Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 91 of 320
Found at i:29113869 original size:20 final size:20
Alignment explanation
Indices: 29113846--29113897 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
29113836 GTGGTCACAC
29113846 ACACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
29113866 ACACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
29113886 ACACGCCCGTGT
1 ACACGCCCGTGT
29113898 CCTCAGCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.33, G:0.37, T:0.19
Consensus pattern (20 bp):
ACACGCCCGTGTGGCTTGGG
Found at i:29115277 original size:42 final size:42
Alignment explanation
Indices: 29115168--29115332 Score: 154
Period size: 42 Copynumber: 3.9 Consensus size: 42
29115158 TAAGATGCCA
* * **
29115168 ATGCCATATCCCAGATATGGTCTTACATGGGATCACATATATCG
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCAC--ATATCG
* ** * *
29115212 ATGCCGATAGCCCA-ACTAT-GTCTTACACGATGTCCCGTATCG
1 ATGCC-ATATCCCAGAC-ATGGTCTTACACGAAATCACATATCG
* * *
29115254 ATGCCATGTCCTAGACATGGTCTTACATGAAATCACATATCG
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCACATATCG
* *
29115296 ATGCCATATCCCAGATATGGTCTTACATGAAATCACA
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCACA
29115333 CATAAGCCTA
Statistics
Matches: 98, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
41 7 0.07
42 64 0.65
44 18 0.18
45 9 0.09
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACACGAAATCACATATCG
Found at i:29121742 original size:27 final size:26
Alignment explanation
Indices: 29121682--29121791 Score: 121
Period size: 27 Copynumber: 4.1 Consensus size: 26
29121672 CATGGCTGCG
* *
29121682 AGAACAGATAATGTGACAGAGTCACC
1 AGAACAGATAATGTGGCAGAGCCACC
* *
29121708 AAATACAGATAATCGTGGCAGAACCACC
1 AGA-ACAGATAAT-GTGGCAGAGCCACC
*
29121736 AGAACAGATATATGTGGCAGAGCCACT
1 AGAACAGATA-ATGTGGCAGAGCCACC
* *
29121763 AGATCAGATAATTGTGGCATAGCCACC
1 AGAACAGATAA-TGTGGCAGAGCCACC
29121790 AG
1 AG
29121792 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
26 3 0.04
27 52 0.74
28 15 0.21
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (26 bp):
AGAACAGATAATGTGGCAGAGCCACC
Found at i:29121771 original size:54 final size:54
Alignment explanation
Indices: 29121682--29121791 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
29121672 CATGGCTGCG
*
29121682 AGAACAGATAATGTGACAGAGTCACCAAATACAGATAATCGTGGCAGAACCACC
1 AGAACAGATAATGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAACCACC
* * * * * *
29121736 AGAACAGATATATGTGGCAGAGCCACTAGAT-CAGATAATTGTGGCATAGCCACC
1 AGAACAGATA-ATGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAACCACC
29121790 AG
1 AG
29121792 GACGCTTCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 32 0.67
55 16 0.33
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (54 bp):
AGAACAGATAATGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAACCACC
Found at i:29123257 original size:24 final size:24
Alignment explanation
Indices: 29123222--29123295 Score: 112
Period size: 24 Copynumber: 3.1 Consensus size: 24
29123212 ACACAGTTCA
*
29123222 CCCTAATCAGCTCCTAAATCCTCT
1 CCCTGATCAGCTCCTAAATCCTCT
*
29123246 CCCTGATTAGCTCCTAAATCCTCT
1 CCCTGATCAGCTCCTAAATCCTCT
* *
29123270 CCCTTATCAGCTCCTAAATCTTCT
1 CCCTGATCAGCTCCTAAATCCTCT
29123294 CC
1 CC
29123296 AGACAGACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.22, C:0.41, G:0.05, T:0.32
Consensus pattern (24 bp):
CCCTGATCAGCTCCTAAATCCTCT
Found at i:29129548 original size:27 final size:26
Alignment explanation
Indices: 29129517--29129621 Score: 129
Period size: 27 Copynumber: 3.9 Consensus size: 26
29129507 TGGCTGCCAA
* *
29129517 AACAGATAATGTGACAGAGTCACCAG
1 AACAGATAATGTGGCAGAGCCACCAG
*
29129543 ACACAGATAATCGTGGCAGAACCACCAG
1 A-ACAGATAAT-GTGGCAGAGCCACCAG
29129571 AACAGATATATGTGGCAGAGCCACCAG
1 AACAGATA-ATGTGGCAGAGCCACCAG
* *
29129598 ATCAGATAATTGTGGCATAGCCAC
1 AACAGATAA-TGTGGCAGAGCCAC
29129622 TAGGACGCTT
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.03
27 51 0.74
28 16 0.23
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
AACAGATAATGTGGCAGAGCCACCAG
Found at i:29131090 original size:24 final size:24
Alignment explanation
Indices: 29131063--29131128 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
29131053 CACCCTAATC
* *
29131063 AGCTCCTAAATCCTCTCCCTGGTT
1 AGCTCCTAAATCCTCTCCCTGATG
*
29131087 AGCTCCTAAATCCTCTCCCTTATG
1 AGCTCCTAAATCCTCTCCCTGATG
*
29131111 AGCTCCTAAATCTTCTCC
1 AGCTCCTAAATCCTCTCC
29131129 AGACAGACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.20, C:0.38, G:0.09, T:0.33
Consensus pattern (24 bp):
AGCTCCTAAATCCTCTCCCTGATG
Found at i:29137810 original size:27 final size:28
Alignment explanation
Indices: 29137780--29137841 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
29137770 GTGATTTTGA
29137780 GTGAAAA-TGCCAAAAT-AGGATTAAATT
1 GTGAAAAGTG-CAAAATAAGGATTAAATT
* *
29137807 GTGAAAAGTGCAAATTGAAGGTTTAAATT
1 GTGAAAAGTGCAAAAT-AAGGATTAAATT
29137836 GTGAAA
1 GTGAAA
29137842 GAAATATGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 12 0.40
28 2 0.07
29 16 0.53
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (28 bp):
GTGAAAAGTGCAAAATAAGGATTAAATT
Found at i:29139038 original size:40 final size:40
Alignment explanation
Indices: 29138859--29139038 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
29138849 ATTAGCTGTG
* *
29138859 TTTTTAAAAAAATGCCACTATAGATCGAGCATTAGCGGCGC
1 TTTTT-AAAAAACGCCGCTATAGATCGAGCATTAGCGGCGC
* * * * * * *
29138900 TTTTTTAAAAACACCACTATAGATCAAGAATTAACAGCGC
1 TTTTTAAAAAACGCCGCTATAGATCGAGCATTAGCGGCGC
* *
29138940 TTTTTTAAAAACGCCGCTATAGATCGAGCATTAGCGGCGT
1 TTTTTAAAAAACGCCGCTATAGATCGAGCATTAGCGGCGC
*
29138980 TTTTTAAAAAACGCCGCTATAGATCGAGCATTAGCGGTG-
1 TTTTTAAAAAACGCCGCTATAGATCGAGCATTAGCGGCGC
*
29139019 TTTTTAAAAAAGCGTCGCTA
1 TTTTTAAAAAA-CGCCGCTA
29139039 ATGCTCGATC
Statistics
Matches: 121, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
39 11 0.09
40 105 0.87
41 5 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (40 bp):
TTTTTAAAAAACGCCGCTATAGATCGAGCATTAGCGGCGC
Found at i:29139385 original size:14 final size:14
Alignment explanation
Indices: 29139366--29139402 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29139356 TAATTATCAT
29139366 TATAGTTTAGGGTA
1 TATAGTTTAGGGTA
*
29139380 TATAGTTTAGGGTT
1 TATAGTTTAGGGTA
*
29139394 TATGGTTTA
1 TATAGTTTA
29139403 TGAGTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (14 bp):
TATAGTTTAGGGTA
Found at i:29139438 original size:21 final size:20
Alignment explanation
Indices: 29139386--29139467 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 20
29139376 GGTATATAGT
* *
29139386 TTAGGGTTTATGGTTTATGAG
1 TTAGAGTTTAAGGTTTA-GAG
* * *
29139407 TTAATATTTTAAGGTTTAGTG
1 TT-AGAGTTTAAGGTTTAGAG
* *
29139428 TTATGGGTTTAGGGTTTAAGAG
1 TTA-GAGTTTAAGGTTT-AGAG
29139450 TTAGAGTTTAAGGTTTAG
1 TTAGAGTTTAAGGTTTAG
29139468 GGGTTAGTGG
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
20 3 0.07
21 26 0.57
22 17 0.37
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.46
Consensus pattern (20 bp):
TTAGAGTTTAAGGTTTAGAG
Found at i:29139473 original size:21 final size:22
Alignment explanation
Indices: 29139414--29139521 Score: 87
Period size: 21 Copynumber: 5.0 Consensus size: 22
29139404 GAGTTAATAT
* *
29139414 TTTAAGGTTTA-GTGTTATGGG
1 TTTAAGGTTTAGGGGTTAGGGG
* * * *
29139435 TTTAGGGTTTAAGAGTTA-GAG
1 TTTAAGGTTTAGGGGTTAGGGG
*
29139456 TTTAAGGTTTAGGGGTTAGTGG
1 TTTAAGGTTTAGGGGTTAGGGG
* *
29139478 -TTAGGGGTTAGGGGTTAGGGG
1 TTTAAGGTTTAGGGGTTAGGGG
* *
29139499 TTAAAGGGTTAGGGGTTAAGGGG
1 TTTAAGGTTTAGGGGTT-AGGGG
29139522 ATAGGGGGTT
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
21 45 0.64
22 20 0.29
23 5 0.07
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.36
Consensus pattern (22 bp):
TTTAAGGTTTAGGGGTTAGGGG
Found at i:29139498 original size:7 final size:7
Alignment explanation
Indices: 29139464--29139528 Score: 85
Period size: 7 Copynumber: 9.0 Consensus size: 7
29139454 AGTTTAAGGT
29139464 TTAGGGG
1 TTAGGGG
*
29139471 TTAGTGG
1 TTAGGGG
29139478 TTAGGGG
1 TTAGGGG
29139485 TTAGGGG
1 TTAGGGG
29139492 TTAGGGG
1 TTAGGGG
*
29139499 TTAAAGGG
1 TT-AGGGG
29139507 TTAGGGG
1 TTAGGGG
29139514 TTAAGGGG
1 TT-AGGGG
*
29139522 ATAGGGG
1 TTAGGGG
29139529 GTTATGGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
7 39 0.76
8 12 0.24
ACGTcount: A:0.20, C:0.00, G:0.52, T:0.28
Consensus pattern (7 bp):
TTAGGGG
Found at i:29139509 original size:15 final size:14
Alignment explanation
Indices: 29139436--29139520 Score: 91
Period size: 14 Copynumber: 6.0 Consensus size: 14
29139426 TGTTATGGGT
* *
29139436 TTAGGGTTTAAGAG
1 TTAGGGGTTAAGGG
* * *
29139450 TTAGAGTTTAAGGT
1 TTAGGGGTTAAGGG
29139464 TTAGGGGTT-AGTGG
1 TTAGGGGTTAAG-GG
*
29139478 TTAGGGGTTAGGGG
1 TTAGGGGTTAAGGG
29139492 TTAGGGGTTAAAGGG
1 TTAGGGGTT-AAGGG
29139507 TTAGGGGTTAAGGG
1 TTAGGGGTTAAGGG
29139521 GATAGGGGGT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
13 2 0.03
14 44 0.73
15 14 0.23
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (14 bp):
TTAGGGGTTAAGGG
Found at i:29139526 original size:15 final size:14
Alignment explanation
Indices: 29139464--29139528 Score: 85
Period size: 15 Copynumber: 4.5 Consensus size: 14
29139454 AGTTTAAGGT
*
29139464 TTAGGGGTTAGTGG
1 TTAGGGGTTAGGGG
29139478 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGGG
*
29139492 TTAGGGGTTAAAGGG
1 TTAGGGGTT-AGGGG
29139507 TTAGGGGTTAAGGGG
1 TTAGGGGTT-AGGGG
*
29139522 ATAGGGG
1 TTAGGGG
29139529 GTTATGGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
14 22 0.48
15 24 0.52
ACGTcount: A:0.20, C:0.00, G:0.52, T:0.28
Consensus pattern (14 bp):
TTAGGGGTTAGGGG
Found at i:29139589 original size:15 final size:15
Alignment explanation
Indices: 29139565--29139599 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29139555 ATATTTTAAG
*
29139565 GTTTATGGATTATGA
1 GTTTAGGGATTATGA
*
29139580 GTTTAGGGATTATGG
1 GTTTAGGGATTATGA
29139595 GTTTA
1 GTTTA
29139600 AAGTTTAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (15 bp):
GTTTAGGGATTATGA
Found at i:29139647 original size:15 final size:15
Alignment explanation
Indices: 29139580--29139648 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
29139570 TGGATTATGA
*
29139580 GTTT-AGGGATTATGG
1 GTTTAAGGGTTTA-GG
*
29139595 GTTTAA-AGTTTAGTG
1 GTTTAAGGGTTTAG-G
*
29139610 G-TT-AGGGGTTAGG
1 GTTTAAGGGTTTAGG
*
29139623 GGTTAAGGGTTTAGG
1 GTTTAAGGGTTTAGG
29139638 GTTTAAGGGTT
1 GTTTAAGGGTT
29139649 AAAAGGACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
13 3 0.07
14 10 0.23
15 29 0.67
16 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (15 bp):
GTTTAAGGGTTTAGG
Found at i:29139685 original size:14 final size:14
Alignment explanation
Indices: 29139666--29139716 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
29139656 CATGGGCTAT
29139666 GGGTTTAGAGTTTA
1 GGGTTTAGAGTTTA
**
29139680 GGGTTTA-AGGGTA
1 GGGTTTAGAGTTTA
* *
29139693 GGGGTTAAAGGTTTA
1 GGGTTTAGA-GTTTA
29139708 GGGTTTAGA
1 GGGTTTAGA
29139717 TTAATTAGTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 10 0.36
14 8 0.29
15 10 0.36
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (14 bp):
GGGTTTAGAGTTTA
Found at i:29140110 original size:43 final size:44
Alignment explanation
Indices: 29140036--29140122 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
29140026 GTCATGCCTG
** *
29140036 ACACTTAGCCATTTCCCCCAAAACCCCAAAACAAATTTTCCCAA
1 ACACTTAGCCATTTCCAACAAAACCCCAAAACAAATTTCCCCAA
* *
29140080 ACACTTAGCCATTT-TAACAAAACCCCAAAACACATTTCCCCAA
1 ACACTTAGCCATTTCCAACAAAACCCCAAAACAAATTTCCCCAA
29140123 TTCTTTGCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 24 0.63
44 14 0.37
ACGTcount: A:0.40, C:0.37, G:0.02, T:0.21
Consensus pattern (44 bp):
ACACTTAGCCATTTCCAACAAAACCCCAAAACAAATTTCCCCAA
Found at i:29142574 original size:16 final size:16
Alignment explanation
Indices: 29142549--29142583 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29142539 GAATTCATTT
*
29142549 TATGTGTGAATGCCTA
1 TATGTATGAATGCCTA
*
29142565 TATGTATGAATGCTTA
1 TATGTATGAATGCCTA
29142581 TAT
1 TAT
29142584 CTATCTTTTG
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:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (16 bp):
TATGTATGAATGCCTA
Found at i:29143640 original size:16 final size:16
Alignment explanation
Indices: 29143619--29143651 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29143609 TAGCATTTTA
29143619 ACTATTAAATTAATTG
1 ACTATTAAATTAATTG
*
29143635 ACTATTGAATTAATTG
1 ACTATTAAATTAATTG
29143651 A
1 A
29143652 TTAAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (16 bp):
ACTATTAAATTAATTG
Found at i:29143733 original size:15 final size:15
Alignment explanation
Indices: 29143713--29143745 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29143703 TAATTTGATG
*
29143713 TTTGGATGTTCCATT
1 TTTGGATGTACCATT
29143728 TTTGGATGTACCATT
1 TTTGGATGTACCATT
29143743 TTT
1 TTT
29143746 ATTCATCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.18, T:0.55
Consensus pattern (15 bp):
TTTGGATGTACCATT
Found at i:29148352 original size:43 final size:43
Alignment explanation
Indices: 29148316--29148447 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 43
29148306 TTACATGTTG
* * *
29148316 TCACATATCGATGCCACTGTCCCAGACAGGGTCTTACACGAAA
1 TCACATATCGATGCCAATGTCCCAGACATGGTCTTACACGTAA
* * *
29148359 TCATATAAT-GATGCCAATATCCGAGACATGGTCTTACACGTAA
1 TCACAT-ATCGATGCCAATGTCCCAGACATGGTCTTACACGTAA
* * *
29148402 TTACA-ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAA
1 TCACATAT-CGATGCCAATGTCCCAGACATGGTCTTACACGTAA
29148445 TCA
1 TCA
29148448 AATCTCGGTA
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 2 0.03
43 69 0.95
44 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (43 bp):
TCACATATCGATGCCAATGTCCCAGACATGGTCTTACACGTAA
Found at i:29153879 original size:42 final size:42
Alignment explanation
Indices: 29153751--29153916 Score: 147
Period size: 42 Copynumber: 3.9 Consensus size: 42
29153741 TAAGATGCCA
* * * *
29153751 ATGCCATATCCTAGATATGGTCTTACA-TAGGATCACATATATCG
1 ATGCCATATCCCAGACATGGTCTTACACGA-AATCAC--ATATCG
* * ** * *
29153795 ATGCCGATAGCCCA-ACTATGGTCTTATACGATGTCCCGTATCG
1 ATGCC-ATATCCCAGAC-ATGGTCTTACACGAAATCACATATCG
*
29153838 ATGCCATATCCCAGACATGGTCTTACATGAAATCACATATCG
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCACATATCG
* * *
29153880 ATGGCATATCCCAAATATGGTCTTACACGAAATCACA
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCACA
29153917 CATAACCCTA
Statistics
Matches: 98, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
42 60 0.61
43 12 0.12
44 6 0.06
45 19 0.19
46 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACACGAAATCACATATCG
Found at i:29157246 original size:50 final size:51
Alignment explanation
Indices: 29157156--29157291 Score: 148
Period size: 50 Copynumber: 2.7 Consensus size: 51
29157146 ACGGTTTTTT
* * * * *
29157156 GGTCGCGTGTGTAGTACTAAGTGCAGGTTACTACGTGTACCAGAT-GGTTA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTA
* * *
29157206 GGTCGCATGTATAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTTC
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTA
* * * * *
29157257 GATCACATGTGTGGTACTAAGTGTAGGCCACTATG
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATG
29157292 TGGAAGAGAC
Statistics
Matches: 71, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 39 0.55
51 32 0.45
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTA
Found at i:29160478 original size:14 final size:14
Alignment explanation
Indices: 29160436--29160480 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
29160426 AACTCTTAAA
*
29160436 TTTGCTGATTTATTA
1 TTTG-TGATTTATTT
* *
29160451 TTTATTATTTATTT
1 TTTGTGATTTATTT
29160465 TTTGTGATTTATTT
1 TTTGTGATTTATTT
29160479 TT
1 TT
29160481 CAGGTATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 22 0.88
15 3 0.12
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (14 bp):
TTTGTGATTTATTT
Found at i:29165668 original size:24 final size:24
Alignment explanation
Indices: 29165636--29165684 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29165626 ACAATGAGTA
29165636 TGCAAATGGATTGAATCATAACTT
1 TGCAAATGGATTGAATCATAACTT
29165660 TGCAAATGGATTGAATCATAACTT
1 TGCAAATGGATTGAATCATAACTT
29165684 T
1 T
29165685 ATGAGAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (24 bp):
TGCAAATGGATTGAATCATAACTT
Found at i:29167396 original size:25 final size:24
Alignment explanation
Indices: 29167327--29167409 Score: 123
Period size: 24 Copynumber: 3.4 Consensus size: 24
29167317 CTGGAGGCCT
*
29167327 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTGATAAACTGGGGCAA
29167351 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTTGATAAACTGGGGCAA
*
29167375 AGCCCTTTTCGGTAAACTGGGGCAA
1 AGCCCTTTT-GATAAACTGGGGCAA
29167400 AGCCCTTTTG
1 AGCCCTTTTG
29167410 CACTTCCTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.13
24 25 0.45
25 23 0.42
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTGGGGCAA
Found at i:29167467 original size:10 final size:10
Alignment explanation
Indices: 29167454--29167492 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
29167444 ATATATGAAT
29167454 ATATCATGGC
1 ATATCATGGC
29167464 ATATCATGTGC
1 ATATCATG-GC
29167475 ATATCATGGC
1 ATATCATGGC
29167485 ATATCATG
1 ATATCATG
29167493 TATAAAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:29167480 original size:21 final size:21
Alignment explanation
Indices: 29167454--29167493 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29167444 ATATATGAAT
29167454 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
29167475 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
29167494 ATAAAACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:29181547 original size:25 final size:24
Alignment explanation
Indices: 29181479--29181560 Score: 114
Period size: 25 Copynumber: 3.4 Consensus size: 24
29181469 CTGGAGGCCT
*
29181479 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTGATAAACTGGGGCAA
29181503 AGCCC-TTTGATAAACTGGGGCAA
1 AGCCCTTTTGATAAACTGGGGCAA
*
29181526 AGCCCTTTTCGGTAAACTGGGGCAA
1 AGCCCTTTT-GATAAACTGGGGCAA
29181551 AGCCCTTTTG
1 AGCCCTTTTG
29181561 CACTTCCTCC
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.09
23 17 0.32
24 8 0.15
25 23 0.43
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTGGGGCAA
Found at i:29181618 original size:10 final size:10
Alignment explanation
Indices: 29181605--29181643 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
29181595 ATATATGAAT
29181605 ATATCATGGC
1 ATATCATGGC
29181615 ATATCATGTGC
1 ATATCATG-GC
29181626 ATATCATGGC
1 ATATCATGGC
29181636 ATATCATG
1 ATATCATG
29181644 TATAAACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:29181631 original size:21 final size:21
Alignment explanation
Indices: 29181605--29181644 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29181595 ATATATGAAT
29181605 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
29181626 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
29181645 ATAAACAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:29189427 original size:25 final size:25
Alignment explanation
Indices: 29189393--29189462 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
29189383 CTCTTTTAAT
* *
29189393 AACTAGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
29189418 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
29189443 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
29189463 GCACTTCTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:29189521 original size:10 final size:10
Alignment explanation
Indices: 29189508--29189546 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
29189498 ATATATGAAT
29189508 ATATCATGGC
1 ATATCATGGC
29189518 ATATCATGTGC
1 ATATCATG-GC
29189529 ATATCATGGC
1 ATATCATGGC
29189539 ATATCATG
1 ATATCATG
29189547 TATAAAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:29189534 original size:21 final size:21
Alignment explanation
Indices: 29189508--29189547 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29189498 ATATATGAAT
29189508 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
29189529 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
29189548 ATAAAACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:29193236 original size:40 final size:40
Alignment explanation
Indices: 29193192--29193299 Score: 191
Period size: 40 Copynumber: 2.7 Consensus size: 40
29193182 AACCAGCACA
29193192 AATGCCTTCGGGACTTAACCCGGTTATAATAACCC-TCACG
1 AATGCCTTCGGGACTTAACCCGGTTATAATAACCCGT-ACG
*
29193232 AATGCCTTCGGGACTTAACCCGGTAATAATAACCCGTACG
1 AATGCCTTCGGGACTTAACCCGGTTATAATAACCCGTACG
29193272 AATGCCTTCGGGACTTAACCCGGTTATA
1 AATGCCTTCGGGACTTAACCCGGTTATA
29193300 TTTTTTTTCC
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 64 0.98
41 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGTTATAATAACCCGTACG
Found at i:29196480 original size:25 final size:25
Alignment explanation
Indices: 29196446--29196517 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
29196436 TCATGTACAT
* *
29196446 GTATGCTCACACAAGCTGTGAATCG
1 GTATGCTCACACGAGCTGTGAACCG
* *
29196471 GTATGATCACACGAGCTGTAAACCG
1 GTATGCTCACACGAGCTGTGAACCG
* *
29196496 ATATGCTCACACGAGTTGTGAA
1 GTATGCTCACACGAGCTGTGAA
29196518 AATAGGCCTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAACCG
Found at i:29216378 original size:33 final size:34
Alignment explanation
Indices: 29216301--29216381 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
29216291 TATGGGCCAT
*
29216301 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
* * **
29216335 AATGTAATCTGAA-AA-GGGCTCTGGCCCAGTATC
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGT-TC
29216368 ACTGTTATCTGAAT
1 ACTGTTATCTGAAT
29216382 GGGCTTAGGC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 13 0.34
33 14 0.37
34 11 0.29
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (34 bp):
ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
Found at i:29216386 original size:32 final size:30
Alignment explanation
Indices: 29216301--29216394 Score: 71
Period size: 32 Copynumber: 2.9 Consensus size: 30
29216291 TATGGGCCAT
* *
29216301 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAAT---GGGCT-TGGCCCAGTTC
* * *
29216335 AATGTAATCTGAAAAGGGCTCTGGCCCAGTATC
1 ACTGTTATCTG-AATGGGCT-TGGCCCAGT-TC
29216368 ACTGTTATCTGAATGGGCTTAGGCCCA
1 ACTGTTATCTGAATGGGCTT-GGCCCA
29216395 ATGGGCTTGA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
31 1 0.02
32 26 0.54
33 10 0.21
34 9 0.19
35 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (30 bp):
ACTGTTATCTGAATGGGCTTGGCCCAGTTC
Found at i:29219866 original size:40 final size:40
Alignment explanation
Indices: 29219807--29219984 Score: 220
Period size: 40 Copynumber: 4.5 Consensus size: 40
29219797 CGGATGGTAA
* *
29219807 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATA-T
* *
29219847 CCAGGCTAAGTCCCCAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
*
29219887 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
* *
29219927 CCGGGCTAAGTCCCAAAGGCATTT-TAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGT-GCAAGTTA-CTATAT
* *
29219967 -CTGGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29219985 TACTTGGTTT
Statistics
Matches: 124, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
39 18 0.15
40 105 0.85
41 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
Found at i:29227913 original size:39 final size:39
Alignment explanation
Indices: 29227857--29228068 Score: 292
Period size: 39 Copynumber: 5.5 Consensus size: 39
29227847 CGGATGGTAA
* *
29227857 CCGGGCTAAGTCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATA-T
*
29227896 CTGGGCTAAGTCCGAAGGCATTTGTGC-AG-TACTATAT
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
29227933 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
29227973 -CGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
*
29228011 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTA-CTATAT
*
29228051 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGT-CCGAAGG
29228069 TACTTGGTTT
Statistics
Matches: 161, Mismatches: 5, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
37 15 0.09
38 47 0.29
39 65 0.40
40 34 0.21
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:29246628 original size:40 final size:39
Alignment explanation
Indices: 29246571--29246747 Score: 214
Period size: 40 Copynumber: 4.5 Consensus size: 39
29246561 GGATGGTAAC
* * *
29246571 CGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTAATT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* *
29246610 CTGGGCTAACTCCAGAAGGCATTTGTGCGAGTTACTATATT
1 C-GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATT
*
29246651 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATT
*
29246691 CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT-ATAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAAT-T
* *
29246730 CCGGCTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
29246748 TACTTGGTTT
Statistics
Matches: 123, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
38 2 0.02
39 19 0.15
40 98 0.80
41 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Found at i:29252628 original size:21 final size:21
Alignment explanation
Indices: 29252604--29252645 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29252594 GCATTTAGGA
29252604 CTCGATATGGTCATTACGAGT
1 CTCGATATGGTCATTACGAGT
29252625 CTCGATATGGTCATTACGAGT
1 CTCGATATGGTCATTACGAGT
29252646 TCCTGGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (21 bp):
CTCGATATGGTCATTACGAGT
Found at i:29257263 original size:33 final size:34
Alignment explanation
Indices: 29257186--29257266 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
29257176 TATAGGCCAT
*
29257186 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
* * **
29257220 AATGTAATCTGAA-AA-GGGCTCTGGCCCAGTATC
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGT-TC
29257253 ACTGTTATCTGAAT
1 ACTGTTATCTGAAT
29257267 GGGCTTAGGC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 13 0.34
33 14 0.37
34 11 0.29
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (34 bp):
ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
Found at i:29257271 original size:32 final size:30
Alignment explanation
Indices: 29257186--29257279 Score: 71
Period size: 32 Copynumber: 2.9 Consensus size: 30
29257176 TATAGGCCAT
* *
29257186 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAAT---GGGCT-TGGCCCAGTTC
* * *
29257220 AATGTAATCTGAAAAGGGCTCTGGCCCAGTATC
1 ACTGTTATCTG-AATGGGCT-TGGCCCAGT-TC
29257253 ACTGTTATCTGAATGGGCTTAGGCCCA
1 ACTGTTATCTGAATGGGCTT-GGCCCA
29257280 ATGGGCTTGA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
31 1 0.02
32 26 0.54
33 10 0.21
34 9 0.19
35 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (30 bp):
ACTGTTATCTGAATGGGCTTGGCCCAGTTC
Found at i:29258962 original size:44 final size:44
Alignment explanation
Indices: 29258875--29258962 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
29258865 ATTACATGTA
* * *
29258875 TCGCATCCATTATGAACTCGAACCAATTCAACGAGTTTGGATGC
1 TCGCATCCATTATGAACTCGAACCAACTCAACGAGCTTAGATGC
* *
29258919 TCGCATCCA-TAGTGAACTCGGACCAACTCAATGAGCTTAGATGC
1 TCGCATCCATTA-TGAACTCGAACCAACTCAACGAGCTTAGATGC
29258963 CTCATATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 2 0.05
44 36 0.95
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (44 bp):
TCGCATCCATTATGAACTCGAACCAACTCAACGAGCTTAGATGC
Found at i:29262870 original size:28 final size:28
Alignment explanation
Indices: 29262810--29262864 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
29262800 AATATATAAT
29262810 AATTA-TAAAATAATTTAATTGTAATTA
1 AATTATTAAAATAATTTAATTGTAATTA
* *
29262837 AATTATTAAAAT-ATTTAGTTTTAATTA
1 AATTATTAAAATAATTTAATTGTAATTA
29262864 A
1 A
29262865 TTTTATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (28 bp):
AATTATTAAAATAATTTAATTGTAATTA
Found at i:29266203 original size:38 final size:37
Alignment explanation
Indices: 29266105--29266446 Score: 506
Period size: 37 Copynumber: 9.1 Consensus size: 37
29266095 ATATTTGATG
29266105 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTAT
1 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTAT
* * *
29266142 TATATCCGGGTTTATCCCACAGGCTTCGTGCTGATAT
1 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTAT
29266179 TATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
1 TATATCCGGG-TTTATCCCGCAGGCTTAGTGCTGGTAT
29266217 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTAT
1 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTAT
* * *
29266254 TATATCCAGGTTTATCCCGTAGGCTTTGTGCTGGTAT
1 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTAT
* *
29266291 TATATCCGGGTTTATCCCACAAGCTTCA-TGCTGGTAT
1 TATATCCGGGTTTATCCCGCAGGCTT-AGTGCTGGTAT
* * *
29266328 TATATCTGGGTTTTATCCCGCAGGCTTCGTGCTGGCAT
1 TATATCCGGG-TTTATCCCGCAGGCTTAGTGCTGGTAT
* *
29266366 TATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAT
1 TATATCCGGGTT-TATCCCGCAGGCTTAGTGCTGGTAT
*
29266404 TATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAT
1 TATATCCGGGTT-TATCCCGCAGGCTTAGTGCTGGTAT
29266442 TATAT
1 TATAT
29266447 TCGAGCTTAA
Statistics
Matches: 276, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
37 147 0.53
38 129 0.47
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.36
Consensus pattern (37 bp):
TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTAT
Found at i:29266302 original size:112 final size:112
Alignment explanation
Indices: 29266105--29266446 Score: 526
Period size: 112 Copynumber: 3.0 Consensus size: 112
29266095 ATATTTGATG
* *
29266105 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTATTATATCCGGGTTTATCCCACAGGCTTCG
1 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTATTATATCCGGGTTTATCCCGCAGGCTTTG
*
29266170 TGCTGATATTATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
66 TGCTGGTATTATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
* *
29266217 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTATTATATCCAGGTTTATCCCGTAGGCTTTG
1 TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTATTATATCCGGGTTTATCCCGCAGGCTTTG
* *
29266282 TGCTGGTATTATATCCGGG-TTTATCCCACAAGCTTCA-TGCTGGTAT
66 TGCTGGTATTATATCCGGGTTTTATCCCGCAGGCTT-AGTGCTGGTAT
* * * *
29266328 TATATCTGGGTTTTATCCCGCAGGCTTCGTGCTGGCATTATATCCGGGTTAAATCCCGCAGGCTT
1 TATATCCGGG-TTTATCCCGCAGGCTTAGTGCTGGTATTATATCCGGGTT-TATCCCGCAGGCTT
**
29266393 TGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAT
64 TGTGCTGGTATTATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
29266442 TATAT
1 TATAT
29266447 TCGAGCTTAA
Statistics
Matches: 208, Mismatches: 17, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
111 32 0.15
112 116 0.56
113 34 0.16
114 26 0.12
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.36
Consensus pattern (112 bp):
TATATCCGGGTTTATCCCGCAGGCTTAGTGCTGGTATTATATCCGGGTTTATCCCGCAGGCTTTG
TGCTGGTATTATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
Found at i:29272571 original size:10 final size:9
Alignment explanation
Indices: 29272556--29272596 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
29272546 ATGCCCGTGA
29272556 AAAAAAAAG
1 AAAAAAAAG
*
29272565 GAAAAAAAG
1 AAAAAAAAG
29272574 AAAAGAAAAG
1 AAAA-AAAAG
*
29272584 AAAAAGAAG
1 AAAAAAAAG
29272593 AAAA
1 AAAA
29272597 GAGAGAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:29272597 original size:19 final size:19
Alignment explanation
Indices: 29272554--29272598 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
29272544 AAATGCCCGT
*
29272554 GAAAAAAAAAGGAAAAAAA
1 GAAAAGAAAAGGAAAAAAA
29272573 GAAAAGAAAA-GAAAAAGAA
1 GAAAAGAAAAGGAAAAA-AA
29272592 GAAAAGA
1 GAAAAGA
29272599 GAGAAGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
GAAAAGAAAAGGAAAAAAA
Found at i:29274115 original size:46 final size:46
Alignment explanation
Indices: 29274063--29274235 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
29274053 TGGTTGAGCA
29274063 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
29274109 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
29274154 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
29274202 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29274236 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.57
47 27 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29274219 original size:93 final size:93
Alignment explanation
Indices: 29274060--29274230 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
29274050 GGATGGTTGA
* **
29274060 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29274125 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
29274153 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29274218 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29274231 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:29279644 original size:46 final size:46
Alignment explanation
Indices: 29279592--29279764 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
29279582 TGGTTGAGCA
29279592 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
29279638 TTCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
29279683 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
29279731 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29279765 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29279748 original size:93 final size:93
Alignment explanation
Indices: 29279589--29279760 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
29279579 GGATGGTTGA
* **
29279589 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29279654 TGAGTCCGAGTTCATGAAATGTAACTAG
66 TGAGTCCGAGTTCATGAAATGTAACTAG
*
29279682 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29279747 TGAGTCCGAGTTCA
66 TGAGTCCGAGTTCA
29279761 CTTAGGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCATGAAATGTAACTAG
Found at i:29281598 original size:27 final size:28
Alignment explanation
Indices: 29281568--29281624 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
29281558 AAAATATAAT
29281568 AATTA-TAAAATAATTAAATTTTA-ATTA
1 AATTATTAAAATAATT-AATTTTATATTA
29281595 AATTATTAAAATAATTAATTTTATATTA
1 AATTATTAAAATAATTAATTTTATATTA
29281623 AA
1 AA
29281625 ATTTGATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTATTAAAATAATTAATTTTATATTA
Found at i:29286291 original size:28 final size:30
Alignment explanation
Indices: 29286242--29286297 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
29286232 ATGTTTCCAT
* *
29286242 TGATGAATATTTGTGATTTTAGATGTTAAA
1 TGATGAATATTTATGATGTTAGATGTTAAA
*
29286272 TGATGAAT-TTTATG-TGTTAGTTGTTA
1 TGATGAATATTTATGATGTTAGATGTTA
29286298 TTTATAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.43
29 5 0.22
30 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (30 bp):
TGATGAATATTTATGATGTTAGATGTTAAA
Found at i:29291131 original size:41 final size:43
Alignment explanation
Indices: 29291067--29291172 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 43
29291057 ATATATATGG
* * *
29291067 TTACGTGTAAGACCATGTATGGGACA-TCAGCATC-ATATTTGA
1 TTACATGTAAGACCATGTCTGGGACAGT-AGCATCGATATGTGA
* * *
29291109 TT-CATGTAAGACCCTGTCTGGGATAGTGGCATCGATATGTGA
1 TTACATGTAAGACCATGTCTGGGACAGTAGCATCGATATGTGA
*
29291151 TTACATGCAAGACCATGTCTGG
1 TTACATGTAAGACCATGTCTGG
29291173 CACGTTGACA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
41 24 0.45
42 12 0.23
43 17 0.32
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTGGGACAGTAGCATCGATATGTGA
Found at i:29291769 original size:23 final size:26
Alignment explanation
Indices: 29291722--29291769 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
29291712 ATACGTGTGG
*
29291722 TATTAGGTTATATTGTTTGACTTGAT
1 TATTAGGTTATATTGTATGACTTGAT
29291748 TATTAGGTTA-ATTG-ATGA-TTGA
1 TATTAGGTTATATTGTATGACTTGA
29291770 GTAATTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 4 0.19
26 10 0.48
ACGTcount: A:0.27, C:0.02, G:0.21, T:0.50
Consensus pattern (26 bp):
TATTAGGTTATATTGTATGACTTGAT
Found at i:29301388 original size:100 final size:100
Alignment explanation
Indices: 29301271--29301461 Score: 346
Period size: 100 Copynumber: 1.9 Consensus size: 100
29301261 GCCGAAGCTA
*
29301271 TCTGGTACGCATAGTAGCCTGAACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTA
1 TCTGGTACGCATAGTAGCCTGAACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTA
*
29301336 GCCTGCACTTAGTACTACACATGTGATCACAGTTT
66 GCCTGCACTTAGTACTACACACGTGATCACAGTTT
* *
29301371 TCTGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTA
1 TCTGGTACGCATAGTAGCCTGAACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTA
29301436 GCCTGCACTTAGTACTACACACGTGA
66 GCCTGCACTTAGTACTACACACGTGA
29301462 CCTCAAAATA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 87 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (100 bp):
TCTGGTACGCATAGTAGCCTGAACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTA
GCCTGCACTTAGTACTACACACGTGATCACAGTTT
Found at i:29301390 original size:51 final size:49
Alignment explanation
Indices: 29301269--29301456 Score: 259
Period size: 49 Copynumber: 3.8 Consensus size: 49
29301259 TAGCCGAAGC
* *
29301269 TATCTGGTACGCATAGTAGCCTGAACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * *
29301318 AATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGATCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* * *
29301369 TTTCTGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* *
29301418 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
29301457 CGTGACCTCA
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 76 0.64
50 2 0.02
51 41 0.34
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:29303972 original size:78 final size:78
Alignment explanation
Indices: 29303755--29303983 Score: 325
Period size: 77 Copynumber: 2.9 Consensus size: 78
29303745 ATAAATTTTA
* * * * * *
29303755 TTTTCTTTCAAACAGAAATTCAATTAAACAATTCTGTTTCAAGATTTTATTCCTGTCATTTAATA
1 TTTTGTTTCAAACAGAAAATCAATTGAACAATTATGTTTCAGGATTTTATTCCTGCCATTTAATA
*
29303820 CGATTTGTTTGAT
66 GGATTTGTTTGAT
* * * *
29303833 TTTTGTTTCAAATAGAAAAT-AATTGAACAATCATGTTTTAGGATTTTATTCCTGCCATTTAACA
1 TTTTGTTTCAAACAGAAAATCAATTGAACAATTATGTTTCAGGATTTTATTCCTGCCATTTAATA
29303897 GGATTTGTTTGAT
66 GGATTTGTTTGAT
* * *
29303910 TTTTGTTTTAAACAGAAAATCAATTGAACAATTTTGTTTCAGGATTTTATTCCTGCCGTTTAATA
1 TTTTGTTTCAAACAGAAAATCAATTGAACAATTATGTTTCAGGATTTTATTCCTGCCATTTAATA
29303975 GGATTTGTT
66 GGATTTGTT
29303984 CAATCTTTTT
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
77 67 0.51
78 65 0.49
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (78 bp):
TTTTGTTTCAAACAGAAAATCAATTGAACAATTATGTTTCAGGATTTTATTCCTGCCATTTAATA
GGATTTGTTTGAT
Found at i:29304008 original size:78 final size:76
Alignment explanation
Indices: 29303768--29304033 Score: 275
Period size: 78 Copynumber: 3.4 Consensus size: 76
29303758 TCTTTCAAAC
* * * * *
29303768 AGAAATTCAATTAAACAATTCTGTTTCAAGATTTTATTCCTGTCATTTAATACGATTTGTTTGAT
1 AGAAA-TCAATTGAACAATTATGTTTCAGGATTTTATTCCTGCCATTTAATAGGATTTGTTTGAT
**
29303833 TTTTGTTTCAAAT
65 TTTT-TTAAAAAT
* * *
29303846 AGAAAAT-AATTGAACAATCATGTTTTAGGATTTTATTCCTGCCATTTAACAGGATTTGTTTGAT
1 AG-AAATCAATTGAACAATTATGTTTCAGGATTTTATTCCTGCCATTTAATAGGATTTGTTTGAT
** *
29303910 TTTTGTTTTAAAC
65 TTTT-TTAAAAAT
* * **
29303923 AGAAAATCAATTGAACAATTTTGTTTCAGGATTTTATTCCTGCCGTTTAATAGGATTTGTTCAAT
1 AG-AAATCAATTGAACAATTATGTTTCAGGATTTTATTCCTGCCATTTAATAGGATTTGTTTGAT
29303988 CTTTTTTAAAAAAT
65 -TTTTTT-AAAAAT
* *
29304002 AGAAATCAATTGAATAATTCA-GTTCCAGGATT
1 AGAAATCAATTGAACAATT-ATGTTTCAGGATT
29304034 CTTTTCTTGT
Statistics
Matches: 160, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
77 67 0.42
78 81 0.51
79 12 0.08
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (76 bp):
AGAAATCAATTGAACAATTATGTTTCAGGATTTTATTCCTGCCATTTAATAGGATTTGTTTGATT
TTTTTAAAAAT
Found at i:29304104 original size:26 final size:28
Alignment explanation
Indices: 29304054--29304109 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
29304044 CTTTAAATAA
29304054 AATTTATTCGATTTTTGTTGTTAA-CAG
1 AATTTATTCGATTTTTGTTGTTAACCAG
29304081 AATTTATTCGATTTTTGTTG-TAACCAG
1 AATTTATTCGATTTTTGTTGTTAACCAG
29304108 AA
1 AA
29304110 ATTGGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (28 bp):
AATTTATTCGATTTTTGTTGTTAACCAG
Found at i:29311266 original size:26 final size:24
Alignment explanation
Indices: 29311183--29311290 Score: 146
Period size: 24 Copynumber: 4.4 Consensus size: 24
29311173 CTGGAGGCCT
29311183 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTAATAAACTGGGGCAA
*
29311207 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTTAATAAACTGGGGCAA
29311231 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTT-AATAAACTGGGGCA-A
* *
29311257 AGCCCTTTTCAATAAACTAGGGCAT
1 AGCCCTTTT-AATAAACTGGGGCAA
29311282 AGCCCTTTT
1 AGCCCTTTT
29311291 GCACTTCATC
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
23 7 0.09
24 24 0.31
25 22 0.29
26 24 0.31
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTGGGGCAA
Found at i:29311403 original size:9 final size:11
Alignment explanation
Indices: 29311357--29311406 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
29311347 GCATTTCATA
29311357 CATATCATGTG
1 CATATCATGTG
*
29311368 CATATCA--TA
1 CATATCATGTG
29311377 CATATCATGTG
1 CATATCATGTG
29311388 CATATCATGT-
1 CATATCATGTG
29311398 CA-ATCATGT
1 CATATCATGT
29311407 ATATCATATC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 15 0.43
10 2 0.06
11 18 0.51
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
CATATCATGTG
Found at i:29311406 original size:20 final size:20
Alignment explanation
Indices: 29311340--29311395 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
29311330 TTATGATTAC
* *
29311340 ATCATATGCATTTCATACAT
1 ATCATGTGCATATCATACAT
29311360 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
29311380 ATCATGTGCATATCAT
1 ATCATGTGCATATCAT
29311396 GTCAATCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29311412 original size:9 final size:10
Alignment explanation
Indices: 29311357--29311413 Score: 66
Period size: 9 Copynumber: 5.8 Consensus size: 10
29311347 GCATTTCATA
29311357 CATATCATGT
1 CATATCATGT
*
29311367 GCATATCAT-A
1 -CATATCATGT
29311377 CATATCATGT
1 CATATCATGT
29311387 GCATATCATGT
1 -CATATCATGT
29311398 CA-ATCATGT
1 CATATCATGT
29311407 -ATATCAT
1 CATATCAT
29311414 ATCCCACGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 1 0.02
9 20 0.49
10 2 0.05
11 18 0.44
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (10 bp):
CATATCATGT
Found at i:29330797 original size:79 final size:80
Alignment explanation
Indices: 29330696--29330842 Score: 224
Period size: 79 Copynumber: 1.9 Consensus size: 80
29330686 TCCTCGTTCA
* * **
29330696 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACATAACCCGGAT
29330760 TTAACAATTCGCACG
66 TTAACAATTCGCACG
* * *
29330775 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACATAACCCGGAT
29330840 TTA
66 TTA
29330843 GTATCTCGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
79 33 0.55
80 27 0.45
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACATAACCCGGAT
TTAACAATTCGCACG
Found at i:29330872 original size:40 final size:40
Alignment explanation
Indices: 29330696--29330918 Score: 220
Period size: 40 Copynumber: 5.6 Consensus size: 40
29330686 TCCTCGTTCA
* * * *
29330696 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* ** *
29330735 AATGCCTTCGGGACATAACCCGGATTTAACAATTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
**
29330775 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* *
29330815 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* * * * *
29330855 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAC-CAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-T-CGCACG
* *
29330895 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29330919 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 36 0.23
40 114 0.72
41 7 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
Found at i:29330918 original size:120 final size:119
Alignment explanation
Indices: 29330696--29330918 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 119
29330686 TCCTCGTTCA
* * * *
29330696 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
*
29330761 TAACAATTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
66 TAACAATTCGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
29330815 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* * *
29330879 TATATTCACTTAC-CAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAATT-CGCACGAAAGCCTTCGGGACTTAACCCGGA
29330919 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 37 0.43
120 42 0.48
121 7 0.08
122 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAATTCGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:29338687 original size:40 final size:40
Alignment explanation
Indices: 29338589--29338758 Score: 216
Period size: 40 Copynumber: 4.3 Consensus size: 40
29338579 TCCTCGTTCA
* * ** *
29338589 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
*
29338628 AATGCCTTCGGGACATAACCCGGATTTAACAATTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
*
29338668 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
* ** * *
29338708 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
*
29338748 AAGGCCTTCGG
1 AATGCCTTCGG
29338759 ATCTTATCCG
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 33 0.28
40 84 0.72
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
Found at i:29338690 original size:79 final size:80
Alignment explanation
Indices: 29338589--29338735 Score: 224
Period size: 79 Copynumber: 1.9 Consensus size: 80
29338579 TCCTCGTTCA
* * **
29338589 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACATAACCCGGAT
29338653 TTAACAATTCGCACG
66 TTAACAATTCGCACG
* * *
29338668 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACATAACCCGGAT
29338733 TTA
66 TTA
29338736 GTATCTCGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
79 33 0.55
80 27 0.45
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACATAACCCGGAT
TTAACAATTCGCACG
Found at i:29338770 original size:119 final size:119
Alignment explanation
Indices: 29338589--29338810 Score: 263
Period size: 119 Copynumber: 1.9 Consensus size: 119
29338579 TCCTCGTTCA
* * * *
29338589 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
*
29338654 TA-ACAATT-CGCACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
66 TATACAATTAC-CAC-AAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
29338708 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATC-TTATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* * *
29338771 TATATTCACTTACCACAAAGCCTTCGGGACTTAGCCCGGA
64 TATATACAATTACCACAAAGCCTTCGGGACTTAACCCGGA
29338811 CAGCATTCAA
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
119 69 0.80
120 16 0.19
121 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TATACAATTACCACAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:29338810 original size:40 final size:39
Alignment explanation
Indices: 29338554--29338810 Score: 123
Period size: 40 Copynumber: 6.5 Consensus size: 39
29338544 AAATCACGTA
* * * ** *
29338554 CCTTCGGGATTTAACCGGATATAGCT-CCTCGTTCAAATG
1 CCTTCGGGACTTACCCGGATATAG-TATCTCGCACAAAGG
* * * * * *
29338593 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATG
1 CCTTCGGGACTTA-CCCGGATATAGTATCTCGCACAAAGG
* * ** * *
29338632 CCTTCGGGACATAACCCGGATTTAACAAT-TCGCACGAATG
1 CCTTCGGGAC-TTACCCGGATAT-AGTATCTCGCACAAAGG
* ** * * *
29338672 CCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTT-ACCCGGATATAGTATCTCGCACAAAGG
*
29338712 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTT-ACCCGGATATAGTATCTCGCACAAAGG
* *
29338752 CCTTC-GGATCTTATCCGGATATATTCA-CTTAC-CACAAA-G
1 CCTTCGGGA-CTTACCCGGATATAGT-ATC-T-CGCACAAAGG
29338791 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTA-CCCGGA
29338811 CAGCATTCAA
Statistics
Matches: 176, Mismatches: 29, Indels: 25
0.77 0.13 0.11
Matches are distributed among these distances:
39 66 0.38
40 109 0.62
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTACCCGGATATAGTATCTCGCACAAAGG
Found at i:29353439 original size:40 final size:40
Alignment explanation
Indices: 29353395--29353626 Score: 306
Period size: 40 Copynumber: 5.8 Consensus size: 40
29353385 ATAACCACAA
*
29353395 GCACAAATGCCCTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
29353435 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
29353475 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* * * *
29353515 GCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * * *
29353555 GCACAAATGCCTTCTGGTCTTGGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* * *
29353595 GCACAATTGCCTTCGGGACTTAGCCTGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
29353627 CATTCAAATG
Statistics
Matches: 166, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
39 4 0.02
40 155 0.93
41 7 0.04
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:29353498 original size:80 final size:80
Alignment explanation
Indices: 29353395--29353626 Score: 349
Period size: 80 Copynumber: 2.9 Consensus size: 80
29353385 ATAACCACAA
* * * *
29353395 GCACAAATGCCCTCGGGTCTTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGTCTTAGC
*
29353459 CCGGATATATCAACTC
65 CCGGATATAGCAACTC
*
29353475 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCC
*
29353540 CGGGTATAGCAACTC
66 CGGATATAGCAACTC
* * *
29353555 GCACAAATGCCTTCTGGTCTTGGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCC
*
29353620 TGGATAT
66 CGGATAT
29353627 CATTCAAATG
Statistics
Matches: 138, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
80 134 0.97
81 4 0.03
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCC
CGGATATAGCAACTC
Found at i:29353599 original size:120 final size:120
Alignment explanation
Indices: 29353366--29353625 Score: 344
Period size: 120 Copynumber: 2.2 Consensus size: 120
29353356 ACCCAAGTTT
* * * *
29353366 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATATC
1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATAGC
* *
29353430 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGC
66 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACTAGCACAAATGC
* * * * * * *
29353485 CTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGC
1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATAGC
* * *
29353550 AACTCGCACAAATGCCTTCTGGTCTTGGCCCGGATAAAATC-ACTAGCACAATTGC
66 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGAT-AAATCAACTAGCACAAATGC
*
29353605 CTTCGGGACTTAGCCTGGATA
1 CTTCGGGACTTAGCCCGGATA
29353626 TCATTCAAAT
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
119 10 0.08
120 107 0.88
121 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (120 bp):
CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATAGC
AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACTAGCACAAATGC
Found at i:29362733 original size:39 final size:39
Alignment explanation
Indices: 29362570--29362749 Score: 157
Period size: 40 Copynumber: 4.5 Consensus size: 39
29362560 TGAATGCTGT
* * * * *
29362570 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTATAA
* * *
29362610 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTA-ATT
1 CCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTATA-A
** * *
29362650 TTGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTATAA
**
29362689 TCCGGGTTAAGTCCCGAAGGCATTGTATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTATAA
* *
29362729 CCGGGCTATGTCCCGAAGGCA
1 CCGGGTTAAGTCCCGAAGGCA
29362750 CTTGAACGAG
Statistics
Matches: 116, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
39 32 0.28
40 76 0.66
41 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTATAA
Found at i:29370532 original size:40 final size:38
Alignment explanation
Indices: 29370477--29370656 Score: 164
Period size: 40 Copynumber: 4.6 Consensus size: 38
29370467 TTGAATGCTG
* *
29370477 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATA
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGC-GAGT-ACTATA
29370517 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTA-A
1 TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAG-TACTATA
* ** *
29370556 TTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 -TCCGGGTTAAGTCCCGAAGGC-TTTGTGCGAGTACT-ATA
* * **
29370597 TCTGGGTTAAGTCCCGAAGGCATTGTATGAGTTACTATA
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAG-TACTATA
* * *
29370636 ACCGGGCTATGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
29370657 ACTTGAACGA
Statistics
Matches: 116, Mismatches: 17, Indels: 15
0.78 0.11 0.10
Matches are distributed among these distances:
39 29 0.25
40 77 0.66
41 10 0.09
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (38 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGTACTATA
Found at i:29378840 original size:34 final size:34
Alignment explanation
Indices: 29378794--29378860 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
29378784 TGATTATTTG
*
29378794 ATCGTACTGATTTAGATCAGGGAAAGAAAAAAGC
1 ATCGTACGGATTTAGATCAGGGAAAGAAAAAAGC
** *
29378828 ATCGTACGGATTTAGATTGGGGAAAGGAAAAAG
1 ATCGTACGGATTTAGATCAGGGAAAGAAAAAAG
29378861 TGTCAGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (34 bp):
ATCGTACGGATTTAGATCAGGGAAAGAAAAAAGC
Found at i:29392949 original size:93 final size:93
Alignment explanation
Indices: 29392836--29393007 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
29392826 CGCCCATAAG
* *
29392836 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
29392901 ACGAGTTCGGATGCCTATTTACATCTCA
66 ACGAGTTCGGATGCCTATTTACATCTCA
*
29392929 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
29392994 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
29393008 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTATTTACATCTCA
Found at i:29393004 original size:46 final size:46
Alignment explanation
Indices: 29392829--29393004 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
29392819 TGTAACCCGC
* * *
29392829 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* **
29392875 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTATTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTCGCAT
*
29392925 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
29392968 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
29393005 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:29396153 original size:20 final size:21
Alignment explanation
Indices: 29396130--29396168 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29396120 CATATCATAT
29396130 AAATAAC-ATTAAATTACTTA
1 AAATAACAATTAAATTACTTA
*
29396150 AAATAACAATTATATTACT
1 AAATAACAATTAAATTACT
29396169 ACATTTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAACAATTAAATTACTTA
Found at i:29397473 original size:31 final size:31
Alignment explanation
Indices: 29397437--29397508 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
29397427 AAGAACTAAT
*
29397437 AATATTTCATTAAACTTCAAAAACCATACTA
1 AATATTTCATTAAACTTAAAAAACCATACTA
*
29397468 AATATTTCATTAAGCTTAAAAAACCATACTA
1 AATATTTCATTAAACTTAAAAAACCATACTA
29397499 AA-ATGTTCAT
1 AATAT-TTCAT
29397509 GGAAAAACCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (31 bp):
AATATTTCATTAAACTTAAAAAACCATACTA
Found at i:29399831 original size:19 final size:20
Alignment explanation
Indices: 29399809--29399870 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
29399799 TAAAGTTAAA
29399809 AAATATTTTAAAAAATTA-T
1 AAATATTTTAAAAAATTATT
*
29399828 AAAT-TTTTAAATACATTATT
1 AAATATTTTAAA-AAATTATT
29399848 AAA-A-TTTATAAAAA-TATT
1 AAATATTTTA-AAAAATTATT
29399866 AAATA
1 AAATA
29399871 AAATTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 14 0.39
19 16 0.44
20 6 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATTTTAAAAAATTATT
Found at i:29399875 original size:22 final size:20
Alignment explanation
Indices: 29399847--29399900 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
29399837 AATACATTAT
*
29399847 TAAAATTTATAAAAATATTAAA
1 TAAAATTTA-AAAAAT-TCAAA
*
29399869 TAAAATTTAAAAAGTTCAAA
1 TAAAATTTAAAAAATTCAAA
29399889 TAAAA-TTAAAAA
1 TAAAATTTAAAAA
29399901 TTAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 7 0.23
20 9 0.30
21 5 0.17
22 9 0.30
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAATTTAAAAAATTCAAA
Found at i:29401728 original size:15 final size:15
Alignment explanation
Indices: 29401708--29401738 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29401698 TTAAAAAGGT
29401708 AAATGTCATTCTAAA
1 AAATGTCATTCTAAA
29401723 AAATGTCATTCTAAA
1 AAATGTCATTCTAAA
29401738 A
1 A
29401739 TCTTACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (15 bp):
AAATGTCATTCTAAA
Found at i:29402444 original size:22 final size:20
Alignment explanation
Indices: 29402418--29402459 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29402408 TCAATTTTAT
29402418 TTGAACCGAATGAATCAGTTAA
1 TTGAACCG-A-GAATCAGTTAA
*
29402440 TTGAACTGAGAATCAGTTAA
1 TTGAACCGAGAATCAGTTAA
29402460 AATATTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (20 bp):
TTGAACCGAGAATCAGTTAA
Found at i:29403314 original size:30 final size:30
Alignment explanation
Indices: 29403279--29403340 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
29403269 ATAATTTAAG
29403279 ATATTAATTACGTAAAAATATATAAAATTT
1 ATATTAATTACGTAAAAATATATAAAATTT
* *
29403309 ATATTAATTACTTAAAAATATTTAAAATTT
1 ATATTAATTACGTAAAAATATATAAAATTT
29403339 AT
1 AT
29403341 TTCATATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (30 bp):
ATATTAATTACGTAAAAATATATAAAATTT
Found at i:29403753 original size:18 final size:19
Alignment explanation
Indices: 29403715--29403754 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
29403705 CTAAGATAGC
**
29403715 AAATACTTAAAAATATTTA
1 AAATACTTAAAAATAAATA
29403734 AAAT-CTTAAAAATAAATA
1 AAATACTTAAAAATAAATA
29403752 AAA
1 AAA
29403755 GTTTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATACTTAAAAATAAATA
Found at i:29405608 original size:26 final size:26
Alignment explanation
Indices: 29405579--29405631 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
29405569 ATATTGAGAT
*
29405579 AGTAGAACTCCCGTTTGAACCTTAGG
1 AGTAGAACTCCCCTTTGAACCTTAGG
29405605 AGTAGAACTCCCCTTTGAACCTTAGG
1 AGTAGAACTCCCCTTTGAACCTTAGG
29405631 A
1 A
29405632 AATAAATCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (26 bp):
AGTAGAACTCCCCTTTGAACCTTAGG
Found at i:29405799 original size:45 final size:46
Alignment explanation
Indices: 29405734--29405895 Score: 129
Period size: 45 Copynumber: 3.5 Consensus size: 46
29405724 GGCGTAAGAC
* * *
29405734 CATGTTTGGGACATGGCATCGTCATTGAGACG-AGAGCTAGTGTAAAA
1 CATGTCTGGGACAT-GCATCGGCATCGAGACGTA-AGCTAGTGTAAAA
* * * *
29405781 CATG-CTGGGGCATGCATCGGCCTCGAGATGTAAGCTAGTGTAAGA
1 CATGTCTGGGACATGCATCGGCATCGAGACGTAAGCTAGTGTAAAA
* * *
29405826 CATGTCTAGGACATGCATCGGC-TACGAGATGT--G-TCAGTGTAAGAC
1 CATGTCTGGGACATGCATCGGCAT-CGAGACGTAAGCT-AGTGTAA-AA
*
29405871 CATGTCTGGGACATGGCACCGGCAT
1 CATGTCTGGGACAT-GCATCGGCAT
29405896 GTATAGAGGT
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 8 0.08
45 43 0.45
46 38 0.40
47 5 0.05
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (46 bp):
CATGTCTGGGACATGCATCGGCATCGAGACGTAAGCTAGTGTAAAA
Found at i:29405854 original size:46 final size:46
Alignment explanation
Indices: 29405675--29405982 Score: 156
Period size: 48 Copynumber: 6.6 Consensus size: 46
29405665 TTATTTGTGT
* * * * * *
29405675 GCTAGTGTAAGACATGTCTAGAACATGCATCGGCCA-TATTATGAAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGTAA
** * * * * *
29405721 GCCGGCGTAAGACCATGTTTGGGACATGGCATCGTC-ATTGAGACG-AGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CGAGATGTA-A
* *
29405769 GCTAGTGTAAAACATG-CTGGGGCATGCATCGGCCT-CGAGATGTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGTAA
*
29405814 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCTACGAGATGT--
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTAA
* * *
29405858 G-TCAGTGTAAGACCATGTCTGGGACATGGCACCGGCATGTA-TAGAGGT--
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC---TACGAGATGTAA
* * * *
29405906 GCCAGTGTAAGACCATATCTGGGACATGGCATCGAC-ACGGATATGTGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTAC-GAGATGT-A-A
29405956 GCTAGTGTAAGACCATGTCT-GGACATG
1 GCTAGTGTAAGA-CATGTCTGGGACATG
29405983 GCGTCAACCT
Statistics
Matches: 204, Mismatches: 35, Indels: 44
0.72 0.12 0.16
Matches are distributed among these distances:
43 1 0.00
44 11 0.05
45 42 0.21
46 51 0.25
47 17 0.08
48 55 0.27
49 9 0.04
50 18 0.09
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTAA
Found at i:29405921 original size:48 final size:50
Alignment explanation
Indices: 29405860--29405984 Score: 157
Period size: 48 Copynumber: 2.6 Consensus size: 50
29405850 CGAGATGTGT
* * * *
29405860 CAGTGTAAGACCATGTCTGGGACATGGCACCGGCATGTATA-GAG-GTGC
1 CAGTGTAAGACCATGTCTGGGACATGGCACCGACACGGATATGAGAGAGC
* * *
29405908 CAGTGTAAGACCATATCTGGGACATGGCATCGACACGGATATGTGAGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCACCGACACGGATATGAGAGAGC
*
29405958 TAGTGTAAGACCATGTCT-GGACATGGC
1 CAGTGTAAGACCATGTCTGGGACATGGC
29405985 GTCAACCTCA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
48 36 0.55
49 11 0.17
50 19 0.29
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (50 bp):
CAGTGTAAGACCATGTCTGGGACATGGCACCGACACGGATATGAGAGAGC
Found at i:29407238 original size:17 final size:19
Alignment explanation
Indices: 29407216--29407252 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
29407206 TTGGGTTTTA
29407216 TGGGCC-ACACGGG-CATG
1 TGGGCCTACACGGGCCATG
*
29407233 TGGGCCTACATGGGCCATG
1 TGGGCCTACACGGGCCATG
29407252 T
1 T
29407253 TATGGGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.16, C:0.27, G:0.38, T:0.19
Consensus pattern (19 bp):
TGGGCCTACACGGGCCATG
Found at i:29416266 original size:16 final size:17
Alignment explanation
Indices: 29416245--29416278 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29416235 TTATTATTAA
*
29416245 GATTAAT-ATAGTAAAT
1 GATTAATAATAGAAAAT
29416261 GATTAATAATAGAAAAT
1 GATTAATAATAGAAAAT
29416278 G
1 G
29416279 TAAAAGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (17 bp):
GATTAATAATAGAAAAT
Found at i:29416568 original size:28 final size:28
Alignment explanation
Indices: 29416532--29416585 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
29416522 AATTTGATAA
29416532 TTGATGATGGATTTTGAATAATTGTTAG
1 TTGATGATGGATTTTGAATAATTGTTAG
29416560 TTGATGATGGATTTTGAATAATTGTT
1 TTGATGATGGATTTTGAATAATTGTT
29416586 GATGGTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (28 bp):
TTGATGATGGATTTTGAATAATTGTTAG
Found at i:29427155 original size:26 final size:24
Alignment explanation
Indices: 29427125--29427174 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
29427115 AAATAAAAAA
*
29427125 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
29427151 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
29427175 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:29434693 original size:24 final size:24
Alignment explanation
Indices: 29434661--29434708 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
29434651 CTATGCAGAG
29434661 TAAGGAAGAAACAATATTGGGTAT
1 TAAGGAAGAAACAATATTGGGTAT
*
29434685 TAAGGAAGAAGCAATATTGGGTAT
1 TAAGGAAGAAACAATATTGGGTAT
29434709 CATCTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.25
Consensus pattern (24 bp):
TAAGGAAGAAACAATATTGGGTAT
Found at i:29445055 original size:40 final size:40
Alignment explanation
Indices: 29445010--29445205 Score: 250
Period size: 40 Copynumber: 4.9 Consensus size: 40
29445000 GGATATAGCT
* * * *
29445010 ACTCGCTCGAATGCCTTCGGGACATAGCCCGGTTATGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
29445050 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* * *
29445090 ACTCACACGAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* * ** *
29445130 ACTCACACAAATGCCTTCGGGGCTTAGCCC-GAAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
*
29445170 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
29445206 CATCCGAATA
Statistics
Matches: 134, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
39 2 0.01
40 130 0.97
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:29445101 original size:80 final size:79
Alignment explanation
Indices: 29444998--29445205 Score: 285
Period size: 80 Copynumber: 2.6 Consensus size: 79
29444988 CGAAATTTAA
* * * *
29444998 CCGGATATAGCTACTCGCTCGAATGCCTTCGGGACATAGCCCGGTTATGGTAACTCGCACAAATG
1 CCGGATATAG-TACTCACACGAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACACAAATG
29445063 CCTTCGGGACTTAGC
65 CCTTCGGGACTTAGC
29445078 CCGGATATAGTAACTCACACGAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACACAAATG
1 CCGGATATAGT-ACTCACACGAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACACAAATG
*
29445143 CCTTCGGGGCTTAGC
65 CCTTCGGGACTTAGC
* * *
29445158 CC-GAAATTAGTCACT-AGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CCGGATA-TAGT-ACTCA-CACGAATGCCTTCGGGACATAGCCCGGTTAT
29445206 CATCCGAATA
Statistics
Matches: 116, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
79 5 0.04
80 111 0.96
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (79 bp):
CCGGATATAGTACTCACACGAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACACAAATGC
CTTCGGGACTTAGC
Found at i:29455517 original size:9 final size:9
Alignment explanation
Indices: 29455503--29455532 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
29455493 ATTGCATACA
29455503 ATTCAAAAC
1 ATTCAAAAC
29455512 ATTCAAAAC
1 ATTCAAAAC
29455521 ATTCAAAAC
1 ATTCAAAAC
29455530 ATT
1 ATT
29455533 TGATTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (9 bp):
ATTCAAAAC
Found at i:29457464 original size:31 final size:31
Alignment explanation
Indices: 29457422--29457498 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
29457412 TAACGGTTAT
29457422 TGGGCCGAAGCCTTTTCATAAATCATATCAC
1 TGGGCCGAAGCCTTTTCATAAATCATATCAC
*
29457453 TGGGCCAAAGCCTTTTCATAAATCATATCAC
1 TGGGCCGAAGCCTTTTCATAAATCATATCAC
29457484 TGGGCCGAAGCCTTT
1 TGGGCCGAAGCCTTT
29457499 ACTGTAACGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (31 bp):
TGGGCCGAAGCCTTTTCATAAATCATATCAC
Found at i:29457572 original size:42 final size:42
Alignment explanation
Indices: 29457525--29457612 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
29457515 CTTTAGGCCT
* ** *
29457525 ATTTCAATATCACATGTAATGTCAATGGATGTATGAAAGCCC
1 ATTTCAATATCACATGAAATACCAATGAATGTATGAAAGCCC
*
29457567 ATTTCAATATCACATGAAATACCAATGAATGTATGCAAGCCC
1 ATTTCAATATCACATGAAATACCAATGAATGTATGAAAGCCC
29457609 ATTT
1 ATTT
29457613 GGGGAGACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (42 bp):
ATTTCAATATCACATGAAATACCAATGAATGTATGAAAGCCC
Found at i:29458673 original size:26 final size:28
Alignment explanation
Indices: 29458629--29458680 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
29458619 TACAAGGGTA
29458629 TTACGGTCACTTTACCCTA-TAGGGGCT
1 TTACGGTCACTTTACCCTATTAGGGGCT
**
29458656 TTACGGTCTTTTTA-CCTATTAGGGG
1 TTACGGTCACTTTACCCTATTAGGGG
29458681 TATTTTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (28 bp):
TTACGGTCACTTTACCCTATTAGGGGCT
Found at i:29458755 original size:27 final size:27
Alignment explanation
Indices: 29458725--29458838 Score: 88
Period size: 27 Copynumber: 4.1 Consensus size: 27
29458715 GTAAATCTAC
29458725 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
** *
29458752 AAACCAATAGTATTCCTA-TAATTTT-T
1 AAACCAAGGGTATT-TTAGTAATTTTGT
* *
29458778 AAAAAAGTCAAGGGTATTTTTGTAATTTTGT
1 ---AAA-CCAAGGGTATTTTAGTAATTTTGT
* * * *
29458809 AAATCAGGGGTATTTTGGTAATTTTAT
1 AAACCAAGGGTATTTTAGTAATTTTGT
29458836 AAA
1 AAA
29458839 TTGAGGGTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
26 1 0.01
27 43 0.62
28 5 0.07
29 4 0.06
30 15 0.22
31 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (27 bp):
AAACCAAGGGTATTTTAGTAATTTTGT
Found at i:29458839 original size:27 final size:26
Alignment explanation
Indices: 29458789--29458885 Score: 97
Period size: 27 Copynumber: 3.6 Consensus size: 26
29458779 AAAAAGTCAA
*
29458789 GGGTATTTTTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTT-TAAATCAG
*
29458816 GGGTATTTTGGTAATTTTATAAAT-TG
1 GGGTATTTTGGTAATTTT-TAAATCAG
* * *
29458842 AGGGTATTTCGGTAATTTCTCAAACCAG
1 -GGGTATTTTGGTAATTT-TTAAATCAG
*
29458870 TGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
29458886 CTATCCTACA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
26 1 0.02
27 55 0.95
28 2 0.03
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTTAAATCAG
Found at i:29458978 original size:27 final size:27
Alignment explanation
Indices: 29458917--29459003 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
29458907 GTAATTTCAC
29458917 AATCGATG-GTAAAACGGTAATTTTGTA
1 AATCGA-GAGTAAAACGGTAATTTTGTA
*
29458944 AA-CTGAGAGTAAAATGGTAATTTTGTA
1 AATC-GAGAGTAAAACGGTAATTTTGTA
* * *
29458971 AATCGAGA-TAAAACGATAATTCTATA
1 AATCGAGAGTAAAACGGTAATTTTGTA
29458997 AATCGAG
1 AATCGAG
29459004 GGTACTTTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
26 23 0.44
27 28 0.54
28 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.30
Consensus pattern (27 bp):
AATCGAGAGTAAAACGGTAATTTTGTA
Found at i:29464460 original size:13 final size:13
Alignment explanation
Indices: 29464442--29464468 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29464432 GCTCGACAGG
29464442 GACACGCCCGTGT
1 GACACGCCCGTGT
29464455 GACACGCCCGTGT
1 GACACGCCCGTGT
29464468 G
1 G
29464469 CGATTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:29483019 original size:15 final size:15
Alignment explanation
Indices: 29482999--29483027 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29482989 AATTTTTCCC
29482999 AAAAATAAAAATAAT
1 AAAAATAAAAATAAT
29483014 AAAAATAAAAATAA
1 AAAAATAAAAATAA
29483028 ACCAATCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAAATAAT
Found at i:29490410 original size:27 final size:27
Alignment explanation
Indices: 29490375--29490426 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
29490365 GGAAGTACTG
*
29490375 TACTGGTGGCTATGCCACAATTACTAA
1 TACTAGTGGCTATGCCACAATTACTAA
* *
29490402 TACTAGTGGCTTTGCCACATTTACT
1 TACTAGTGGCTATGCCACAATTACT
29490427 GTTTCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (27 bp):
TACTAGTGGCTATGCCACAATTACTAA
Found at i:29490621 original size:28 final size:27
Alignment explanation
Indices: 29490585--29490649 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
29490575 ATTACACTGC
* *
29490585 ACTGATACTATATTGGGCTTAGGCCCAG
1 ACTG-TACTATATAGGGCTAAGGCCCAG
* *
29490613 ACTGTTACTGTATAGGGCTAAGGCCTAG
1 ACTG-TACTATATAGGGCTAAGGCCCAG
29490641 ACTGTACTA
1 ACTGTACTA
29490650 ATACTGTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (27 bp):
ACTGTACTATATAGGGCTAAGGCCCAG
Found at i:29491773 original size:12 final size:12
Alignment explanation
Indices: 29491756--29491785 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29491746 CAGTTCAATA
29491756 ATATTTCTACAC
1 ATATTTCTACAC
*
29491768 ATATTTCTTCAC
1 ATATTTCTACAC
29491780 ATATTT
1 ATATTT
29491786 TCTCTGTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATTTCTACAC
Found at i:29493804 original size:90 final size:90
Alignment explanation
Indices: 29493537--29493856 Score: 437
Period size: 90 Copynumber: 3.6 Consensus size: 90
29493527 TCAAAATAAT
* * * *
29493537 TGTATT-ATTTCTTTAGAATGTTTGAATTTTTTTTATATCTGTGAATTTAATGTAGTTGTTTAGG
1 TGTATTAATTTC-TTAGAATGTTTGTA-TTTTTTTATATCTATAAATTTAATATAGTTGTTTAGG
*
29493601 AATTAAGGTATCATTTTTATATTTTCA
64 ATTTAAGGTATCATTTTTATATTTTCA
* * * *
29493628 TGTATTAATTTCTTAGAATGTTTCTA-TTTTTTACATCTATAAATTTATTATAGTTATTTAGGAT
1 TGTATTAATTTCTTAGAATGTTTGTATTTTTTTATATCTATAAATTTAATATAGTTGTTTAGGAT
* *
29493692 GTAAGGTATCATTTTTATATTTTCG
66 TTAAGGTATCATTTTTATATTTTCA
* *
29493717 TGTATTAATTTCTTAGAATGTTTGTATTTTATTATATCTATAAATTTAATATAGTTGTCTAGGAT
1 TGTATTAATTTCTTAGAATGTTTGTATTTTTTTATATCTATAAATTTAATATAGTTGTTTAGGAT
*
29493782 TTAAGGTTTCATTTTTATATTTTCA
66 TTAAGGTATCATTTTTATATTTTCA
* * * * *
29493807 TCTATTAATTTCTCAGAATGTTTGTATTTTTTTGTATTTGTAAATTTAAT
1 TGTATTAATTTCTTAGAATGTTTGTATTTTTTTATATCTATAAATTTAAT
29493857 TTAATCCATA
Statistics
Matches: 201, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
89 79 0.39
90 99 0.49
91 18 0.09
92 5 0.02
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.55
Consensus pattern (90 bp):
TGTATTAATTTCTTAGAATGTTTGTATTTTTTTATATCTATAAATTTAATATAGTTGTTTAGGAT
TTAAGGTATCATTTTTATATTTTCA
Found at i:29496421 original size:48 final size:49
Alignment explanation
Indices: 29496204--29496419 Score: 206
Period size: 49 Copynumber: 4.4 Consensus size: 49
29496194 ACCACGATTA
* *
29496204 ATGAGATCTC-GTGTAAGACCATGTCTGGGACATGGCATTGGCATTCGAG
1 ATGAGATC-CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCGAG
* * **
29496253 ATGAGATCCGGTGTAAGACCATGTTTGGGACATGGCATCAACATCCGAG
1 ATGAGATCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCGAG
* ** * *
29496302 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTGT-TGAT
1 ATGAGATCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCGAG
* * * * * *
29496350 ATGTG-TGCTAGTGTAAGACCATATTTGGGACATGGCATCGGCA-CCAAT
1 ATGAGAT-CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCGAG
* * *
29496398 ATGTGATCCCGTATAAGACCAT
1 ATGAGATCCAGTGTAAGACCAT
29496420 ATCAGGGATA
Statistics
Matches: 137, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
48 57 0.42
49 80 0.58
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (49 bp):
ATGAGATCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCGAG
Found at i:29498452 original size:20 final size:20
Alignment explanation
Indices: 29498427--29498474 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
29498417 CAGGTTGAAG
29498427 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
29498447 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
29498467 ACACGGGC
1 ACACGGGC
29498475 ATATGTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.40, G:0.31, T:0.08
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAGCC
Found at i:29500423 original size:16 final size:16
Alignment explanation
Indices: 29500404--29500490 Score: 67
Period size: 16 Copynumber: 5.5 Consensus size: 16
29500394 TTCATAATCA
*
29500404 TCATTTAATTTTATAT
1 TCATTTAATTTCATAT
29500420 TCATTTAA---CAT-T
1 TCATTTAATTTCATAT
29500432 TCATTTAATTTCATAT
1 TCATTTAATTTCATAT
* *
29500448 TCATTACAAATTACAT-T
1 TCATT--TAATTTCATAT
*
29500465 TCATTTCATATTCATATT
1 TCATTTAAT-TTCATA-T
29500483 TCATTTAA
1 TCATTTAA
29500491 CATTTCATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
12 9 0.16
13 2 0.04
15 5 0.09
16 18 0.33
17 6 0.11
18 15 0.27
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTAATTTCATAT
Found at i:29500436 original size:12 final size:12
Alignment explanation
Indices: 29500419--29500502 Score: 57
Period size: 12 Copynumber: 6.8 Consensus size: 12
29500409 TAATTTTATA
29500419 TTCATTTAACAT
1 TTCATTTAACAT
29500431 TTCATTTAATTTCAT
1 TTCATTTAA---CAT
*
29500446 ATTCA-TTACAAAT
1 -TTCATTTA-ACAT
*
29500459 TACATTT--CAT
1 TTCATTTAACAT
* *
29500469 TTCATATTCATAT
1 TTCAT-TTAACAT
29500482 TTCATTTAACAT
1 TTCATTTAACAT
29500494 TTCATTTAA
1 TTCATTTAA
29500503 ATTAATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
10 6 0.11
11 2 0.04
12 26 0.46
13 11 0.20
15 6 0.11
16 5 0.09
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (12 bp):
TTCATTTAACAT
Done.