i:29075976 original size:45 final size:44
Alignment explanation
Indices: 29075912--29076067 Score: 151
Period size: 45 Copynumber: 3.6 Consensus size: 44
29075902 CACCGGTGGT
*
29075912 TTCTTGGGAGGTTCATAAACTGGTGGTTTGGGTTCTGGCTTTTCC
1 TTCTTTGGAGGTTCATAAACTGGTGGTTTGGGTTCTGGC-TTTCC
* * * * *
29075957 TTCTTTGGAGGTTCGTAAACCGGTGGCTTGGGCTCCGGCTTCTCC
1 TTCTTTGGAGGTTCATAAACTGGTGGTTTGGGTTCTGGCTT-TCC
* * * * *
29076002 TTCTTTGGGGGTTCATAGACAGGGGGTTGGGGTTCTGG-----C
1 TTCTTTGGAGGTTCATAAACTGGTGGTTTGGGTTCTGGCTTTCC
*
29076041 TTCTTTGGAGGTTCGTAAACTGGTGGT
1 TTCTTTGGAGGTTCATAAACTGGTGGT
29076068 GGTTTGTAAA
Statistics
Matches: 90, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
39 23 0.26
44 2 0.02
45 65 0.72
ACGTcount: A:0.11, C:0.17, G:0.35, T:0.37
Consensus pattern (44 bp):
TTCTTTGGAGGTTCATAAACTGGTGGTTTGGGTTCTGGCTTTCC
Found at i:29082289 original size:18 final size:18
Alignment explanation
Indices: 29082263--29082298 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29082253 AGTACTTCAT
* *
29082263 AAAATAAAAAAGAACAAA
1 AAAAAAAAAAAAAACAAA
29082281 AAAAAAAAAAAAAACAAA
1 AAAAAAAAAAAAAACAAA
29082299 GAATTGAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.89, C:0.06, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAAAAACAAA
Found at i:29083004 original size:51 final size:51
Alignment explanation
Indices: 29082921--29083334 Score: 765
Period size: 51 Copynumber: 8.1 Consensus size: 51
29082911 AGCTTGTCGT
* *
29082921 GGCGGCTTGTGGGGTGGTTCATCATGTGGAGGCTCAACGGGCGGTTGGTCA
1 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
* *
29082972 GGAGGCTGGTGGGGTGGTTCATCATGTGGAGGCTCAACGGGCGGTTGGTCA
1 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
*
29083023 GGAGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
1 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
29083074 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
1 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
*
29083125 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCTCAACGGGCGGTTGGTCA
1 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
*
29083176 GGAGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
1 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
29083227 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
1 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
29083278 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
1 GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
29083329 GGCGGC
1 GGCGGC
29083335 CCAAGTGGAG
Statistics
Matches: 355, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 355 1.00
ACGTcount: A:0.12, C:0.18, G:0.47, T:0.22
Consensus pattern (51 bp):
GGCGGCTGGTGGGGTGGTTCATCATGTGGAGGCCCAACGGGCGGTTGGTCA
Found at i:29086439 original size:201 final size:201
Alignment explanation
Indices: 29085967--29086474 Score: 793
Period size: 201 Copynumber: 2.5 Consensus size: 201
29085957 TTGTGCTCAA
* * *
29085967 GTGGAGGCGTCTCCCCCTTACCCTTGGGTGGTTTTCCACCGGAAAATATTGGTGGCTTGTGCGAG
1 GTGGAGGCTTCTCTCCCTTACCCTTGGGTGGTTTACCACCGGAAAATATTGGTGGCTTGTGCGAG
29086032 TCCTCAACATCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTCC
66 TCCTCAACATCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTCC
29086097 CTCACCCTTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTCAT
131 CTCACCCTTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTCAT
29086162 GTCCAT
196 GTCCAT
* * * * * *
29086168 GTGGAGGCTTCTCTCCCGTGCCCTTGGGTGGTTTACCACCGGAAAATCTTGGTGGCTCGCGGGAG
1 GTGGAGGCTTCTCTCCCTTACCCTTGGGTGGTTTACCACCGGAAAATATTGGTGGCTTGTGCGAG
*
29086233 TCCTCAACATCCTCACCTAGGAGGCGTCTGTGGGGAGGTTTGTGGTCATGGGGTGGCTCCTTTCC
66 TCCTCAACATCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTCC
29086298 CTCACCCTTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTCAT
131 CTCACCCTTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTCAT
*
29086363 GTCCTT
196 GTCCAT
* * **** * * * * *
29086369 GTGGAGGCTTCTCTCCCTTACCCTTGGGTGGTTTACCGCCTGTGGTTTTTGGAGGTTTGTGTGTG
1 GTGGAGGCTTCTCTCCCTTACCCTTGGGTGGTTTACCACCGGAAAATATTGGTGGCTTGTGCGAG
*
29086434 TCCTCAACATCCTCA-CTCAGGAGGTGTCTGTGAGGAGGTTT
66 TCCTCAACATCCTCACCT-AGGAGGCGTCTGTGAGGAGGTTT
29086475 TTCCCCATGT
Statistics
Matches: 278, Mismatches: 28, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
200 2 0.01
201 276 0.99
ACGTcount: A:0.13, C:0.25, G:0.30, T:0.32
Consensus pattern (201 bp):
GTGGAGGCTTCTCTCCCTTACCCTTGGGTGGTTTACCACCGGAAAATATTGGTGGCTTGTGCGAG
TCCTCAACATCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTCC
CTCACCCTTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTCAT
GTCCAT
Found at i:29089456 original size:26 final size:26
Alignment explanation
Indices: 29089427--29089477 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
29089417 GATTAATTCT
*
29089427 AAATAATTATAAAAATAT-AAGATAAA
1 AAATAATAATAAAAAT-TGAAGATAAA
*
29089453 AAATAATAATTAAAATTGAAGATAA
1 AAATAATAATAAAAATTGAAGATAA
29089478 TTCATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (26 bp):
AAATAATAATAAAAATTGAAGATAAA
Found at i:29091515 original size:100 final size:100
Alignment explanation
Indices: 29091403--29091604 Score: 350
Period size: 100 Copynumber: 2.0 Consensus size: 100
29091393 AATAATTATT
*
29091403 TTATTTTATTCTTATCTATTCTGCAAACTAAACATATTTATGATGCTACGTCCATTTCCATCAAT
1 TTATTTTATTCTTATCTATTCTGCAAACTAAACATATTTACGATGCTACGTCCATTTCCATCAAT
* *
29091468 TAGGATTATGACTAAAATTAAATTACGCGCCTAAC
66 TAGGATTAGGACTAAAAGTAAATTACGCGCCTAAC
*
29091503 TTATTTTATTCTTATCTATTCTGCAAACTAAACATATTTACGATGCTACGTCCATTTCCGTCAAT
1 TTATTTTATTCTTATCTATTCTGCAAACTAAACATATTTACGATGCTACGTCCATTTCCATCAAT
* *
29091568 TAGGATTAGGATTAAAAGTAGATTACGCGCCTAAC
66 TAGGATTAGGACTAAAAGTAAATTACGCGCCTAAC
29091603 TT
1 TT
29091605 TTCTGATCAT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (100 bp):
TTATTTTATTCTTATCTATTCTGCAAACTAAACATATTTACGATGCTACGTCCATTTCCATCAAT
TAGGATTAGGACTAAAAGTAAATTACGCGCCTAAC
Found at i:29097448 original size:19 final size:19
Alignment explanation
Indices: 29097421--29097467 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
29097411 ATCTTCTTGG
29097421 CTTTC-TGTTATTCTTCTT
1 CTTTCTTGTTATTCTTCTT
*
29097439 CTTTCTTGTTTCTTCTTCTT
1 CTTTCTTG-TTATTCTTCTT
29097459 -TTTCTTGTT
1 CTTTCTTGTT
29097468 TGGTCCAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 7 0.27
19 9 0.35
20 10 0.38
ACGTcount: A:0.02, C:0.21, G:0.06, T:0.70
Consensus pattern (19 bp):
CTTTCTTGTTATTCTTCTT
Found at i:29103463 original size:14 final size:14
Alignment explanation
Indices: 29103444--29103470 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29103434 CATATTTGTA
29103444 TATATTAGTCACTT
1 TATATTAGTCACTT
29103458 TATATTAGTCACT
1 TATATTAGTCACT
29103471 ATCATAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (14 bp):
TATATTAGTCACTT
Found at i:29111840 original size:2 final size:2
Alignment explanation
Indices: 29111829--29111875 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
29111819 TCGGAATTAA
* *
29111829 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29111870 AT AT AT
1 AT AT AT
29111876 CACAATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:29113542 original size:49 final size:48
Alignment explanation
Indices: 29113489--29113582 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 48
29113479 TAGCATACTG
29113489 TTTATAATTAGTTATTATTTATACAAATTTTGATATAAAATATTATAA
1 TTTATAATTAGTTATTATTTATACAAATTTTGATATAAAATATTATAA
*
29113537 NTTTATAATTAGTTTTTATTTATACAAATTTTGATATAAAATATTA
1 -TTTATAATTAGTTATTATTTATACAAATTTTGATATAAAATATTA
29113583 AAACATATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.51
Consensus pattern (48 bp):
TTTATAATTAGTTATTATTTATACAAATTTTGATATAAAATATTATAA
Found at i:29126540 original size:26 final size:24
Alignment explanation
Indices: 29126488--29126537 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
29126478 AGTTAAATTG
*
29126488 TTACACGTTATATATAAAAATATA
1 TTACACGTCATATATAAAAATATA
*
29126512 TTACACGTCATGTATAAAAA-ATA
1 TTACACGTCATATATAAAAATATA
29126535 TTA
1 TTA
29126538 TTATTACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (24 bp):
TTACACGTCATATATAAAAATATA
Found at i:29126614 original size:29 final size:29
Alignment explanation
Indices: 29126581--29126648 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
29126571 GTTATATTAG
* * *
29126581 AAAAATGTTAATGTTCCACATTATGTTGA
1 AAAAATATTAATGTTACACATCATGTTGA
* * *
29126610 AAAAATATTATTGTTATACGTCATGTTGA
1 AAAAATATTAATGTTACACATCATGTTGA
29126639 AAAAATATTA
1 AAAAATATTA
29126649 TTATTAATGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (29 bp):
AAAAATATTAATGTTACACATCATGTTGA
Found at i:29158713 original size:29 final size:29
Alignment explanation
Indices: 29158680--29158736 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
29158670 CTTATCATCC
29158680 CCTTCTCGACAAATGAAATCTCATTTTGA
1 CCTTCTCGACAAATGAAATCTCATTTTGA
29158709 CCTTCTCGACAAATGAAATCTCATTTTG
1 CCTTCTCGACAAATGAAATCTCATTTTG
29158737 GTAATTACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (29 bp):
CCTTCTCGACAAATGAAATCTCATTTTGA
Found at i:29159539 original size:2 final size:2
Alignment explanation
Indices: 29159532--29159562 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29159522 TATCAACAAT
*
29159532 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29159563 TTGAGATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:29176599 original size:32 final size:32
Alignment explanation
Indices: 29176559--29176622 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
29176549 GCTGCCCATA
29176559 CCATCACTGGCAA-CCACCAACTGCCATCCTTC
1 CCATCACTGG-AAGCCACCAACTGCCATCCTTC
29176591 CCATCACTGGAAGCCACCAACTGCCATCCTTC
1 CCATCACTGGAAGCCACCAACTGCCATCCTTC
29176623 TCTATTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.25, C:0.45, G:0.11, T:0.19
Consensus pattern (32 bp):
CCATCACTGGAAGCCACCAACTGCCATCCTTC
Found at i:29180057 original size:24 final size:23
Alignment explanation
Indices: 29180000--29180061 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
29179990 ATACAATAAC
*
29180000 CTTATACTAATATAATTAGGAAT
1 CTTATTCTAATATAATTAGGAAT
29180023 CTTATTCTAATATAATTAGGAATT
1 CTTATTCTAATATAATTAGGAA-T
* *
29180047 GTTATTTTAATATAA
1 CTTATTCTAATATAA
29180062 CTAGATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 21 0.60
24 14 0.40
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.45
Consensus pattern (23 bp):
CTTATTCTAATATAATTAGGAAT
Found at i:29183530 original size:23 final size:23
Alignment explanation
Indices: 29183504--29183549 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
29183494 ATACAATAAC
*
29183504 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
29183527 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
29183550 TGTTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:29197534 original size:16 final size:15
Alignment explanation
Indices: 29197513--29197552 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
29197503 CTCTCTTCTT
29197513 TCTCTTCTTTGTCCTC
1 TCTCTTCTTTGTCC-C
29197529 TCTCTTC-TTGTCCC
1 TCTCTTCTTTGTCCC
29197543 TCTTCTTCTT
1 TC-TCTTCTT
29197553 CTTCTTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 11 0.50
16 8 0.36
ACGTcount: A:0.00, C:0.38, G:0.05, T:0.57
Consensus pattern (15 bp):
TCTCTTCTTTGTCCC
Found at i:29200296 original size:13 final size:13
Alignment explanation
Indices: 29200266--29200304 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
29200256 TTAGATATCA
*
29200266 ATAATTTATT-AT
1 ATAAATTATTAAT
29200278 -TAAATTATTAAT
1 ATAAATTATTAAT
29200290 ATAAATTATTAAT
1 ATAAATTATTAAT
29200303 AT
1 AT
29200305 TTTGAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 8 0.33
12 2 0.08
13 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATAAATTATTAAT
Found at i:29200338 original size:20 final size:20
Alignment explanation
Indices: 29200274--29200339 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
29200264 CAATAATTTA
* *
29200274 TTATTAAATTATTAATATAAA
1 TTATTAAATTATTGA-ATAAT
*
29200295 TTATTAATATT-TTGAAT-TT
1 TTATTAA-ATTATTGAATAAT
29200314 ATTATTAAATTATTGAATAAT
1 -TTATTAAATTATTGAATAAT
29200335 TTATT
1 TTATT
29200340 TTTAAATTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
19 3 0.08
20 20 0.54
21 11 0.30
22 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATTAAATTATTGAATAAT
Found at i:29200360 original size:23 final size:23
Alignment explanation
Indices: 29200265--29200348 Score: 72
Period size: 23 Copynumber: 3.9 Consensus size: 23
29200255 ATTAGATATC
*
29200265 AATAATTTATTATTAAATTATT-
1 AATAATTTATTTTTAAATTATTG
** *
29200287 AAT-ATAAATTATTAATATT-TTG
1 AATAATTTATTTTTAA-ATTATTG
*
29200309 ---AATTTATTATTAAATTATTG
1 AATAATTTATTTTTAAATTATTG
29200329 AATAATTTATTTTTAAATTA
1 AATAATTTATTTTTAAATTA
29200349 GTTGGATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
19 3 0.06
20 13 0.26
21 12 0.24
22 6 0.12
23 16 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AATAATTTATTTTTAAATTATTG
Found at i:29200469 original size:14 final size:14
Alignment explanation
Indices: 29200444--29200480 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29200434 AACATCAATA
29200444 ATTTATTATTAAATT
1 ATTTA-TATTAAATT
29200459 ATTTATATTAAATT
1 ATTTATATTAAATT
*
29200473 AGTTATAT
1 ATTTATAT
29200481 AATTTTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
ATTTATATTAAATT
Found at i:29203506 original size:4 final size:4
Alignment explanation
Indices: 29203497--29203531 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
29203487 AAAGAAAAAG
*
29203497 ATAC ATAC ATAC ATAC ATAC AAAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
29203532 TAAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:29203555 original size:17 final size:17
Alignment explanation
Indices: 29203529--29203562 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29203519 ACATACATAC
29203529 ATATAAATATAAATATT
1 ATATAAATATAAATATT
* *
29203546 ATATATATATATATATT
1 ATATAAATATAAATATT
29203563 TATCTAGAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAAATATAAATATT
Found at i:29205741 original size:27 final size:27
Alignment explanation
Indices: 29205696--29205750 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
29205686 CAAGCGTTTT
29205696 AATCATTCATCAGGCTTGCATGTGAGG
1 AATCATTCATCAGGCTTGCATGTGAGG
* * *
29205723 AATCGTTCATCTGGTTTGCATGTGAGG
1 AATCATTCATCAGGCTTGCATGTGAGG
29205750 A
1 A
29205751 GGCATGTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (27 bp):
AATCATTCATCAGGCTTGCATGTGAGG
Found at i:29207823 original size:3 final size:3
Alignment explanation
Indices: 29207812--29207846 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
29207802 TTTTTTTTTT
29207812 TTG TT- TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
29207847 GAGATATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:29213005 original size:45 final size:45
Alignment explanation
Indices: 29212941--29213082 Score: 257
Period size: 45 Copynumber: 3.2 Consensus size: 45
29212931 CTATTACAAG
*
29212941 AGAGGCAGCACCTCAACAAAGCTCACAAATAGAATCAAGTTCGTC
1 AGAGGCTGCACCTCAACAAAGCTCACAAATAGAATCAAGTTCGTC
*
29212986 AGAGGCTGCACCTCAACAAATCTCACAAATAGAATCAAGTTCGTC
1 AGAGGCTGCACCTCAACAAAGCTCACAAATAGAATCAAGTTCGTC
*
29213031 AGAGGCTGCACCTCAACAAAGCTCACAAATAGAATCAAGGTCGTC
1 AGAGGCTGCACCTCAACAAAGCTCACAAATAGAATCAAGTTCGTC
29213076 AGAGGCT
1 AGAGGCT
29213083 TCAGCAATTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 93 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (45 bp):
AGAGGCTGCACCTCAACAAAGCTCACAAATAGAATCAAGTTCGTC
Found at i:29213602 original size:14 final size:14
Alignment explanation
Indices: 29213585--29213642 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 14
29213575 ATTAAGATTT
29213585 AATTATATAATATA
1 AATTATATAATATA
*
29213599 AATTGTATAA-ATTA
1 AATTATATAATA-TA
29213613 AATTATATATTATATA
1 AATTATATA--ATATA
29213629 AA-TATTATAATATA
1 AATTA-TATAATATA
29213643 TTTAATATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 1 0.03
14 24 0.65
15 2 0.05
16 9 0.24
17 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
AATTATATAATATA
Found at i:29213858 original size:28 final size:28
Alignment explanation
Indices: 29213803--29213860 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
29213793 TTGCATACAG
*
29213803 CATACATGCATACACACATACAAGCACA
1 CATACATGCATACACACAAACAAGCACA
*
29213831 CATACATGCATAGACACAAACATA-CACA
1 CATACATGCATACACACAAACA-AGCACA
29213859 CA
1 CA
29213861 CAAAGAATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.48, C:0.31, G:0.07, T:0.14
Consensus pattern (28 bp):
CATACATGCATACACACAAACAAGCACA
Found at i:29214686 original size:2 final size:2
Alignment explanation
Indices: 29214679--29214704 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29214669 ACATACATAC
29214679 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29214705 GTACACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29219046 original size:21 final size:21
Alignment explanation
Indices: 29219020--29219060 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
29219010 CAATTGATTC
29219020 CAGTCCGATTGATATGTCTTT
1 CAGTCCGATTGATATGTCTTT
*
29219041 CAGTCCTATTGATATGTCTT
1 CAGTCCGATTGATATGTCTT
29219061 CCTCAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (21 bp):
CAGTCCGATTGATATGTCTTT
Found at i:29230055 original size:21 final size:21
Alignment explanation
Indices: 29229980--29230062 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
29229970 TTCTCAAATT
**
29229980 GATTTTAAGGTTTAATGAATC
1 GATTTTAAGGTTTCGTGAATC
* *
29230001 GATTCT-AGTGTTTGGTGAA-C
1 GATTTTAAG-GTTTCGTGAATC
* *
29230021 TAGTTTT-AGAGTTTCTTGAATC
1 GA-TTTTAAG-GTTTCGTGAATC
29230043 GATTTTAAGGTTTCGTGAAT
1 GATTTTAAGGTTTCGTGAAT
29230063 AGAGTTTAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
20 4 0.08
21 40 0.83
22 4 0.08
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (21 bp):
GATTTTAAGGTTTCGTGAATC
Found at i:29230070 original size:21 final size:22
Alignment explanation
Indices: 29230022--29230070 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
29230012 TTGGTGAACT
* * *
29230022 AGTTTTAGAGTTTCTTGAATCG
1 AGTTTAAGAGTTTCGTGAATAG
*
29230044 ATTTTAAG-GTTTCGTGAATAG
1 AGTTTAAGAGTTTCGTGAATAG
29230065 AGTTTA
1 AGTTTA
29230071 GGATTTTCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (22 bp):
AGTTTAAGAGTTTCGTGAATAG
Found at i:29231053 original size:22 final size:21
Alignment explanation
Indices: 29231023--29231066 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 21
29231013 TTTGCAAAGC
*
29231023 TCAATGTAATATTGACCACGTTT
1 TCAATGTAAT-TTG-CAACGTTT
29231046 TCAA-GTAATTTGCAACGTTT
1 TCAATGTAATTTGCAACGTTT
29231066 T
1 T
29231067 GGATAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 5 0.25
23 4 0.20
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (21 bp):
TCAATGTAATTTGCAACGTTT
Found at i:29235722 original size:6 final size:6
Alignment explanation
Indices: 29235713--29235739 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29235703 CAAAAGCATT
29235713 GAATGG GAATGG GAATGG GAATGG GAA
1 GAATGG GAATGG GAATGG GAATGG GAA
29235740 GACTGTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.48, T:0.15
Consensus pattern (6 bp):
GAATGG
Found at i:29245699 original size:3 final size:3
Alignment explanation
Indices: 29245693--29245724 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29245683 GGAGGAGGAG
29245693 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
29245725 GAACGCGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29247405 original size:6 final size:6
Alignment explanation
Indices: 29247394--29247423 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
29247384 GCAACTCAAT
29247394 GCAAAG GCAAAG GCAAAG GCAAAG GCAAAG
1 GCAAAG GCAAAG GCAAAG GCAAAG GCAAAG
29247424 CTTCCAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (6 bp):
GCAAAG
Found at i:29258398 original size:3 final size:3
Alignment explanation
Indices: 29258390--29258416 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29258380 TTTTGGGGGA
29258390 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
29258417 GGTATTTTGT
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):
ATT
Found at i:29263832 original size:2 final size:2
Alignment explanation
Indices: 29263827--29263852 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29263817 TTTTTTGGAT
29263827 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
29263853 AACCGGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29263985 original size:2 final size:2
Alignment explanation
Indices: 29263978--29264010 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29263968 TATGATGATT
*
29263978 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
29264011 GGGGCCGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29264456 original size:2 final size:2
Alignment explanation
Indices: 29264449--29264484 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29264439 GTGTNATCAG
29264449 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
29264485 ACAAAGGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29270829 original size:12 final size:12
Alignment explanation
Indices: 29270812--29270836 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29270802 TCTCGTTTTC
29270812 ATATTACTCCTT
1 ATATTACTCCTT
29270824 ATATTACTCCTT
1 ATATTACTCCTT
29270836 A
1 A
29270837 GAAATGCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATTACTCCTT
Found at i:29278407 original size:2 final size:2
Alignment explanation
Indices: 29278400--29278430 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29278390 AGAAATTTGC
29278400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29278431 TACAATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29281205 original size:38 final size:38
Alignment explanation
Indices: 29281163--29281239 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
29281153 TTTTTGAAAG
29281163 ATAGTTATTTAGTATGTTAATCTTTAATTTGATATTGT
1 ATAGTTATTTAGTATGTTAATCTTTAATTTGATATTGT
29281201 ATAGTTATTTAGTATGTTAATCTTTAATTTGATATTGT
1 ATAGTTATTTAGTATGTTAATCTTTAATTTGATATTGT
29281239 A
1 A
29281240 CTTGGATTGG
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:0.30, C:0.03, G:0.13, T:0.55
Consensus pattern (38 bp):
ATAGTTATTTAGTATGTTAATCTTTAATTTGATATTGT
Found at i:29303486 original size:2 final size:2
Alignment explanation
Indices: 29303479--29303544 Score: 73
Period size: 2 Copynumber: 32.5 Consensus size: 2
29303469 TGGAGAAAAT
* *
29303479 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GTA G- GT CA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA
29303520 TGNA GA GA GA GA GA GA GA GA GA GA G
1 -G-A GA GA GA GA GA GA GA GA GA GA G
29303545 TGGGAAATGG
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
1 2 0.04
2 51 0.91
3 2 0.04
4 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.48, T:0.05
Consensus pattern (2 bp):
GA
Found at i:29306167 original size:3 final size:3
Alignment explanation
Indices: 29306153--29306182 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
29306143 CAAAATGGTG
*
29306153 TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
29306183 CAGTAGTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:29306758 original size:21 final size:21
Alignment explanation
Indices: 29306734--29306773 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
29306724 AAACATCAGA
29306734 TTCTGAAGTTGA-CATGACAGC
1 TTCTGAAGTT-ACCATGACAGC
29306755 TTCTGAAGTTACCATGACA
1 TTCTGAAGTTACCATGACA
29306774 CTAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
TTCTGAAGTTACCATGACAGC
Found at i:29319860 original size:24 final size:25
Alignment explanation
Indices: 29319828--29319875 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29319818 TAATATAGAA
29319828 TCATAATAA-TAAAAGATTTAATTT
1 TCATAATAATTAAAAGATTTAATTT
* *
29319852 TCATGATAATTAAAAGGTTTAATT
1 TCATAATAATTAAAAGATTTAATT
29319876 AATTTTATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (25 bp):
TCATAATAATTAAAAGATTTAATTT
Found at i:29321570 original size:22 final size:23
Alignment explanation
Indices: 29321543--29321587 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
29321533 ACACCATGGA
29321543 GATCTTTTTAATCAAAA-AAATT
1 GATCTTTTTAATCAAAAGAAATT
*
29321565 GATCTTTTTAATGAAAAGAAATT
1 GATCTTTTTAATCAAAAGAAATT
29321588 TCATTCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (23 bp):
GATCTTTTTAATCAAAAGAAATT
Found at i:29322920 original size:2 final size:2
Alignment explanation
Indices: 29322913--29322946 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29322903 TATAAAACAA
29322913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29322947 GAATAAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29323742 original size:16 final size:17
Alignment explanation
Indices: 29323721--29323765 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
29323711 TTTTATTTTT
29323721 ATATTTTAAAATATT-A
1 ATATTTTAAAATATTCA
*
29323737 ATA-TTTAAATTATTCA
1 ATATTTTAAAATATTCA
29323753 ATATTATTAAAAT
1 ATATT-TTAAAAT
29323766 TAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.42
16 7 0.29
17 1 0.04
18 6 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTTTAAAATATTCA
Found at i:29323800 original size:18 final size:17
Alignment explanation
Indices: 29323741--29323806 Score: 51
Period size: 18 Copynumber: 3.7 Consensus size: 17
29323731 ATATTAATAT
* *
29323741 TTAAATTATTCAATATTA
1 TTAAATTATTTAAT-TAA
* *
29323759 TTAAAATTAATAAATTAA
1 TT-AAATTATTTAATTAA
*
29323777 TAAAATTATTTAATGTAA
1 TTAAATTATTTAAT-TAA
*
29323795 TTAAATTTTTTA
1 TTAAATTATTTA
29323807 TTTATAAACT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 10 0.26
18 18 0.47
19 10 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TTAAATTATTTAATTAA
Found at i:29327979 original size:3 final size:3
Alignment explanation
Indices: 29327971--29328002 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29327961 CAAGATATCT
29327971 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
29328003 GTTCTTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29347077 original size:16 final size:17
Alignment explanation
Indices: 29347058--29347095 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
29347048 CTCTTTATGA
*
29347058 AAAAACCATGAA-AAAT
1 AAAAACCATGAATAAAG
*
29347074 AAAAATCATGAATAAAG
1 AAAAACCATGAATAAAG
29347091 AAAAA
1 AAAAA
29347096 GAATACCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.71, C:0.08, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAAACCATGAATAAAG
Found at i:29347140 original size:26 final size:26
Alignment explanation
Indices: 29347111--29347165 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
29347101 CCCTTGGAAT
29347111 CATATAATTATTGGGATTACAATATC
1 CATATAATTATTGGGATTACAATATC
29347137 CATATAATTATTGGGATTACAATATC
1 CATATAATTATTGGGATTACAATATC
29347163 CAT
1 CAT
29347166 CCTCAACCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (26 bp):
CATATAATTATTGGGATTACAATATC
Found at i:29349329 original size:15 final size:16
Alignment explanation
Indices: 29349303--29349332 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29349293 TTTTTAATTT
29349303 TTAAAAATTAAAATCA
1 TTAAAAATTAAAATCA
29349319 TTAAAAA-TAAAATC
1 TTAAAAATTAAAATC
29349333 TACATAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAAAATCA
Found at i:29349502 original size:20 final size:20
Alignment explanation
Indices: 29349469--29349507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29349459 GAATAGAATT
* *
29349469 GAAAAAAATGAATATAAATA
1 GAAAAAAATAAATAAAAATA
*
29349489 GAAAAAATTAAATAAAAAT
1 GAAAAAAATAAATAAAAAT
29349508 TTATCTCTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (20 bp):
GAAAAAAATAAATAAAAATA
Found at i:29350657 original size:21 final size:21
Alignment explanation
Indices: 29350633--29350673 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29350623 TTATGAATAT
29350633 ATATAATT-ATATTATATATAC
1 ATATAATTAAT-TTATATATAC
*
29350654 ATATATTTAATTTATATATA
1 ATATAATTAATTTATATATA
29350674 AACATTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATAATTAATTTATATATAC
Found at i:29350671 original size:23 final size:23
Alignment explanation
Indices: 29350629--29350698 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
29350619 AATGTTATGA
*
29350629 ATATATATAATTATATTATATATAC
1 ATATATATAATT-TA-TATATAAAC
*
29350654 ATATATTTAATTTATATATAAAC
1 ATATATATAATTTATATATAAAC
29350677 AT-TACTATAATTTATA-ATAAAC
1 ATATA-TATAATTTATATATAAAC
29350699 TTTATTTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.20
23 20 0.49
24 2 0.05
25 11 0.27
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATATATAATTTATATATAAAC
Found at i:29350879 original size:217 final size:212
Alignment explanation
Indices: 29350635--29351270 Score: 836
Period size: 210 Copynumber: 3.0 Consensus size: 212
29350625 ATGAATATAT
* *
29350635 ATAATTATATTATATATACATATATTTAATTTATATATAAACATTACTATAATTTATAATAAACT
1 ATAA-TATATTATATATACATATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACT
* * * *
29350700 TTATTTATATGGTTATACTTAATAACTTTATTAGCTATCACTTTATATTTTATAATATATTGTTT
65 TTATTTATATGATTACACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATTGTTT
* * *
29350765 ATAATTAGTTATCATTATATAAAGTTTGATATAAAATATTATAACATATAAGTTATGTCATTAAT
130 ATAATTAGTTATTATTATATAAACTTTGATATAAAACATTATAACATATAAGTTATGT-ATTAAT
29350830 TTCATATATATATAATAAA
194 TTCATATATATATAATAAA
* * * * *
29350849 GTCATATATTATGTATATATATATATATTTAATTTATACATAGGCATTACTATAACTTATAATAG
1 AT-A-ATA-TAT-TATATATACATATATTTAATTTATACATAAGCATTACTATAATTTATAATAA
* *
29350914 ATTTTATTTATATGATTACACTTAATAACTTTATTAGTTATCA-TCTTAGATTTTATAACATATT
62 ACTTTATTTATATGATTACACTTAATAACTTTATTAGCTATCACT-TTAGATTTTATAACATATT
* *
29350978 ATTTATAATTAGTTATTATT-TATACGAACTTTGATATAAAACATTTTAACATATAA-TT-TGTA
126 GTTTATAATTAGTTATTATTATATA--AACTTTGATATAAAACATTATAACATATAAGTTATGTA
* *
29351040 TT-A-TTAATTTTATATATAATAAA
189 TTAATTTCA-TATATATATAATAAA
*
29351063 ATAATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAATTTATAATAAACTT
1 ATAATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTT
* * * * * *
29351128 CATTAATATGATTACACTTAAAAAGTTTATTAGCTATCACCTTAGATTTTATAGCATATTGTTTA
66 TATTTATATGATTACACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATTGTTTA
* * * *
29351193 TGATTAGTTATTATTTATACAAACTTTAATAT-AAACATTATAACATATAAGTTATATAATTAAT
131 TAATTAGTTATTA-TTATATAAACTTTGATATAAAACATTATAACATATAAGTTATGT-ATTAAT
29351257 TTCATATATATATA
194 TTCATATATATATA
29351271 TAATTATGGA
Statistics
Matches: 364, Mismatches: 42, Indels: 33
0.83 0.10 0.08
Matches are distributed among these distances:
209 17 0.05
210 130 0.36
211 7 0.02
212 9 0.02
213 14 0.04
214 20 0.05
215 6 0.02
216 12 0.03
217 122 0.34
218 27 0.07
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (212 bp):
ATAATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTT
TATTTATATGATTACACTTAATAACTTTATTAGCTATCACTTTAGATTTTATAACATATTGTTTA
TAATTAGTTATTATTATATAAACTTTGATATAAAACATTATAACATATAAGTTATGTATTAATTT
CATATATATATAATAAA
Found at i:29353950 original size:10 final size:10
Alignment explanation
Indices: 29353937--29353972 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
29353927 TATAATTAAT
29353937 TATATAAAAA
1 TATATAAAAA
29353947 TATATAAAAA
1 TATATAAAAA
29353957 T-TA-AAAAA
1 TATATAAAAA
29353965 -ATATAAAA
1 TATATAAAA
29353973 GTAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.29
9 6 0.25
10 11 0.46
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TATATAAAAA
Found at i:29353961 original size:17 final size:17
Alignment explanation
Indices: 29353941--29353982 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
29353931 ATTAATTATA
29353941 TAAAAATATATAAAAAT
1 TAAAAATATATAAAAAT
* *
29353958 TAAAAAAATATAAAAGT
1 TAAAAATATATAAAAAT
*
29353975 AAAAAATA
1 TAAAAATA
29353983 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
TAAAAATATATAAAAAT
Done.