Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008033.1 Hibiscus syriacus cultivar Beakdansim tig00110515_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3048429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2575967 original size:13 final size:13
Alignment explanation
Indices: 2575943--2576004 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
2575933 TCTTTTTTAA
2575943 TTTCTTTTTTTCT
1 TTTCTTTTTTTCT
2575956 TTTCTTTTTTTCT
1 TTTCTTTTTTTCT
* *
2575969 AAATT-TTTTCTTCT
1 --TTTCTTTTTTTCT
*
2575983 TTT-TGTCTTTTCT
1 TTTCT-TTTTTTCT
2575996 TTTCTTTTT
1 TTTCTTTTT
2576005 GTAGTCCAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 3 0.08
13 25 0.64
14 9 0.23
15 2 0.05
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:2575993 original size:18 final size:18
Alignment explanation
Indices: 2575950--2576006 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
2575940 TAATTTCTTT
*
2575950 TTTTCTTTTCTTTTTTTC
1 TTTTCTTTTCTTTTTGTC
*
2575968 TAAATTTTTTCTTCTTTTTGTC
1 T---TTTCTT-TTCTTTTTGTC
2575990 TTTTCTTTTCTTTTTGT
1 TTTTCTTTTCTTTTTGT
2576007 AGTCCAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 11 0.34
19 5 0.16
21 5 0.16
22 11 0.34
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTGTC
Found at i:2576753 original size:19 final size:20
Alignment explanation
Indices: 2576712--2576762 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2576702 GAAACCCCTT
*
2576712 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
2576732 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
2576751 TGAAGATACATG
1 TGAAAATACATG
2576763 CTCTTGTCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:2577552 original size:2 final size:2
Alignment explanation
Indices: 2577545--2577580 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2577535 AGTTATTTTC
2577545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2577581 CCTATAGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2579225 original size:17 final size:16
Alignment explanation
Indices: 2579202--2579262 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
2579192 ATTGGAGTGC
2579202 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
*
2579218 ACAAAAGAAGAGAAAAATC
1 A-AAAAGAA-AGAAAAA-G
2579237 AGAAAAG-AA-AAAAAG
1 A-AAAAGAAAGAAAAAG
2579252 AAAAA-AAAGAA
1 AAAAAGAAAGAA
2579263 TTTCAAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 6 0.16
17 8 0.22
18 8 0.22
19 6 0.16
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:2588659 original size:18 final size:19
Alignment explanation
Indices: 2588618--2588656 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2588608 TATCCTTTCT
*
2588618 TTATTTCATTTTATTCTTA
1 TTATTTCATTTCATTCTTA
2588637 TTATTT-ATTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
2588656 T
1 T
2588657 ATTATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:2593523 original size:17 final size:18
Alignment explanation
Indices: 2593503--2593562 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 18
2593493 TTGGAGTACA
2593503 AAAAGAA-AGAAAAAGAC
1 AAAAGAAGAGAAAAAGAC
*
2593520 AAAAGAAGAGAAAAA-TC
1 AAAAGAAGAGAAAAAGAC
* *
2593537 AAAA-AAGAAAAAAAGAA
1 AAAAGAAGAGAAAAAGAC
*
2593554 AAAAAAAGA
1 AAAAGAAGA
2593563 ATTTCAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 9 0.25
17 16 0.44
18 11 0.31
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAGAAAAAGAC
Found at i:2593523 original size:18 final size:17
Alignment explanation
Indices: 2593500--2593563 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 17
2593490 GAATTGGAGT
2593500 ACAAAAAGAAAGAAAAAG
1 ACAAAAA-AAAGAAAAAG
*
2593518 ACAAAAGAAGAGAAAAA-
1 ACAAAA-AAAAGAAAAAG
*
2593535 TCAAAAAAGAA-AAAAAG
1 ACAAAAAA-AAGAAAAAG
2593552 A-AAAAAAAAGAA
1 ACAAAAAAAAGAA
2593564 TTTCAAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
15 2 0.05
16 15 0.39
17 6 0.16
18 14 0.37
19 1 0.03
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (17 bp):
ACAAAAAAAAGAAAAAG
Found at i:2593548 original size:8 final size:8
Alignment explanation
Indices: 2593502--2593558 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
2593492 ATTGGAGTAC
2593502 AAAAAGAAA
1 AAAAAG-AA
2593511 GAAAAAGACA
1 -AAAAAGA-A
*
2593521 AAAGAAGAG
1 AAA-AAGAA
**
2593530 AAAAATCA
1 AAAAAGAA
2593538 AAAAAGAA
1 AAAAAGAA
2593546 AAAAAGAA
1 AAAAAGAA
2593554 AAAAA
1 AAAAA
2593559 AAGAATTTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 21 0.54
9 7 0.18
10 11 0.28
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:2593550 original size:16 final size:15
Alignment explanation
Indices: 2593508--2593557 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
2593498 GTACAAAAAG
*
2593508 AAAGAAAAAGACAAA
1 AAAGAAAAAAACAAA
*
2593523 AGAAGAGAAAAATCAAA
1 A-AAGA-AAAAAACAAA
*
2593540 AAAGAAAAAAAGAAA
1 AAAGAAAAAAACAAA
2593555 AAA
1 AAA
2593558 AAAGAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.41
16 8 0.28
17 9 0.31
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAAACAAA
Found at i:2615558 original size:30 final size:31
Alignment explanation
Indices: 2615524--2615583 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2615514 CTTAGCTTTA
**
2615524 TATTATGCTTACATATGTTTTAGAT-TCATT
1 TATTATGCTTACATATCATTTAGATATCATT
* *
2615554 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGCTTACATATCATTTAGATATCAT
2615584 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
TATTATGCTTACATATCATTTAGATATCATT
Found at i:2616516 original size:19 final size:21
Alignment explanation
Indices: 2616492--2616543 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2616482 CGGCCAAGAG
*
2616492 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2616511 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2616532 CATGTATTTTCA
1 CATGTATTTTCA
2616544 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:2617869 original size:14 final size:14
Alignment explanation
Indices: 2617850--2617884 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2617840 TTCATCATTC
*
2617850 CAAACATTAGAGAA
1 CAAACATTAAAGAA
*
2617864 CAAACAGTAAAGAA
1 CAAACATTAAAGAA
2617878 CAAACAT
1 CAAACAT
2617885 ATTTCACACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.11
Consensus pattern (14 bp):
CAAACATTAAAGAA
Found at i:2619748 original size:30 final size:31
Alignment explanation
Indices: 2619714--2619773 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2619704 CTTAGCTTTA
**
2619714 TATTATGCTTACATATGTTTTAGAT-TCATT
1 TATTATGCTTACATATCATTTAGATATCATT
* *
2619744 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGCTTACATATCATTTAGATATCAT
2619774 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
TATTATGCTTACATATCATTTAGATATCATT
Found at i:2621442 original size:25 final size:25
Alignment explanation
Indices: 2621414--2621461 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2621404 GAAAAAAGAA
2621414 AGAAAAGACA-AAAAGAAAAAAAATC
1 AGAAAAGA-AGAAAAGAAAAAAAATC
*
2621439 AGAATAGAAGAAAAGAAAAAAAA
1 AGAAAAGAAGAAAAGAAAAAAAA
2621462 AGAATTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (25 bp):
AGAAAAGAAGAAAAGAAAAAAAATC
Found at i:2627654 original size:26 final size:26
Alignment explanation
Indices: 2627604--2627667 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
2627594 CTTGGCTTGC
2627604 TTTTCTCTTTT-TGAAATCTTTTTCT
1 TTTTCTCTTTTCTGAAATCTTTTTCT
2627629 TTTTCTTCTTTTCTG-AAT-TTTCTTCT
1 TTTTC-TCTTTTCTGAAATCTTT-TTCT
*
2627655 TTTTGTCTTTTCT
1 TTTTCTCTTTTCT
2627668 TTTTTTTGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 16 0.46
26 17 0.49
27 2 0.06
ACGTcount: A:0.08, C:0.17, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTTCTCTTTTCTGAAATCTTTTTCT
Found at i:2627667 original size:16 final size:15
Alignment explanation
Indices: 2627620--2627675 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
2627610 CTTTTTGAAA
*
2627620 TCTTTTTCTTTTTCT
1 TCTTTTTGTTTTTCT
*
2627635 TCTTTTCTGAATTTTCT
1 TCTTTT-TG-TTTTTCT
2627652 TCTTTTTGTCTTTTCT
1 TCTTTTTGT-TTTTCT
*
2627668 TTTTTTTG
1 TCTTTTTG
2627676 CACTCCAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 6 0.18
16 16 0.47
17 12 0.35
ACGTcount: A:0.04, C:0.16, G:0.05, T:0.75
Consensus pattern (15 bp):
TCTTTTTGTTTTTCT
Found at i:2631488 original size:36 final size:36
Alignment explanation
Indices: 2631436--2631548 Score: 167
Period size: 36 Copynumber: 3.2 Consensus size: 36
2631426 GATACTATTT
2631436 TCATCACCATAATCCAT-ATCCATTATCACGCCTATA
1 TCATCACCATAATCCATCA-CCATTATCACGCCTATA
*
2631472 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
2631508 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
2631543 ACATCA
1 TCATCA
2631549 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 17 0.24
36 54 0.75
37 1 0.01
ACGTcount: A:0.34, C:0.35, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:2631491 original size:13 final size:11
Alignment explanation
Indices: 2631469--2631534 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
2631459 TATCACGCCT
2631469 ATATCATCACC
1 ATATCATCACC
2631480 ATAGTCCATCACC
1 ATA-T-CATCACC
*
2631493 ATTATCA-CGCC
1 A-TATCATCACC
2631504 TATATCATCACC
1 -ATATCATCACC
2631516 ATATTCCATCACC
1 ATA-T-CATCACC
2631529 ATATCA
1 ATATCA
2631535 CGCCAATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:2631563 original size:33 final size:33
Alignment explanation
Indices: 2631437--2631563 Score: 105
Period size: 36 Copynumber: 3.6 Consensus size: 33
2631427 ATACTATTTT
* *
2631437 CATCACCATAATCCAT-ATCCATTATCACGCCTATAT
1 CATCACCAT--TCCATCA-CCA-TATCACGCCAATAA
* *
2631473 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCAT--TCCATCACCA-TATCACGCCAATAA
2631509 CATCACCATATTCCATCACCATATCACGCCAATAA
1 CATCACC--ATTCCATCACCATATCACGCCAATAA
*
2631544 CATCATCC-TTCCATTACCAT
1 CATCA-CCATTCCATCACCAT
2631564 TTCATCACCA
Statistics
Matches: 83, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
33 11 0.13
35 17 0.20
36 52 0.63
37 1 0.01
38 2 0.02
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.28
Consensus pattern (33 bp):
CATCACCATTCCATCACCATATCACGCCAATAA
Found at i:2632033 original size:14 final size:15
Alignment explanation
Indices: 2631999--2632045 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2631989 AATTTGGAGT
2631999 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
2632014 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
2632028 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
2632045 G
1 G
2632046 TGAAACAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:2632199 original size:16 final size:15
Alignment explanation
Indices: 2632173--2632224 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
2632163 GAGTTGTAAG
2632173 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
2632187 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
2632203 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
2632220 CTTAT
1 -TTAT
2632225 TTCATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:2635566 original size:36 final size:36
Alignment explanation
Indices: 2635514--2635626 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
2635504 GATACTATTT
* *
2635514 TCATCACCATAATCCATCTCCATTATCATGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
2635550 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
2635586 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
2635621 ACATCA
1 TCATCA
2635627 TCCTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.24
36 54 0.76
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:2635569 original size:13 final size:11
Alignment explanation
Indices: 2635514--2635612 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
2635504 GATACTATTT
2635514 TCATCACCATAA
1 TCATCACCAT-A
*
2635526 TCCATCTCCATTA
1 T-CATCACCA-TA
*
2635539 TCATGC-CTATA
1 TCAT-CACCATA
2635550 TCATCACCATA
1 TCATCACCATA
2635561 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
2635575 TCA-CGCCTATA
1 TCATCACC-ATA
2635586 TCATCACCATA
1 TCATCACCATA
2635597 TTCCATCACCATA
1 -T-CATCACCATA
2635610 TCA
1 TCA
2635613 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.01
11 23 0.32
12 15 0.21
13 29 0.41
14 3 0.04
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:2635641 original size:33 final size:33
Alignment explanation
Indices: 2635562--2635665 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2635552 ATCACCATAG
* *
2635562 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2635598 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2635631 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2635664 TC
1 TC
2635666 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2636396 original size:19 final size:21
Alignment explanation
Indices: 2636372--2636423 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2636362 CGACCAAGAG
*
2636372 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2636391 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2636412 CATGTATTTTCA
1 CATGTATTTTCA
2636424 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:2646579 original size:17 final size:17
Alignment explanation
Indices: 2646557--2646606 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2646547 ATAAAGTTAG
*
2646557 TTCATTAATTAAACTAA
1 TTCATTTATTAAACTAA
* * *
2646574 TTCATTTGTCAAACTAG
1 TTCATTTATTAAACTAA
2646591 TTCATTTATTAAACTA
1 TTCATTTATTAAACTA
2646607 CCTCTTAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (17 bp):
TTCATTTATTAAACTAA
Found at i:2648450 original size:17 final size:17
Alignment explanation
Indices: 2648428--2648497 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
2648418 TGAATAAAGT
* *
2648428 TAGTTCATTAATTAAAC
1 TAGTTCATTCATCAAAC
2648445 TAGTTCATTCATCAAAC
1 TAGTTCATTCATCAAAC
** *
2648462 TAGTTCACCCATCAACC
1 TAGTTCATTCATCAAAC
* *
2648479 TAGTTCATTTATTAAAC
1 TAGTTCATTCATCAAAC
2648496 TA
1 TA
2648498 ACTCTTAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (17 bp):
TAGTTCATTCATCAAAC
Found at i:2655835 original size:15 final size:15
Alignment explanation
Indices: 2655811--2655841 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2655801 TCTTTTCACA
*
2655811 ACTTTGCAAGAGAGG
1 ACTTTACAAGAGAGG
2655826 ACTTTACAAGAGAGG
1 ACTTTACAAGAGAGG
2655841 A
1 A
2655842 ACGAGTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.19
Consensus pattern (15 bp):
ACTTTACAAGAGAGG
Found at i:2669729 original size:20 final size:20
Alignment explanation
Indices: 2669706--2669747 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2669696 TCCCTTAGGG
*
2669706 TTCCATGTGATGCCTTGTAC
1 TTCCATGAGATGCCTTGTAC
* *
2669726 TTCCCTGAGCTGCCTTGTAC
1 TTCCATGAGATGCCTTGTAC
2669746 TT
1 TT
2669748 TGTAAGCTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.29, G:0.19, T:0.40
Consensus pattern (20 bp):
TTCCATGAGATGCCTTGTAC
Found at i:2685441 original size:56 final size:56
Alignment explanation
Indices: 2685376--2685487 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
2685366 AAATGCCAAG
2685376 GACGTCCTAATATAATGTGGCTTGCACTCATGGGCACCACGTCACAAAGGACTTCA
1 GACGTCCTAATATAATGTGGCTTGCACTCATGGGCACCACGTCACAAAGGACTTCA
2685432 GACGTCCTAATATAATGTGGCTTGCACTCATGGGCACCACGTCACAAAGGACTTCA
1 GACGTCCTAATATAATGTGGCTTGCACTCATGGGCACCACGTCACAAAGGACTTCA
2685488 TCATTGTATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (56 bp):
GACGTCCTAATATAATGTGGCTTGCACTCATGGGCACCACGTCACAAAGGACTTCA
Found at i:2691317 original size:14 final size:14
Alignment explanation
Indices: 2691298--2691340 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2691288 ATAAGATACT
* *
2691298 ATCTATTCATCATC
1 ATCTATCCATCACC
2691312 ATCTATCCATCACC
1 ATCTATCCATCACC
*
2691326 ATC-CTCCATCACC
1 ATCTATCCATCACC
2691339 AT
1 AT
2691341 TCATCCTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:2696937 original size:16 final size:16
Alignment explanation
Indices: 2696916--2696950 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2696906 ATTATTATTA
2696916 TAACTCAAGTATAGTC
1 TAACTCAAGTATAGTC
2696932 TAACTCAAGTATAGTC
1 TAACTCAAGTATAGTC
2696948 TAA
1 TAA
2696951 TATGCAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (16 bp):
TAACTCAAGTATAGTC
Found at i:2704918 original size:20 final size:19
Alignment explanation
Indices: 2704881--2704919 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2704871 ACGATAATGC
*
2704881 ATGAAGCTTAAGAGCTAAT
1 ATGAAGCTTAAGAACTAAT
*
2704900 ATGAATGCTTATGAACTAAT
1 ATGAA-GCTTAAGAACTAAT
2704920 GAAATGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
ATGAAGCTTAAGAACTAAT
Found at i:2708232 original size:19 final size:20
Alignment explanation
Indices: 2708190--2708240 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
2708180 AAAACCCCTT
*
2708190 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
2708210 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
2708229 TGAAAATACATG
1 TGAAAATACATG
2708241 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2711228 original size:47 final size:48
Alignment explanation
Indices: 2711081--2711252 Score: 301
Period size: 48 Copynumber: 3.6 Consensus size: 48
2711071 ATTCAAGAAT
*
2711081 CATGACTTTTGGAGAACTAAAGGATGTGTTATTTGAATCACCAATAGA
1 CATGACTTCTGGAGAACTAAAGGATGTGTTATTTGAATCACCAATAGA
2711129 CATGACTTCTGGAGAACTAAAGGATGTGTTATTTGAATCACCAATAGA
1 CATGACTTCTGGAGAACTAAAGGATGTGTTATTTGAATCACCAATAGA
*
2711177 CATGACTTCTGGAGAACTAAAGGATGT-TCATTTGAATCACCAATAGA
1 CATGACTTCTGGAGAACTAAAGGATGTGTTATTTGAATCACCAATAGA
* *
2711224 CATGACTTTTGGAGAACTAAAGAATGTGT
1 CATGACTTCTGGAGAACTAAAGGATGTGT
2711253 GATGTGATCC
Statistics
Matches: 119, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
47 44 0.37
48 75 0.63
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (48 bp):
CATGACTTCTGGAGAACTAAAGGATGTGTTATTTGAATCACCAATAGA
Found at i:2712591 original size:36 final size:36
Alignment explanation
Indices: 2712568--2712699 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 36
2712558 TTCCACCTTT
*
2712568 ATTATCACGCCTATATCATCACCATAGTCCATCACC
1 ATTATCACGCCTATATCATCACCATAGTCCACCACC
* * *
2712604 ATTATCACGCCTTTATCATCACCATAGTCCATCTCC
1 ATTATCACGCCTATATCATCACCATAGTCCACCACC
* *
2712640 ATTATCACGCCTATATCGTCACCATATTCCACCACC
1 ATTATCACGCCTATATCATCACCATAGTCCACCACC
* *
2712676 ATTATCACGCCCATATTATCACCA
1 ATTATCACGCCTATATCATCACCA
2712700 ACTTATAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 86 1.00
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
ATTATCACGCCTATATCATCACCATAGTCCACCACC
Found at i:2717077 original size:36 final size:36
Alignment explanation
Indices: 2717054--2717185 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 36
2717044 TTCCACCTTT
*
2717054 ATTATCACGCCTATATCATCACCATAGTCCATCACC
1 ATTATCACGCCTATATCATCACCATAGTCCACCACC
* * *
2717090 ATTATCACGCCTTTATCATCACCATAGTCCATCTCC
1 ATTATCACGCCTATATCATCACCATAGTCCACCACC
* *
2717126 ATTATCACGCCTATATCGTCACCATATTCCACCACC
1 ATTATCACGCCTATATCATCACCATAGTCCACCACC
* *
2717162 ATTATCACGCCCATATTATCACCA
1 ATTATCACGCCTATATCATCACCA
2717186 ACTTATAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 86 1.00
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
ATTATCACGCCTATATCATCACCATAGTCCACCACC
Found at i:2719360 original size:25 final size:25
Alignment explanation
Indices: 2719332--2719380 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2719322 AGGTCCAAGT
*
2719332 CTTTTATTACCACCTCTTGTAAAGG
1 CTTTTATTACCACCCCTTGTAAAGG
2719357 CTTTTATTACCACCCCTTGTAAAG
1 CTTTTATTACCACCCCTTGTAAAG
2719381 ACATATATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (25 bp):
CTTTTATTACCACCCCTTGTAAAGG
Found at i:2726653 original size:20 final size:20
Alignment explanation
Indices: 2726624--2726672 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2726614 CATATTCATC
* *
2726624 TCCATCACCTCCATTCTACT
1 TCCATTACCTCCATTATACT
*
2726644 TCCATTACCTTCATTATACT
1 TCCATTACCTCCATTATACT
2726664 TCCATTACC
1 TCCATTACC
2726673 ATACTTCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (20 bp):
TCCATTACCTCCATTATACT
Found at i:2729758 original size:24 final size:21
Alignment explanation
Indices: 2729723--2729765 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2729713 GGCTCATTCT
*
2729723 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2729746 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2729766 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2731008 original size:15 final size:15
Alignment explanation
Indices: 2730973--2731001 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2730963 GTGCTTCAAC
2730973 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
2730987 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
2731002 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:2735073 original size:187 final size:187
Alignment explanation
Indices: 2734758--2735132 Score: 732
Period size: 187 Copynumber: 2.0 Consensus size: 187
2734748 TCCATCTTGA
*
2734758 TTCCTAAATTCCTAGATTGATATCTAGTGGGTTGAAGACACAATCACCACCCCTCAAGCAAGTTT
1 TTCCTAAATTCCTAGATTGAGATCTAGTGGGTTGAAGACACAATCACCACCCCTCAAGCAAGTTT
*
2734823 GTGAAGATTGGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCGAGTTTGAGATACAACATCAC
66 GTGAAGACTGGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCGAGTTTGAGATACAACATCAC
2734888 CACCATCTTCATTTCATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAAT
131 CACCATCTTCATTTCATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAAT
2734945 TTCCTAAATTCCTAGATTGAGATCTAGTGGGTTGAAGACACAATCACCACCCCTCAAGCAAGTTT
1 TTCCTAAATTCCTAGATTGAGATCTAGTGGGTTGAAGACACAATCACCACCCCTCAAGCAAGTTT
2735010 GTGAAGACTGGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCGAGTTTGAGATACAACATCAC
66 GTGAAGACTGGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCGAGTTTGAGATACAACATCAC
2735075 CACCATCTTCATTTCATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAAT
131 CACCATCTTCATTTCATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAAT
2735132 T
1 T
2735133 CCTCAGCCAT
Statistics
Matches: 186, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 186 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (187 bp):
TTCCTAAATTCCTAGATTGAGATCTAGTGGGTTGAAGACACAATCACCACCCCTCAAGCAAGTTT
GTGAAGACTGGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCGAGTTTGAGATACAACATCAC
CACCATCTTCATTTCATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAAT
Found at i:2735656 original size:132 final size:132
Alignment explanation
Indices: 2735419--2735679 Score: 486
Period size: 132 Copynumber: 2.0 Consensus size: 132
2735409 GGATGATGCG
* *
2735419 ATCATGCCAAGGACCAAACTTCTTCAACACATGATCACTTCATGGACATTCTGCCTTGTTAATTC
1 ATCATGCCAAGGACCAAACTTCTTCAACACATGATCACTTCATGGACATTATGCCTTGTTAATTA
*
2735484 TAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATTCATTACATGTCACGTGAATAC
66 TAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATTAATTACATGTCACGTGAATAC
2735549 GC
131 GC
*
2735551 ATCATGCCAAGGACCAAACTTCTTCAACACATGATCACTTCATGGACGTTATGCCTTGTTAATTA
1 ATCATGCCAAGGACCAAACTTCTTCAACACATGATCACTTCATGGACATTATGCCTTGTTAATTA
2735616 TAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATTAATTACATGTCACGTGAATA
66 TAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATTAATTACATGTCACGTGAATA
2735680 TGTTTATCTT
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 125 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (132 bp):
ATCATGCCAAGGACCAAACTTCTTCAACACATGATCACTTCATGGACATTATGCCTTGTTAATTA
TAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATTAATTACATGTCACGTGAATAC
GC
Found at i:2737410 original size:14 final size:14
Alignment explanation
Indices: 2737391--2737433 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2737381 ATAAGATACT
* *
2737391 ATCTATTCATCATC
1 ATCTATCCATCACC
2737405 ATCTATCCATCACC
1 ATCTATCCATCACC
*
2737419 ATC-CTCCATCACC
1 ATCTATCCATCACC
2737432 AT
1 AT
2737434 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:2741253 original size:19 final size:21
Alignment explanation
Indices: 2741210--2741261 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
2741200 GAAACCCCTT
2741210 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
2741231 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
2741250 TGAAGATACATG
1 TGAAAATACATG
2741262 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:2742095 original size:19 final size:20
Alignment explanation
Indices: 2742053--2742103 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
2742043 AAAACCCCTT
*
2742053 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
2742073 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
2742092 TGAAAATACATG
1 TGAAAATACATG
2742104 CTCTTGGACG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2744112 original size:24 final size:24
Alignment explanation
Indices: 2744085--2744144 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
2744075 ATTGGTTCTT
2744085 CAAAAGACATGTCTTGTGGATCAC
1 CAAAAGACATGTCTTGTGGATCAC
* * * * * **
2744109 CAAAGGTCATGACTTTTGGTTCTT
1 CAAAAGACATGTCTTGTGGATCAC
2744133 CAAAAGACATGT
1 CAAAAGACATGT
2744145 TTCTTGAATC
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (24 bp):
CAAAAGACATGTCTTGTGGATCAC
Found at i:2746055 original size:19 final size:20
Alignment explanation
Indices: 2746013--2746063 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2746003 AAAACCCCTT
*
2746013 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
*
2746033 TGAAAATATATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2746052 TGAAGATACATG
1 TGAAAATACATG
2746064 CTCTTTGACG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2751301 original size:8 final size:8
Alignment explanation
Indices: 2751288--2751332 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
2751278 ATCTTTTTCT
2751288 TTTTCTTC
1 TTTTCTTC
2751296 TTTTCTTC
1 TTTTCTTC
2751304 TTTTCTTC
1 TTTTCTTC
2751312 TTTT-TGTC
1 TTTTCT-TC
2751320 TTTTCTTTC
1 TTTTC-TTC
2751329 TTTT
1 TTTT
2751333 TGCACTCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 26 0.76
9 6 0.18
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTTC
Found at i:2751334 original size:17 final size:16
Alignment explanation
Indices: 2751279--2751334 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
2751269 CTTTTTGAAA
*
2751279 TCTTTTTCT-TTTTCT
1 TCTTTTTGTCTTTTCT
2751294 TCTTTTCT-TCTTTTCT
1 TCTTTT-TGTCTTTTCT
2751310 TCTTTTTGTCTTTTCTT
1 TCTTTTTGTCTTTTC-T
2751327 TCTTTTTG
1 TCTTTTTG
2751335 CACTCCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.22
16 20 0.54
17 9 0.24
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.77
Consensus pattern (16 bp):
TCTTTTTGTCTTTTCT
Found at i:2756429 original size:13 final size:13
Alignment explanation
Indices: 2756413--2756442 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2756403 CTTTTTGAAC
2756413 TTCTCTTTTTCTT
1 TTCTCTTTTTCTT
*
2756426 TTCTTTTTTTCTT
1 TTCTCTTTTTCTT
2756439 TTCT
1 TTCT
2756443 GATTTCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTCTTTTTCTT
Found at i:2757220 original size:19 final size:21
Alignment explanation
Indices: 2757177--2757227 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2757167 GAAACCCCTT
2757177 TGAAAATACATTACTTTTAAA
1 TGAAAATACATTACTTTTAAA
2757198 TGAAAATACATTA-TTTT-AA
1 TGAAAATACATTACTTTTAAA
*
2757217 TGAAGATACAT
1 TGAAAATACAT
2757228 GCTCTTGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (21 bp):
TGAAAATACATTACTTTTAAA
Found at i:2763155 original size:20 final size:21
Alignment explanation
Indices: 2763118--2763156 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2763108 GATGGTCTTG
*
2763118 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
2763139 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
2763157 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:2763530 original size:20 final size:21
Alignment explanation
Indices: 2763491--2763530 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2763481 GAAACCCCTT
2763491 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
2763512 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGACTTTTAA
2763531 GGAAGATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:2763541 original size:19 final size:21
Alignment explanation
Indices: 2763492--2763542 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
2763482 AAACCCCTTT
*
2763492 GAAAATACATGACTTTTAAAT
1 GAAAATACATGACTTTTAAAG
2763513 GAAAATACATGA-TTTT-AAG
1 GAAAATACATGACTTTTAAAG
*
2763532 GAAGATACATG
1 GAAAATACATG
2763543 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (21 bp):
GAAAATACATGACTTTTAAAG
Found at i:2767471 original size:19 final size:21
Alignment explanation
Indices: 2767428--2767479 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
2767418 GAAACCCCTT
2767428 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
2767449 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
2767468 TGAAGATACATG
1 TGAAAATACATG
2767480 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:2771365 original size:18 final size:20
Alignment explanation
Indices: 2771323--2771373 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
2771313 GAAACCCCTT
2771323 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGAC-TTTAAA
2771344 TGAAAATACATGAC-TT-AA
1 TGAAAATACATGACTTTAAA
*
2771362 TGAAGATACATG
1 TGAAAATACATG
2771374 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 13 0.45
19 2 0.07
21 14 0.48
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (20 bp):
TGAAAATACATGACTTTAAA
Found at i:2774604 original size:24 final size:23
Alignment explanation
Indices: 2774555--2774604 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
2774545 AAAAAAAATA
**
2774555 AAAGCACTTAAAAGAAGAAATTG
1 AAAGCACTTAAAAGAAGAAAAAG
2774578 AAAGCACTTGAAAAGAAGAAAAAG
1 AAAGCACTT-AAAAGAAGAAAAAG
2774602 AAA
1 AAA
2774605 TAAAGAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.62, C:0.08, G:0.18, T:0.12
Consensus pattern (23 bp):
AAAGCACTTAAAAGAAGAAAAAG
Found at i:2793314 original size:24 final size:21
Alignment explanation
Indices: 2793279--2793321 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2793269 GGCTCATTCT
*
2793279 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2793302 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2793322 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2796872 original size:13 final size:11
Alignment explanation
Indices: 2796853--2796916 Score: 58
Period size: 13 Copynumber: 5.4 Consensus size: 11
2796843 ATACTATTTT
2796853 TCATCACCATA
1 TCATCACCATA
2796864 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
2796878 TCA-CGCCTATA
1 TCATCACC-ATA
2796889 TCATCACCATA
1 TCATCACCATA
2796900 TTCCATCACCATA
1 -T-CATCACCATA
2796913 TCAT
1 TCAT
2796917 GCCAATAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.32
12 9 0.20
13 19 0.43
14 2 0.05
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:2796893 original size:36 final size:35
Alignment explanation
Indices: 2796853--2796929 Score: 109
Period size: 36 Copynumber: 2.2 Consensus size: 35
2796843 ATACTATTTT
*
2796853 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCA-TATCACGCCAATA
* *
2796889 TCATCACCATATTCCATCACCATATCATGCCAATA
1 TCATCACCATAGTCCATCACCATATCACGCCAATA
*
2796924 ACATCA
1 TCATCA
2796930 TCCTTCCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 16 0.43
36 21 0.57
ACGTcount: A:0.34, C:0.35, G:0.04, T:0.27
Consensus pattern (35 bp):
TCATCACCATAGTCCATCACCATATCACGCCAATA
Found at i:2796944 original size:33 final size:33
Alignment explanation
Indices: 2796900--2796968 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2796890 CATCACCATA
*
2796900 TTCCATCACCATATCAT-GCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
2796933 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
2796966 TTC
1 TTC
2796969 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:2810783 original size:32 final size:33
Alignment explanation
Indices: 2810722--2810788 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
2810712 ACAAAATTAA
* *
2810722 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
2810754 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGATAG
2810787 AA
1 AA
2810789 ATGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:2811982 original size:26 final size:26
Alignment explanation
Indices: 2811946--2812013 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
2811936 ATGAACCTAC
*
2811946 ATGCAAGGCACATGGGGCCTGGTCAT
1 ATGCAAGGCACATGGGGCCTGATCAT
*
2811972 ATGCAAGGCACATGGGGGCTGATCAT
1 ATGCAAGGCACATGGGGCCTGATCAT
*
2811998 ATGCAAAGCACATGGG
1 ATGCAAGGCACATGGG
2812014 TGTTCTAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.28, C:0.21, G:0.34, T:0.18
Consensus pattern (26 bp):
ATGCAAGGCACATGGGGCCTGATCAT
Found at i:2813045 original size:16 final size:16
Alignment explanation
Indices: 2813024--2813070 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
2813014 CAAAGCCTAT
2813024 TAGAAATGGTTATGAA
1 TAGAAATGGTTATGAA
*
2813040 TAGAAATGGTTAGGAA
1 TAGAAATGGTTATGAA
2813056 TAGAAATGGTTATGA
1 TAGAAATGGTTATGA
2813071 CAAGGGTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.30
Consensus pattern (16 bp):
TAGAAATGGTTATGAA
Found at i:2819725 original size:164 final size:158
Alignment explanation
Indices: 2819507--2819831 Score: 596
Period size: 164 Copynumber: 2.0 Consensus size: 158
2819497 TTTTGCTTGA
2819507 TATTATATGCTGTCATTTATTGTATATATATGATCATGCATGACTTTTTAATTCACATCTTTATA
1 TATTATATGCTGTCATTTATTGTATATATATGATCATGCATGACTTTTTAATTCACATCTTTATA
2819572 TAACTCATTCAATGCATATGCATTCATAGTTAGTTCATTTTCATTATTAACATAGGTGGAAGCAT
66 TAACTCATTCAATGCATATGCATTCATAGTTAGTTCATTTTCATTATTAACATAGGTGGAAGCAT
2819637 GAATTCATAATTATCATAGCTCAATTCC
131 GAATTCATAATTATCATAGCTCAATTCC
2819665 TATTATTATGCTGTCATTTATATGTATAATATATGATATTCATGCATGACTTTTTAATTCACATC
1 TATTA-TATGCTGTCATTTAT-TGTAT-ATATATG--A-TCATGCATGACTTTTTAATTCACATC
2819730 TTTATATAACTCATTCAATGCATATGCATTCATAGTTAGTTCATTTTCATTATTAACATAGGTGG
60 TTTATATAACTCATTCAATGCATATGCATTCATAGTTAGTTCATTTTCATTATTAACATAGGTGG
2819795 AAGCATGAATTCATAATTATCATAGCTCAATTCC
125 AAGCATGAATTCATAATTATCATAGCTCAATTCC
2819829 TAT
1 TAT
2819832 CTAATTAATT
Statistics
Matches: 161, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
158 5 0.03
159 15 0.09
160 5 0.03
161 7 0.04
163 1 0.01
164 128 0.80
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (158 bp):
TATTATATGCTGTCATTTATTGTATATATATGATCATGCATGACTTTTTAATTCACATCTTTATA
TAACTCATTCAATGCATATGCATTCATAGTTAGTTCATTTTCATTATTAACATAGGTGGAAGCAT
GAATTCATAATTATCATAGCTCAATTCC
Found at i:2830325 original size:91 final size:91
Alignment explanation
Indices: 2830150--2830320 Score: 225
Period size: 91 Copynumber: 1.9 Consensus size: 91
2830140 CCTAGAACAC
* * *
2830150 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCCTTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAAGATG
* * *
2830215 AAGTGTTCTCTCCCTATTCGGCCAAG
66 AAGAGATCTATCCCTATTCGGCCAAG
** * * *
2830241 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATATGGTTCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAAGATG
2830306 AATGGAGATCTATCC
66 AA--GAGATCTATCC
2830321 ATTCGTCCAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
91 59 0.88
93 8 0.12
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAAGATG
AAGAGATCTATCCCTATTCGGCCAAG
Found at i:2833896 original size:22 final size:22
Alignment explanation
Indices: 2833846--2833897 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2833836 TGCAAGAAGA
*
2833846 CCATGTACGTTCAAGTAGGCTG
1 CCATGTGCGTTCAAGTAGGCTG
*
2833868 CCATGTGCGTTCAAGTAGGCTT
1 CCATGTGCGTTCAAGTAGGCTG
2833890 CCATGTGC
1 CCATGTGC
2833898 ATCATTCAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (22 bp):
CCATGTGCGTTCAAGTAGGCTG
Found at i:2834092 original size:19 final size:20
Alignment explanation
Indices: 2834068--2834118 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2834058 CGGCCAAGAG
* *
2834068 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
2834087 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2834107 CATGTATTTTCA
1 CATGTATTTTCA
2834119 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:2834555 original size:19 final size:20
Alignment explanation
Indices: 2834535--2834570 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
2834525 GTTTCTTTAT
2834535 TTTA-TTTCATT-CTTATTA
1 TTTATTTTCATTACTTATTA
2834553 TTTATTTTCATTACTTAT
1 TTTATTTTCATTACTTAT
2834571 ATTATTATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 7 0.44
20 5 0.31
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTTCATTACTTATTA
Found at i:2834573 original size:19 final size:17
Alignment explanation
Indices: 2834531--2834573 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
2834521 TATCGTTTCT
2834531 TTAT-TTTATTTCATTC
1 TTATATTTATTTCATTC
2834547 TTATTATTTATTTTCATTAC
1 TTA-TATTTA-TTTCATT-C
2834567 TTATATT
1 TTATATT
2834574 ATTATCCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 1 0.04
18 4 0.17
19 11 0.48
20 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTTATTTCATTC
Found at i:2838932 original size:59 final size:59
Alignment explanation
Indices: 2838840--2838958 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
2838830 CTTTGTCAAC
2838840 ATGTCTGCCGGATTTTGAGCTCCACTAATCTTTTCAAGTTCCAAAATCCCATCTTCCAG
1 ATGTCTGCCGGATTTTGAGCTCCACTAATCTTTTCAAGTTCCAAAATCCCATCTTCCAG
2838899 ATGTCTGCCGGATTTTGAGCTCCACTAATCTTTTCAAGTTCCAAAATCCCATCTTCCAG
1 ATGTCTGCCGGATTTTGAGCTCCACTAATCTTTTCAAGTTCCAAAATCCCATCTTCCAG
2838958 A
1 A
2838959 AGAGACCGGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (59 bp):
ATGTCTGCCGGATTTTGAGCTCCACTAATCTTTTCAAGTTCCAAAATCCCATCTTCCAG
Found at i:2843900 original size:64 final size:65
Alignment explanation
Indices: 2843799--2843929 Score: 237
Period size: 64 Copynumber: 2.0 Consensus size: 65
2843789 ATCAAGTATT
2843799 TTATACTTGTGGCGTCAACCCCTTCCTTTCATCTTGATACTTC-TTCCTATTCATATAACTAGTG
1 TTATACTTGTGGCGTCAACCCCTTCCTTTCATCTTGATACTTCGTTCCTATTCATATAACTAGTG
2843863 TTATACTTGTGGCGTCAACCCCTTCCTTTCATCTTGATACTTCTGGTTCCTATTCATATAACTAG
1 TTATACTTGTGGCGTCAACCCCTTCCTTTCATCTTGATACTTC--GTTCCTATTCATATAACTAG
2843928 TG
64 TG
2843930 GGTCAAAGTA
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
64 43 0.67
67 21 0.33
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (65 bp):
TTATACTTGTGGCGTCAACCCCTTCCTTTCATCTTGATACTTCGTTCCTATTCATATAACTAGTG
Found at i:2850713 original size:36 final size:35
Alignment explanation
Indices: 2850620--2850730 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
2850610 TTGGTGGTTA
* * * * *
2850620 TATAGGTGTGAAATGGTGATAGAAGATGGTAAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
2850655 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
2850690 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
2850726 T-TAGG
1 TATAGG
2850731 TAGTATCTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 42 0.64
36 24 0.36
ACGTcount: A:0.32, C:0.03, G:0.38, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:2854479 original size:25 final size:26
Alignment explanation
Indices: 2854424--2854489 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
2854414 AAATGGTTAG
2854424 GGATAGAAATGGTTATGATAGGGGTA
1 GGATAGAAATGGTTATGATAGGGGTA
2854450 GGATAGAAATGGTTATGATA-GGGTA
1 GGATAGAAATGGTTATGATAGGGGTA
*
2854475 GGATAGAAAAGGTTA
1 GGATAGAAATGGTTA
2854490 AGAAAAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 19 0.49
26 20 0.51
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.26
Consensus pattern (26 bp):
GGATAGAAATGGTTATGATAGGGGTA
Found at i:2854981 original size:16 final size:15
Alignment explanation
Indices: 2854956--2854994 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
2854946 TTTGATAATT
2854956 AAGAAATGAAAATGGA
1 AAGAAATG-AAATGGA
*
2854972 AAGAATTGAAATGGA
1 AAGAAATGAAATGGA
2854987 AAGAAATG
1 AAGAAATG
2854995 TTATCAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (15 bp):
AAGAAATGAAATGGA
Found at i:2855233 original size:36 final size:35
Alignment explanation
Indices: 2855140--2855250 Score: 116
Period size: 35 Copynumber: 3.2 Consensus size: 35
2855130 TTGGTGGTTA
* * * * *
2855140 TATAGGCGTGAAATGATGATAGAAGATGGTAAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
2855175 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* **
2855210 TATAGGCATGAAAATGGTGATGGAAGACAGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
2855246 T-TAGG
1 TATAGG
2855251 TAGTATCTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
35 41 0.65
36 22 0.35
ACGTcount: A:0.34, C:0.05, G:0.35, T:0.26
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:2879372 original size:12 final size:12
Alignment explanation
Indices: 2879347--2879381 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2879337 TGTCTTTTAT
2879347 TTATCTTG-TTC
1 TTATCTTGTTTC
2879358 TTATCTTGTTTC
1 TTATCTTGTTTC
2879370 TTATCTTGTTTC
1 TTATCTTGTTTC
2879382 CATCACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.09, C:0.17, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:2879719 original size:13 final size:13
Alignment explanation
Indices: 2879701--2879729 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2879691 TTTTTTTTCA
2879701 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
2879714 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
2879727 AAA
1 AAA
2879730 CAAAGCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:2879740 original size:17 final size:17
Alignment explanation
Indices: 2879700--2879733 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2879690 ATTTTTTTTC
2879700 AAAAAAAAAAAAACAAA
1 AAAAAAAAAAAAACAAA
*
2879717 AAAAAAAAACAAACAAA
1 AAAAAAAAAAAAACAAA
2879734 GCAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAACAAA
Found at i:2880838 original size:72 final size:71
Alignment explanation
Indices: 2880720--2880858 Score: 174
Period size: 72 Copynumber: 1.9 Consensus size: 71
2880710 AATACATCAT
* * * * * *
2880720 TTGGCTGAATTCATCCCACCTTGTGTGAACTTGTTGATTTGTCTTCTATGGATGAATGTTCATGA
1 TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCT-TGCATGAATATGCATGA
2880785 ATGTATC
65 ATGTATC
*
2880792 TTGGCTGAAATTCTTCCC-CCTTGTGTGAACATGACT-ATTTGGCTTCTTGCATGAATATGCATG
1 TTGGCTG-AATTCATCCCACCTTGTGTGAACATG-CTGATTTGGCTTCTTGCATGAATATGCATG
2880855 AATG
64 AATG
2880859 GATGAATTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
71 17 0.29
72 31 0.53
73 10 0.17
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (71 bp):
TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCTTGCATGAATATGCATGAA
TGTATC
Found at i:2884556 original size:13 final size:11
Alignment explanation
Indices: 2884537--2884599 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 11
2884527 GATACTATTT
2884537 TCATCACCATA
1 TCATCACCATA
2884548 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
2884562 TCA-CGCCTATA
1 TCATCACC-ATA
2884573 TCATCACCATA
1 TCATCACCATA
2884584 TTCCATCACCATA
1 -T-CATCACCATA
2884597 TCA
1 TCA
2884600 CGCCAATAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
11 13 0.30
12 9 0.21
13 19 0.44
14 2 0.05
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:2884589 original size:36 final size:35
Alignment explanation
Indices: 2884537--2884612 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 35
2884527 GATACTATTT
*
2884537 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCA-TATCACGCCAATA
*
2884573 TCATCACCATATTCCATCACCATATCACGCCAATA
1 TCATCACCATAGTCCATCACCATATCACGCCAATA
*
2884608 ACATC
1 TCATC
2884613 CTTCCATTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 16 0.43
36 21 0.57
ACGTcount: A:0.33, C:0.37, G:0.04, T:0.26
Consensus pattern (35 bp):
TCATCACCATAGTCCATCACCATATCACGCCAATA
Found at i:2885079 original size:14 final size:14
Alignment explanation
Indices: 2885056--2885101 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
2885046 TTTGGAGTGC
2885056 AAAAGAAAGAAAAGA
1 AAAAG-AAGAAAAGA
*
2885071 AAAAGAAGAATA-A
1 AAAAGAAGAAAAGA
*
2885084 AAAA-AAGCAAAGA
1 AAAAGAAGAAAAGA
2885097 AAAAG
1 AAAAG
2885102 TGAAGCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 6 0.23
15 5 0.19
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Found at i:2885111 original size:26 final size:27
Alignment explanation
Indices: 2885054--2885111 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
2885044 AATTTGGAGT
*
2885054 GCAAAAGAAAGAAAAGAAAAAGAAGAA
1 GCAAAAAAAAGAAAAGAAAAAGAAGAA
* * *
2885081 -TAAAAAAAAGCAAAGAAAAAG-TGAA
1 GCAAAAAAAAGAAAAGAAAAAGAAGAA
2885106 GCAAAA
1 GCAAAA
2885112 TTGCAAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.72, C:0.05, G:0.19, T:0.03
Consensus pattern (27 bp):
GCAAAAAAAAGAAAAGAAAAAGAAGAA
Found at i:2888554 original size:13 final size:11
Alignment explanation
Indices: 2888535--2888597 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 11
2888525 GATACTATTT
2888535 TCATCACCATA
1 TCATCACCATA
2888546 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
2888560 TCA-CGCCTATA
1 TCATCACC-ATA
2888571 TCATCACCATA
1 TCATCACCATA
2888582 TTCCATCACCATA
1 -T-CATCACCATA
2888595 TCA
1 TCA
2888598 CGCCAATAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
11 13 0.30
12 9 0.21
13 19 0.44
14 2 0.05
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:2888587 original size:36 final size:35
Alignment explanation
Indices: 2888535--2888611 Score: 118
Period size: 36 Copynumber: 2.2 Consensus size: 35
2888525 GATACTATTT
*
2888535 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCA-TATCACGCCAATA
*
2888571 TCATCACCATATTCCATCACCATATCACGCCAATA
1 TCATCACCATAGTCCATCACCATATCACGCCAATA
*
2888606 ACATCA
1 TCATCA
2888612 TCCTTCCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 17 0.45
36 21 0.55
ACGTcount: A:0.34, C:0.36, G:0.04, T:0.26
Consensus pattern (35 bp):
TCATCACCATAGTCCATCACCATATCACGCCAATA
Found at i:2888626 original size:33 final size:33
Alignment explanation
Indices: 2888547--2888650 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2888537 ATCACCATAG
* *
2888547 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2888583 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2888616 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2888649 TC
1 TC
2888651 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2892577 original size:13 final size:11
Alignment explanation
Indices: 2892558--2892620 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 11
2892548 GATACTATTT
2892558 TCATCACCATA
1 TCATCACCATA
2892569 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
2892583 TCA-CGCCTATA
1 TCATCACC-ATA
2892594 TCATCACCATA
1 TCATCACCATA
2892605 TTCCATCACCATA
1 -T-CATCACCATA
2892618 TCA
1 TCA
2892621 CGCCAATAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
11 13 0.30
12 9 0.21
13 19 0.44
14 2 0.05
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:2892610 original size:36 final size:35
Alignment explanation
Indices: 2892558--2892634 Score: 118
Period size: 36 Copynumber: 2.2 Consensus size: 35
2892548 GATACTATTT
*
2892558 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCA-TATCACGCCAATA
*
2892594 TCATCACCATATTCCATCACCATATCACGCCAATA
1 TCATCACCATAGTCCATCACCATATCACGCCAATA
*
2892629 ACATCA
1 TCATCA
2892635 TCCTTCCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 17 0.45
36 21 0.55
ACGTcount: A:0.34, C:0.36, G:0.04, T:0.26
Consensus pattern (35 bp):
TCATCACCATAGTCCATCACCATATCACGCCAATA
Found at i:2892649 original size:33 final size:33
Alignment explanation
Indices: 2892570--2892673 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2892560 ATCACCATAG
* *
2892570 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2892606 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2892639 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2892672 TC
1 TC
2892674 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2899262 original size:11 final size:11
Alignment explanation
Indices: 2899248--2899272 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2899238 AAAGCAACGG
2899248 AAAAGAAAAGA
1 AAAAGAAAAGA
2899259 AAAAGAAAAGA
1 AAAAGAAAAGA
2899270 AAA
1 AAA
2899273 GACTCCTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:2901874 original size:33 final size:33
Alignment explanation
Indices: 2901830--2901898 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2901820 CATCACCATA
*
2901830 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
2901863 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
2901896 TTC
1 TTC
2901899 ATTCATAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:2905167 original size:9 final size:9
Alignment explanation
Indices: 2905155--2905204 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
2905145 TTGAAACTTT
2905155 TTCTTTTTC
1 TTCTTTTTC
2905164 TTC--TTTC
1 TTCTTTTTC
2905171 TTCTTTTTC
1 TTCTTTTTC
2905180 TTCTTTTT-
1 TTCTTTTTC
*
2905188 GTC-TTTTC
1 TTCTTTTTC
2905196 TTTCTTTTT
1 -TTCTTTTT
2905205 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
7 11 0.32
8 2 0.06
9 17 0.50
10 4 0.12
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:2905192 original size:17 final size:16
Alignment explanation
Indices: 2905152--2905204 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
2905142 CTTTTGAAAC
2905152 TTTTTCTTTTTCTTCT
1 TTTTTCTTTTTCTTCT
*
2905168 TTCTTCTTTTTCTTCT
1 TTTTTCTTTTTCTTCT
2905184 TTTTGTC-TTTTCTTTCT
1 TTTT-TCTTTTTC-TTCT
2905201 TTTT
1 TTTT
2905205 GCACTCCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 23 0.70
17 10 0.30
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTTCTTCT
Found at i:2905205 original size:17 final size:17
Alignment explanation
Indices: 2905159--2905205 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2905149 AACTTTTTCT
*
2905159 TTTTC-TTCTTTCT-TC
1 TTTTCTTTCTTTTTGTC
2905174 TTTT-TCTTCTTTTTGTC
1 TTTTCT-TTCTTTTTGTC
2905191 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
2905206 CACTCCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 7 0.26
17 15 0.56
18 1 0.04
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:2913165 original size:71 final size:71
Alignment explanation
Indices: 2913048--2913185 Score: 165
Period size: 71 Copynumber: 1.9 Consensus size: 71
2913038 AATACATCAT
* * * * * *
2913048 TTGGCTGAATTCATCTCACCTTGTGTGAACTTGTTGATTTGTCTTCTATGGATGAATGTTCATGA
1 TTGGCTGAATTCATCTCACCTTGTGTGAACATGCTGATTTGGCTTCT-TGCATGAATATGCATGA
2913113 ATGTATC
65 ATGTATC
*
2913120 TTGGCTGAAATTC-T-TCCCCTTGTGTGAACATGACT-ATTTGGCTTCTTGCATGAATATGCATG
1 TTGGCTG-AATTCATCTCACCTTGTGTGAACATG-CTGATTTGGCTTCTTGCATGAATATGCATG
2913182 AATG
64 AATG
2913186 GATGAATTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
70 17 0.30
71 26 0.46
72 9 0.16
73 5 0.09
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.41
Consensus pattern (71 bp):
TTGGCTGAATTCATCTCACCTTGTGTGAACATGCTGATTTGGCTTCTTGCATGAATATGCATGAA
TGTATC
Found at i:2915843 original size:36 final size:36
Alignment explanation
Indices: 2915790--2915919 Score: 188
Period size: 36 Copynumber: 3.6 Consensus size: 36
2915780 TTCCACCTTT
2915790 ATTATCACGCCTATATCATCACCATAGTCCATCACC
1 ATTATCACGCCTATATCATCACCATAGTCCATCACC
* * *
2915826 ATTATCAGGCCTTTATCATCACCATAGTCCATCTCC
1 ATTATCACGCCTATATCATCACCATAGTCCATCACC
* * *
2915862 ATTATCACGCCTATATCGTCACCATATTCCACCACC
1 ATTATCACGCCTATATCATCACCATAGTCCATCACC
* *
2915898 ATTATCACGCCCATATTATCAC
1 ATTATCACGCCTATATCATCAC
2915920 AAACTTATAA
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.28, C:0.35, G:0.06, T:0.30
Consensus pattern (36 bp):
ATTATCACGCCTATATCATCACCATAGTCCATCACC
Found at i:2918681 original size:36 final size:36
Alignment explanation
Indices: 2918629--2918741 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
2918619 GATACTATTT
*
2918629 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
2918665 TCATCACCATAGTCCATCACCATTATCATGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
2918701 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
2918736 ACATCA
1 TCATCA
2918742 TCCTCCATTA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:2918684 original size:13 final size:11
Alignment explanation
Indices: 2918629--2918727 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
2918619 GATACTATTT
2918629 TCATCACCATAA
1 TCATCACCAT-A
*
2918641 TCCATCTCCATTA
1 T-CATCACCA-TA
*
2918654 TCA-CGCCTATA
1 TCATCACC-ATA
2918665 TCATCACCATA
1 TCATCACCATA
2918676 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
2918690 TCATGC-CTATA
1 TCAT-CACCATA
2918701 TCATCACCATA
1 TCATCACCATA
2918712 TTCCATCACCATA
1 -T-CATCACCATA
2918725 TCA
1 TCA
2918728 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.01
11 23 0.32
12 15 0.21
13 29 0.41
14 3 0.04
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:2918755 original size:32 final size:32
Alignment explanation
Indices: 2918713--2918782 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
2918703 ATCACCATAT
* *
2918713 TCCATCACCATATCA-CGCCAATAACATCATCC
1 TCCATTACCATATCATCACCAATAA-ATCATCC
* *
2918745 TCCATTACCATTTCATCACCATTAAATCATCC
1 TCCATTACCATATCATCACCAATAAATCATCC
*
2918777 TTCATT
1 TCCATT
2918783 CATCAACAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.31, C:0.36, G:0.01, T:0.31
Consensus pattern (32 bp):
TCCATTACCATATCATCACCAATAAATCATCC
Found at i:2921997 original size:22 final size:22
Alignment explanation
Indices: 2921971--2922012 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2921961 TATTTATAGT
2921971 TATGATGATGA-TATTATGAATG
1 TATGATG-TGATTATTATGAATG
*
2921993 TATGATGTTATTATTATGAA
1 TATGATGTGATTATTATGAA
2922013 CCACATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (22 bp):
TATGATGTGATTATTATGAATG
Found at i:2923186 original size:36 final size:36
Alignment explanation
Indices: 2923134--2923246 Score: 167
Period size: 36 Copynumber: 3.2 Consensus size: 36
2923124 GATACTATTT
* *
2923134 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
2923170 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
2923206 TCATCACCAT-GTTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAG-TCCATCACCATTATCACGCCTATA
*
2923241 ACATCA
1 TCATCA
2923247 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 18 0.25
36 54 0.75
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:2923261 original size:33 final size:33
Alignment explanation
Indices: 2923146--2923285 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
2923136 ATCACCATAA
* * *
2923146 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
2923180 AGTCCATCACCATTATCACGCCTATATCATCA-CCATGT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
2923218 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2923251 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2923284 TC
1 TC
2923286 ATTCATCAAC
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.47
38 1 0.01
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2927825 original size:36 final size:36
Alignment explanation
Indices: 2927773--2927885 Score: 167
Period size: 36 Copynumber: 3.2 Consensus size: 36
2927763 GATACTATTT
* *
2927773 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
2927809 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
2927845 TCATCACCAT-GTTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAG-TCCATCACCATTATCACGCCTATA
*
2927880 ACATCA
1 TCATCA
2927886 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 18 0.25
36 54 0.75
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:2927900 original size:33 final size:33
Alignment explanation
Indices: 2927785--2927924 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
2927775 ATCACCATAA
* * *
2927785 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
2927819 AGTCCATCACCATTATCACGCCTATATCATCA-CCATGT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
2927857 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2927890 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2927923 TC
1 TC
2927925 ATTCATCAAC
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.47
38 1 0.01
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2932464 original size:36 final size:36
Alignment explanation
Indices: 2932441--2932572 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 36
2932431 TTCCACCTTT
*
2932441 ATTATCACGCCTATATCATCACCATAGTCCATCACC
1 ATTATCACGCCTATATCATCACCATAGTCCACCACC
* * *
2932477 ATTATCACGCCTTTATCATCACCATAGTCCATCTCC
1 ATTATCACGCCTATATCATCACCATAGTCCACCACC
* *
2932513 ATTATCACGCCTATATCGTCACCATATTCCACCACC
1 ATTATCACGCCTATATCATCACCATAGTCCACCACC
* *
2932549 ATTATCACGCCCATATTATCACCA
1 ATTATCACGCCTATATCATCACCA
2932573 ACTTATAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 86 1.00
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
ATTATCACGCCTATATCATCACCATAGTCCACCACC
Found at i:2955089 original size:19 final size:21
Alignment explanation
Indices: 2955042--2955090 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
2955032 AATAAAGGGT
2955042 AATAATATAAGTAATGAAAATA
1 AATAA-ATAAGTAATGAAAATA
*
2955064 AAT-AATAAG-AATG-AAATG
1 AATAAATAAGTAATGAAAATA
2955082 AATAAATAA
1 AATAAATAA
2955091 AAAGATAGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 5 0.20
21 1 0.04
22 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.24
Consensus pattern (21 bp):
AATAAATAAGTAATGAAAATA
Found at i:2959330 original size:5 final size:5
Alignment explanation
Indices: 2959320--2959374 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
2959310 GAACTTCTCT
2959320 TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TTCTT- TTTGTC TTTTC
1 TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC TT-TTC TTT-TC TTTTC
2959367 -TTTC TTTT
1 TTTTC TTTT
2959375 TGCACTCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 5 0.11
5 30 0.68
6 9 0.20
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:2959338 original size:8 final size:8
Alignment explanation
Indices: 2959327--2959374 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
2959317 TCTTTTTCTT
2959327 TTCTTTTC
1 TTCTTTTC
2959335 TTCTTTTC
1 TTCTTTTC
2959343 TTCTTTTC
1 TTCTTTTC
2959351 TTCTTTT-
1 TTCTTTTC
2959358 TGTCTTTTC
1 T-TCTTTTC
2959367 TTTCTTTT
1 -TTCTTTT
2959375 TGCACTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 29 0.78
9 6 0.16
10 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:2965255 original size:13 final size:11
Alignment explanation
Indices: 2965214--2965298 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
2965204 TACAATCTTC
2965214 CATCACCATTAT
1 CATCACCA-TAT
*
2965226 CACTC-CTATAT
1 CA-TCACCATAT
2965237 CATCACCATAGT
1 CATCACCATA-T
2965249 CCATCACCATTAT
1 -CATCACCA-TAT
*
2965262 CA-CGCCTATAT
1 CATCACC-ATAT
2965273 CATCACCATATT
1 CATCACCATA-T
2965285 CCATCACCATAT
1 -CATCACCATAT
2965297 CA
1 CA
2965299 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 2 0.03
11 22 0.37
12 13 0.22
13 21 0.35
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:2965259 original size:36 final size:36
Alignment explanation
Indices: 2965212--2965315 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
2965202 GATACAATCT
*
2965212 TCCATCACCATTATCACTCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
2965248 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
2965284 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
2965316 ACTTCTAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:2980433 original size:20 final size:19
Alignment explanation
Indices: 2980396--2980433 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2980386 AGAGCATGTA
*
2980396 TTTTCATTAAAGTCTTGTT
1 TTTTCATTAAAATCTTGTT
2980415 TTTTCATTAAAAATCTTGT
1 TTTTCATT-AAAATCTTGT
2980434 CATTTTAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (19 bp):
TTTTCATTAAAATCTTGTT
Found at i:2984697 original size:16 final size:16
Alignment explanation
Indices: 2984663--2984696 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2984653 TTCAACTTTC
*
2984663 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
2984679 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
2984694 TTT
1 TTT
2984697 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:2984724 original size:23 final size:25
Alignment explanation
Indices: 2984685--2984738 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
2984675 TTCTTTTCTT
2984685 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
2984710 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
2984733 TTTCTT
1 TTTCTT
2984739 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:2986495 original size:17 final size:17
Alignment explanation
Indices: 2986473--2986512 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2986463 TTAATTAATT
2986473 AAACTAGTTCATTCATC
1 AAACTAGTTCATTCATC
* *
2986490 AAACTAGTTCATTTATT
1 AAACTAGTTCATTCATC
2986507 AAACTA
1 AAACTA
2986513 ACTCTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (17 bp):
AAACTAGTTCATTCATC
Found at i:2988766 original size:15 final size:15
Alignment explanation
Indices: 2988732--2988770 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2988722 GAAATGGAAG
2988732 AAGAAATGAAATGAT
1 AAGAAATGAAATGAT
*
2988747 AAGAATTGAAATGGAT
1 AAGAAATGAAAT-GAT
2988763 -AGAAATGA
1 AAGAAATGA
2988771 TATCAAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (15 bp):
AAGAAATGAAATGAT
Found at i:2990113 original size:73 final size:72
Alignment explanation
Indices: 2990005--2990167 Score: 267
Period size: 73 Copynumber: 2.3 Consensus size: 72
2989995 AATAAGCTAA
*
2990005 ATAA-TATAAGATATAAT-AATGTAAATATGTGGTTCATAATAATAACTTCATACATTCATAATA
1 ATAACTATAA-ATATAATGTATGTAAATATGTGGTTCATAATAATAACTTCATACATTCATAATA
2990068 TCATCATC
65 TCATCATC
*
2990076 ATAACTATAAATATAATGTATGTAAGTTATGTGGTTCATAATAATAACTTCATACATTCATAATA
1 ATAACTATAAATATAATGTATGTAA-ATATGTGGTTCATAATAATAACTTCATACATTCATAATA
*
2990141 TTATCATC
65 TCATCATC
2990149 ATAACTATAAATATAATGT
1 ATAACTATAAATATAATGT
2990168 TTATAAGCAC
Statistics
Matches: 86, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
71 11 0.13
72 11 0.13
73 64 0.74
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (72 bp):
ATAACTATAAATATAATGTATGTAAATATGTGGTTCATAATAATAACTTCATACATTCATAATAT
CATCATC
Found at i:2990150 original size:22 final size:22
Alignment explanation
Indices: 2990110--2990151 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2990100 AGTTATGTGG
*
2990110 TTCATAATAATAACTTCATACA
1 TTCATAATAATAACATCATACA
* *
2990132 TTCATAATATTATCATCATA
1 TTCATAATAATAACATCATA
2990152 ACTATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATAACATCATACA
Done.