Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006856.1 Hibiscus syriacus cultivar Beakdansim tig00017446_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: 1184065
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 4
Found at i:720632 original size:23 final size:25
Alignment explanation
Indices: 720604--720654 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
720594 AATAGCAAAG
720604 AAATTG-AAGCACTCAAAA-GAAGA
1 AAATTGCAAGCACTCAAAAGGAAGA
720627 AAATTGCAAGCACTCAAAAGGAAGA
1 AAATTGCAAGCACTCAAAAGGAAGA
720652 AAA
1 AAA
720655 AGAGAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.23
24 12 0.46
25 8 0.31
ACGTcount: A:0.57, C:0.14, G:0.18, T:0.12
Consensus pattern (25 bp):
AAATTGCAAGCACTCAAAAGGAAGA
Found at i:734781 original size:23 final size:23
Alignment explanation
Indices: 734749--734801 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
734739 TTGGTTTTAT
* *
734749 GGTGAATAAGAATATTCATTAAG
1 GGTGATTAAGAATATTCAGTAAG
734772 GGTGATTAAGAATATTCAGTAAG
1 GGTGATTAAGAATATTCAGTAAG
734795 GGTGATT
1 GGTGATT
734802 TGGTCTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (23 bp):
GGTGATTAAGAATATTCAGTAAG
Found at i:736488 original size:59 final size:59
Alignment explanation
Indices: 736389--736525 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 59
736379 TAGCAGGCTG
** * * *
736389 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTTT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** *
736448 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
736507 CATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
736526 CGGTGCTTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:736676 original size:44 final size:46
Alignment explanation
Indices: 736626--736737 Score: 147
Period size: 47 Copynumber: 2.5 Consensus size: 46
736616 GTAAGCATAC
*
736626 AAATAAGCTTACGAGCTTTTGGAA-T-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGCAAGTATATGGGTA
* * * * *
736670 AAATAAGTTTACTAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TTAAATGGCAAGTATATGGGTA
736717 AAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
736738 AGATCAATGG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 21 0.37
46 1 0.02
47 35 0.61
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGCAAGTATATGGGTA
Found at i:738333 original size:11 final size:12
Alignment explanation
Indices: 738293--738336 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
738283 TATTTAAACG
*
738293 GGTATTGGGCCA
1 GGTATTGGGTCA
*
738305 GGTATTGGGTCG
1 GGTATTGGGTCA
738317 GGTATTGGGTC-
1 GGTATTGGGTCA
738328 GGTATTGGG
1 GGTATTGGG
738337 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:738335 original size:23 final size:24
Alignment explanation
Indices: 738291--738336 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
738281 ATTATTTAAA
738291 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
738315 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
738337 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:738414 original size:24 final size:25
Alignment explanation
Indices: 738354--738414 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
738344 TCGGGCCGGG
738354 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
738377 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
738401 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
738415 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:738480 original size:13 final size:13
Alignment explanation
Indices: 738450--738494 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
738440 TTTAATATTT
*
738450 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
738462 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
738475 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
738488 ATCGGGG
1 ATCGGGG
738495 TAATCGGGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.35
13 20 0.65
ACGTcount: A:0.13, C:0.16, G:0.53, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:743756 original size:44 final size:46
Alignment explanation
Indices: 743706--743817 Score: 140
Period size: 47 Copynumber: 2.5 Consensus size: 46
743696 GTAAGCATAC
* *
743706 AAATAAGCTTACGAGCTTTTGGAA-T-AATGGCAAGT-ATATGGGTA
1 AAATAAGCTTAAGAGCTTATGGAATTAAATGGCAAGTAAT-TGGGTA
* * *
743750 AAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTAATTTGGTA
1 AAATAAGCTTAAGAGCTTATGGAA-TTAAATGGCAAGTAATTGGGTA
743797 AAATAAGCTTAAGAGCTTATG
1 AAATAAGCTTAAGAGCTTATG
743818 AGATAAATGG
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
44 22 0.37
46 1 0.02
47 34 0.58
48 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTAAGAGCTTATGGAATTAAATGGCAAGTAATTGGGTA
Found at i:747848 original size:30 final size:30
Alignment explanation
Indices: 747812--747871 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
747802 TGTGTACACT
*
747812 TTAGAAATGAAAGGTTCCCAAATCAAAGAA
1 TTAGAAAAGAAAGGTTCCCAAATCAAAGAA
747842 TTAGAAAAGAAAGGTTCCCAAATCAAAGAA
1 TTAGAAAAGAAAGGTTCCCAAATCAAAGAA
747872 AGTCCAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.18
Consensus pattern (30 bp):
TTAGAAAAGAAAGGTTCCCAAATCAAAGAA
Found at i:749999 original size:14 final size:14
Alignment explanation
Indices: 749982--750010 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
749972 GAGATTTCTA
749982 TGTAGGGAATTATT
1 TGTAGGGAATTATT
749996 TGTAGGGAATTATT
1 TGTAGGGAATTATT
750010 T
1 T
750011 ACAGGGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (14 bp):
TGTAGGGAATTATT
Found at i:753786 original size:2 final size:2
Alignment explanation
Indices: 753774--753808 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
753764 TTGCTATAAC
*
753774 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
753809 ACTACATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:755403 original size:19 final size:20
Alignment explanation
Indices: 755358--755406 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
755348 AACCCCTTTA
**
755358 AAAATACATGATTTTTGATG
1 AAAATACATGATTTTAAATG
755378 AAAATACATGA-TTTAAATG
1 AAAATACATGATTTTAAATG
*
755397 AAGATACATG
1 AAAATACATG
755407 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
AAAATACATGATTTTAAATG
Found at i:758726 original size:5 final size:5
Alignment explanation
Indices: 758716--758784 Score: 58
Period size: 5 Copynumber: 13.8 Consensus size: 5
758706 TTGAATTTAT
758716 TTTTC TTTTC TTTTC TTTTC --TTC TTTTC TGATTT- TTTTC TTCTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T--TTTC TTTTC TT-TTC
758761 TTCTT- TTTTC GTTTTC -TTTC TTTT
1 TT-TTC TTTTC -TTTTC TTTTC TTTT
758785 TGCACTCCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
3 3 0.05
4 9 0.16
5 26 0.47
6 14 0.25
7 3 0.05
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:758741 original size:13 final size:13
Alignment explanation
Indices: 758718--758779 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
758708 GAATTTATTT
758718 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
758731 TT-TTCTTCTTTTC
1 TTCTT-TTCTTTTC
**
758744 -TGATTT-TTTTC
1 TTCTTTTCTTTTC
758755 TTCTTCTTCTTTT-
1 TTCTT-TTCTTTTC
758768 TTCGTTTTCTTT
1 TTC-TTTTCTTT
758780 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
11 5 0.12
12 7 0.17
13 22 0.55
14 6 0.15
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:758755 original size:19 final size:19
Alignment explanation
Indices: 758696--758764 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
758686 CTTGGCTTAC
* *
758696 TTTC-TCTTTTTTGAATTTA
1 TTTCTTCTTTTCTG-ATTTT
758715 TTT-TTCTTTTCT--TTTCT
1 TTTCTTCTTTTCTGATTT-T
758732 TTTCTTCTTTTCTGATTTT
1 TTTCTTCTTTTCTGATTTT
758751 TTTCTTCTTCTTCT
1 TTTCTTCTT-TTCT
758765 TTTTTCGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 3 0.07
17 3 0.07
18 9 0.21
19 20 0.48
20 7 0.17
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTCTTCTTTTCTGATTTT
Found at i:758759 original size:37 final size:37
Alignment explanation
Indices: 758696--758767 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
758686 CTTGGCTTAC
*
758696 TTTCTCTTTTTTGAATTTATTTTTCTT-TTCTTTTCT
1 TTTCTCTTTTCTGAATTTATTTTTCTTCTTCTTTTCT
*
758732 TTTCTTCTTTTCTG-ATTTTTTTCTTCTTCTTCTTTT
1 TTTC-TCTTTTCTGAATTTATTT-TTCTTCTTCTTTT
758768 TTCGTTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 11 0.35
37 13 0.42
38 7 0.23
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (37 bp):
TTTCTCTTTTCTGAATTTATTTTTCTTCTTCTTTTCT
Found at i:758767 original size:16 final size:15
Alignment explanation
Indices: 758715--758785 Score: 63
Period size: 17 Copynumber: 4.3 Consensus size: 15
758705 TTTGAATTTA
758715 TTTTTCTTTTCTTTTCT
1 TTTTTCTTTTC--TTCT
758732 TTTCTTCTTTTCTGAT-T
1 TTT-TTCTTTTCT--TCT
758749 TTTTTCTTCTTCTTCT
1 TTTTTCTT-TTCTTCT
758765 TTTTTCGTTTTCTTTCT
1 TTTTTC-TTTTC-TTCT
758782 TTTT
1 TTTT
758786 GCACTCCAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
15 1 0.02
16 16 0.34
17 21 0.45
18 9 0.19
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTTCTTTTCTTCT
Found at i:758768 original size:18 final size:17
Alignment explanation
Indices: 758718--758769 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 17
758708 GAATTTATTT
758718 TTCTTTTCTTTTCTTTTC
1 TTCTTTTCTTTT-TTTTC
758736 TTCTTTTCTGATTTTTTTC
1 TTCTTTTCT--TTTTTTTC
758755 TTCTTCTTCTTTTTT
1 TTCTT-TTCTTTTTT
758770 CGTTTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 14 0.45
19 10 0.32
20 7 0.23
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (17 bp):
TTCTTTTCTTTTTTTTC
Found at i:758785 original size:33 final size:32
Alignment explanation
Indices: 758714--758777 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
758704 TTTTGAATTT
758714 ATTTTTCTT-TTCTTTTCTTTTCTTCTTTTCTG
1 ATTTTT-TTCTTCTTTTCTTTTCTTCTTTTCTG
758746 ATTTTTTTCTTCTTCTTCTTTT-TTCGTTTTCT
1 ATTTTTTTCTTCTT-TTCTTTTCTTC-TTTTCT
758778 TTCTTTTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 2 0.07
32 14 0.48
33 13 0.45
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (32 bp):
ATTTTTTTCTTCTTTTCTTTTCTTCTTTTCTG
Found at i:759527 original size:19 final size:20
Alignment explanation
Indices: 759480--759530 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
759470 GAAACCTCTT
**
759480 TGAAAATACATGATGTTTTA
1 TGAAAATACATGATGTTAAA
759500 TGAAAATACATGAT-TTAAA
1 TGAAAATACATGATGTTAAA
*
759519 TGAAGATACATG
1 TGAAAATACATG
759531 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATGTTAAA
Found at i:764624 original size:40 final size:42
Alignment explanation
Indices: 764572--764667 Score: 117
Period size: 40 Copynumber: 2.3 Consensus size: 42
764562 AGGATCAGAC
* *
764572 TTATTATTTTATTAGAAATTA-A-AAACAATATTTTTAG-TTA
1 TTATTATTTTATTAGAAATTAGAGAAA-AACATGTTTAGTTTA
* *
764612 TTATTATTTTATTAGGAATTAGAGTTAAAACATGTTTAGTTTA
1 TTATTATTTTATTAGAAATTAGAG-AAAAACATGTTTAGTTTA
764655 TTATTATTTTATT
1 TTATTATTTTATT
764668 CTTTTGTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 20 0.42
41 1 0.02
42 9 0.19
43 18 0.38
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.53
Consensus pattern (42 bp):
TTATTATTTTATTAGAAATTAGAGAAAAACATGTTTAGTTTA
Found at i:765482 original size:10 final size:9
Alignment explanation
Indices: 765457--765481 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
765447 CAAAACAAAA
765457 CAAAAAAGG
1 CAAAAAAGG
765466 CAAAAAAGG
1 CAAAAAAGG
765475 CAAAAAA
1 CAAAAAA
765482 AAAAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (9 bp):
CAAAAAAGG
Found at i:769709 original size:20 final size:22
Alignment explanation
Indices: 769669--769714 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
769659 TGCTTGAATG
769669 ATGCACATGGCAGCCTACTTG-A
1 ATGCACATGG-AGCCTACTTGCA
*
769691 ATGCACATGG-GCCTTCTTGCA
1 ATGCACATGGAGCCTACTTGCA
769712 ATG
1 ATG
769715 ATTTGGTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (22 bp):
ATGCACATGGAGCCTACTTGCA
Found at i:784089 original size:19 final size:20
Alignment explanation
Indices: 784065--784114 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
784055 GGTCAAGAGC
*
784065 ATGTATATTCATT-AAAATA
1 ATGTATTTTCATTAAAAATA
* *
784084 ATGTATTTTAATTAAAAATC
1 ATGTATTTTCATTAAAAATA
784104 ATGTATTTTCA
1 ATGTATTTTCA
784115 AAGGGTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (20 bp):
ATGTATTTTCATTAAAAATA
Found at i:793523 original size:61 final size:61
Alignment explanation
Indices: 793331--793527 Score: 243
Period size: 61 Copynumber: 3.2 Consensus size: 61
793321 GTAAAAACAA
* * * * * *
793331 CATGGTACATGCTGGTAATAGCATGGTTGAGCATTATAAAGACATATATAATTCACTAGAG
1 CATGGTACACGTTGATAAAAGCCTGGTGGAGCATTATAAAGACATATATAATTCACTAGAG
* * *
793392 CATGGTACACGGTGATAAAAGCCTGGTGGAGTATTATAAAGATATATATAATTCACTAGAG
1 CATGGTACACGTTGATAAAAGCCTGGTGGAGCATTATAAAGACATATATAATTCACTAGAG
* * * *
793453 CATGGTACACGTTGATAACAA-CTTGGTGGAGCATTATAAAGACATATACAATTCAATAAAG
1 CATGGTACACGTTGATAA-AAGCCTGGTGGAGCATTATAAAGACATATATAATTCACTAGAG
**
793514 CATTATACACGTTG
1 CATGGTACACGTTG
793528 GAAGACATAA
Statistics
Matches: 118, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
61 116 0.98
62 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (61 bp):
CATGGTACACGTTGATAAAAGCCTGGTGGAGCATTATAAAGACATATATAATTCACTAGAG
Found at i:797397 original size:13 final size:12
Alignment explanation
Indices: 797378--797463 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
797368 ATATAGGCGT
797378 GATATGGTGATG
1 GATATGGTGATG
797390 GAATATGGTGAT-
1 G-ATATGGTGATG
*
797402 GATATAGG-CAT-
1 GATAT-GGTGATG
797413 GATAATGGTGATG
1 GAT-ATGGTGATG
797426 GACTATGGTGAT-
1 GA-TATGGTGATG
*
797438 GATATAGGCG-T-
1 GATAT-GGTGATG
797449 GATAATGGTGATG
1 GAT-ATGGTGATG
797462 GA
1 GA
797464 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:797433 original size:36 final size:36
Alignment explanation
Indices: 797360--797464 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
797350 ATTTATAAGT
* *
797360 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
797395 TGGTGATGATATAGGCATGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
797431 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
797465 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:809627 original size:44 final size:44
Alignment explanation
Indices: 809563--809659 Score: 185
Period size: 44 Copynumber: 2.2 Consensus size: 44
809553 AAACCACATC
*
809563 TTTATATTACTTGATGCATTATCTTATTTAAAGCATATTATTTA
1 TTTATATTACTTGATACATTATCTTATTTAAAGCATATTATTTA
809607 TTTATATTACTTGATACATTATCTTATTTAAAGCATATTATTTA
1 TTTATATTACTTGATACATTATCTTATTTAAAGCATATTATTTA
809651 TTTATATTA
1 TTTATATTA
809660 GTCTTGCATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (44 bp):
TTTATATTACTTGATACATTATCTTATTTAAAGCATATTATTTA
Found at i:811389 original size:14 final size:14
Alignment explanation
Indices: 811367--811406 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
811357 TAAGATACTA
*
811367 TTTCTATCACCATC
1 TTTCCATCACCATC
811381 TTTCCATCACCATC
1 TTTCCATCACCATC
*
811395 -CTCCATCACCAT
1 TTTCCATCACCAT
811407 TCATACCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:811401 original size:13 final size:14
Alignment explanation
Indices: 811372--811406 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
811362 TACTATTTCT
*
811372 ATCACCATCTTTCC
1 ATCACCATCTCTCC
811386 ATCACCATC-CTCC
1 ATCACCATCTCTCC
811399 ATCACCAT
1 ATCACCAT
811407 TCATACCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.26, C:0.46, G:0.00, T:0.29
Consensus pattern (14 bp):
ATCACCATCTCTCC
Found at i:812040 original size:16 final size:16
Alignment explanation
Indices: 812019--812055 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
812009 GTAAGTTATC
*
812019 TTCATTTTCTTAATAT
1 TTCATTTCCTTAATAT
*
812035 TTCATTTCCTTAATCT
1 TTCATTTCCTTAATAT
812051 TTCAT
1 TTCAT
812056 CTTTTCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (16 bp):
TTCATTTCCTTAATAT
Found at i:817040 original size:198 final size:198
Alignment explanation
Indices: 816725--817108 Score: 705
Period size: 198 Copynumber: 1.9 Consensus size: 198
816715 CTCTCTTTCT
* *
816725 TTAAAAAGATTCGACCTTGAATCTGAAACATTAAAGGGAGCAACATTAGAATCGTTTAATGATTC
1 TTAAAAAGATTCGACCTCGAATATGAAACATTAAAGGGAGCAACATTAGAATCGTTTAATGATTC
*
816790 ATTCACATTATACTTACCGAATAGATATGCTTTGAATCTTTGAGACTTTGTTCTTCTAATAGGTT
66 ATTCACATTATACTTACCGAATAGATATGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTT
*
816855 CGAGTAGAAACATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTGCATGTATCATTCCCCCAC
131 CGAGTAGAAACATTAGTCCAAAGAAGAATGTATTATGGACTCTGGTGCATGTATCATTCCCCCAC
816920 TCC
196 TCC
* *
816923 TTAAAAGGATTCGTCCTCGAATATGAAACATTAAAGGGAGCAACATTAGAATCGTTTAATGATTC
1 TTAAAAAGATTCGACCTCGAATATGAAACATTAAAGGGAGCAACATTAGAATCGTTTAATGATTC
816988 ATTCACATTATACTTACCGAATAGATATGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTT
66 ATTCACATTATACTTACCGAATAGATATGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTT
*
817053 TGAGTAGAAACATTAGTCCAAAGAAGAATGTATTATGGACTCTGGTGCATGTATCA
131 CGAGTAGAAACATTAGTCCAAAGAAGAATGTATTATGGACTCTGGTGCATGTATCA
817109 CTTGAGTTGT
Statistics
Matches: 179, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
198 179 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (198 bp):
TTAAAAAGATTCGACCTCGAATATGAAACATTAAAGGGAGCAACATTAGAATCGTTTAATGATTC
ATTCACATTATACTTACCGAATAGATATGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTT
CGAGTAGAAACATTAGTCCAAAGAAGAATGTATTATGGACTCTGGTGCATGTATCATTCCCCCAC
TCC
Found at i:821626 original size:15 final size:15
Alignment explanation
Indices: 821590--821619 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
821580 GTGCTTCAAC
821590 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
821604 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
821619 T
1 T
821620 CTTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:821642 original size:27 final size:28
Alignment explanation
Indices: 821612--821673 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
821602 CTTTTCTTTG
* *
821612 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
*
821639 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGCTTCAATTT
821667 CTTTTCT
1 CTTTTCT
821674 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 8 0.28
29 4 0.14
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAATTT
Found at i:832701 original size:35 final size:35
Alignment explanation
Indices: 832656--832734 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
832646 CTATATGTCC
* * *
832656 ATCAGCATCTTCCATTACCATTTCATGCCTATATA
1 ATCACCATCTTCCATCACCATTTCACGCCTATATA
*
832691 ATCACCATCTTCCATCACCATTTCACGCCTATATC
1 ATCACCATCTTCCATCACCATTTCACGCCTATATA
832726 ATCACCATC
1 ATCACCATC
832735 CCTTAACCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.28, C:0.35, G:0.04, T:0.33
Consensus pattern (35 bp):
ATCACCATCTTCCATCACCATTTCACGCCTATATA
Found at i:838845 original size:19 final size:20
Alignment explanation
Indices: 838813--838863 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
838803 CGGCCAAGAG
*
838813 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
*
838832 CATTTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
838852 CATGTATTTTCA
1 CATGTATTTTCA
838864 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:839252 original size:35 final size:35
Alignment explanation
Indices: 839207--839286 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
839197 ACTATATGTC
* *
839207 CATCACCATCTTCCATTACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCATATAT
*
839242 CATCGCCATCTTCCATCACCATTTCACGCATATAT
1 CATCACCATCTTCCATCACCATTTCACGCATATAT
*
839277 CATCATCATC
1 CATCACCATC
839287 CCTTAACCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.26, C:0.38, G:0.04, T:0.33
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACGCATATAT
Found at i:844020 original size:19 final size:18
Alignment explanation
Indices: 843998--844060 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
843988 TTTTGAATTT
843998 TTCTTTTTCTTTTCTTCTC
1 TTCTTTTTCTTTT-TTCTC
844017 TTC-TTTTCTGATTTTTCTC
1 TTCTTTTTCT--TTTTTCTC
844036 TTCTTTTGTC-TTTTTCT-
1 TTCTTTT-TCTTTTTTCTC
844053 TTCTTTTT
1 TTCTTTTT
844061 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.03
17 7 0.17
18 13 0.32
19 11 0.28
20 6 0.15
21 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.75
Consensus pattern (18 bp):
TTCTTTTTCTTTTTTCTC
Found at i:853306 original size:21 final size:21
Alignment explanation
Indices: 853267--853311 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
853257 AAGGAAGATT
* *
853267 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAAG
853288 AATGAAATGA-AATAAATAAAG
1 AATGAAATGATAA-AAATAAAG
853309 AAT
1 AAT
853312 AGAGATGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAAG
Found at i:854821 original size:35 final size:36
Alignment explanation
Indices: 854727--854831 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
854717 AGATACAATC
* *
854727 TTCCATCACCATTATCACGCCTATATCACCACCATA
1 TTCCATCACCATTATCACGCCTATATTATCACCATA
*
854763 GTCCATCACCATTATCACGCCTATATTATCACCATA
1 TTCCATCACCATTATCACGCCTATATTATCACCATA
854799 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 TTCCATCACCATTATCACGCCTATATTATCACCA
854832 ACTTTTAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 22 0.34
36 43 0.66
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.30
Consensus pattern (36 bp):
TTCCATCACCATTATCACGCCTATATTATCACCATA
Found at i:855460 original size:16 final size:15
Alignment explanation
Indices: 855434--855485 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
855424 GAGTTGTAAG
855434 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
855448 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
855464 TTATTCTTTCATATTTT
1 TTA-TCTTTCAT-TTTT
855481 CTTAT
1 -TTAT
855486 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:0.17, C:0.15, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:859201 original size:11 final size:11
Alignment explanation
Indices: 859178--859249 Score: 67
Period size: 11 Copynumber: 6.2 Consensus size: 11
859168 TACAATCTTC
859178 CATCACCATTAT
1 CATCACCA-TAT
859190 CA-CACCTATAT
1 CATCACC-ATAT
859201 CATCACCATAGT
1 CATCACCATA-T
859213 CCATCACCATTAT
1 -CATCACCA-TAT
*
859226 CA-CGCCTATAT
1 CATCACC-ATAT
859237 CATCACCATAT
1 CATCACCATAT
859248 CA
1 CA
859250 CGCCTATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
11 26 0.51
12 14 0.27
13 9 0.18
14 2 0.04
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:859248 original size:22 final size:23
Alignment explanation
Indices: 859214--859266 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
859204 CACCATAGTC
859214 CATCACCATTATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
859237 CATCACCA-TATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
*
859259 TATCACCA
1 CATCACCA
859267 ACTTCTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCACGCCTATAT
Found at i:859264 original size:36 final size:36
Alignment explanation
Indices: 859176--859246 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
859166 GATACAATCT
859176 TCCATCACCATTATCACACCTATATCATCACCATAG
1 TCCATCACCATTATCACACCTATATCATCACCATAG
*
859212 TCCATCACCATTATCACGCCTATATCATCACCATA
1 TCCATCACCATTATCACACCTATATCATCACCATA
859247 TCACGCCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACACCTATATCATCACCATAG
Found at i:869626 original size:19 final size:21
Alignment explanation
Indices: 869587--869628 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
869577 GGGACTCATC
869587 CTTTCATTTAAAGCATTATGTA
1 CTTTCATTTAAAG-ATTATGTA
869609 CTTTCATTT-AAG-TTATGTA
1 CTTTCATTTAAAGATTATGTA
869628 C
1 C
869629 GTAGCCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
21 3 0.15
22 9 0.45
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (21 bp):
CTTTCATTTAAAGATTATGTA
Found at i:871174 original size:25 final size:24
Alignment explanation
Indices: 871128--871174 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
871118 TAGTTCATAT
*
871128 CTTTATAATATGCATATTCTTATA
1 CTTTATAATATGCATATACTTATA
*
871152 CTTTATAATAATTCATATACTTA
1 CTTTATAAT-ATGCATATACTTA
871175 GTTGATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (24 bp):
CTTTATAATATGCATATACTTATA
Found at i:871982 original size:19 final size:20
Alignment explanation
Indices: 871958--872001 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
871948 CGGCCAAGAG
*
871958 CATGTATCTTCATT-TAAAT
1 CATGTATCTTCATTAAAAAT
*
871977 CATGTATTTTCATTAAAAAT
1 CATGTATCTTCATTAAAAAT
871997 CATGT
1 CATGT
872002 GTTTTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (20 bp):
CATGTATCTTCATTAAAAAT
Found at i:871998 original size:20 final size:19
Alignment explanation
Indices: 871958--872008 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
871948 CGGCCAAGAG
* *
871958 CATGTATCTTCATTTAAAT
1 CATGTATTTTCATTAAAAT
871977 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
*
871997 CATGTGTTTTCA
1 CATGTATTTTCA
872009 AAAGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:874837 original size:91 final size:91
Alignment explanation
Indices: 874669--874904 Score: 366
Period size: 91 Copynumber: 2.6 Consensus size: 91
874659 CCCATGTGCC
* * * * *
874669 TTGCATATGACCA-CCCCCTTGTACCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATAAAGAGTTCT
874733 CTCCCTATTCGGCCAAGCAATTTGTT
66 CTCCCTATTCGGCCAAGCAATTTGTT
874759 TTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATAAAGAGTTCT
1 TTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATAAAGAGTTCT
*
874824 CTCCCTATTCGGCCAAGCCATTTGTT
66 CTCCCTATTCGGCCAAGCAATTTGTT
* * * * *
874850 TTTCATGTGATCAGCCCCCATGTGCTTTGCATATAGTTCATTTAGGCGCCAAGAT
1 TTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGAT
874905 GAATGGCCAT
Statistics
Matches: 134, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
90 11 0.08
91 123 0.92
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (91 bp):
TTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATAAAGAGTTCT
CTCCCTATTCGGCCAAGCAATTTGTT
Found at i:875764 original size:27 final size:28
Alignment explanation
Indices: 875703--875764 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
875693 AAAGAAAATC
*
875703 AGAAAAGAAATTAAAGCACTCCAAAAGA
1 AGAAAAGAAATTAAAGCACTCAAAAAGA
* *
875731 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTAAAGCACTCAAAAAGA
875758 AGAAAAG
1 AGAAAAG
875765 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTAAAGCACTCAAAAAGA
Found at i:888410 original size:23 final size:23
Alignment explanation
Indices: 888365--888410 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
888355 TTATACCTAT
*
888365 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
888388 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
888411 TATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:893222 original size:23 final size:23
Alignment explanation
Indices: 893177--893222 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
893167 TTATACCTAT
* *
893177 AGATACTTATTTCATATGTTATA
1 AGATAATTATTTCATATGATATA
893200 AGATAATTATTTTCATAT-ATATA
1 AGATAATTA-TTTCATATGATATA
893223 TATATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (23 bp):
AGATAATTATTTCATATGATATA
Found at i:901018 original size:25 final size:24
Alignment explanation
Indices: 900964--901019 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
900954 TTCTTTGTTT
* *
900964 TTTTCTTTTTGAGTGCTGAAATTT
1 TTTTCTTTTGGAGTGCTGAAATTC
**
900988 TCTTTCTTTTGGAGTGCTTCAATTCC
1 T-TTTCTTTTGGAGTGCTGAAATT-C
901014 TTTTCT
1 TTTTCT
901020 GATTTTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 24 0.92
26 1 0.04
ACGTcount: A:0.12, C:0.16, G:0.14, T:0.57
Consensus pattern (24 bp):
TTTTCTTTTGGAGTGCTGAAATTC
Found at i:903668 original size:38 final size:38
Alignment explanation
Indices: 903598--903695 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 38
903588 GGTCGGACAT
*
903598 GTTCTTCTCATTATAAACTTCTTCTCCCTCATTAGATGA
1 GTTCTTCTCATTATGAAC-TCTTCTCCCTCATTAGATGA
* * *
903637 GTTCTTCTCATTATGAACTCTTCTGCCTCATTGGATGG
1 GTTCTTCTCATTATGAACTCTTCTCCCTCATTAGATGA
903675 GTTCTTCTCATTATGAACTCT
1 GTTCTTCTCATTATGAACTCT
903696 CTAATGGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
38 38 0.69
39 17 0.31
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.44
Consensus pattern (38 bp):
GTTCTTCTCATTATGAACTCTTCTCCCTCATTAGATGA
Found at i:903990 original size:123 final size:123
Alignment explanation
Indices: 903636--904334 Score: 757
Period size: 123 Copynumber: 5.6 Consensus size: 123
903626 TCATTAGATG
** * * * * ** *
903636 AGTTCTTCTCATTATGAAC-TCTTCTGCCTCATT-GGATGGGTTCTTCTCATTATGAACTCTCTA
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTC-TTCAGATGAGTTCTTCTTATTACAAACTC-CTT
* * * ** *
903699 ATGGAAATGTTGATGCTGCTCTATCTCCTTCTGTGATAGAGTTAAGTAAAAGGTTGAATA
64 CTGGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATA
* * * * * * *
903759 AGTCCTTTATATTACGAACTTCTTTTTCCTCTTCAGATGAGTTATTCTTATTTACGAACTCCTTC
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTA-TTACAAACTCCTTC
* * * *
903824 TGGAAATATTGATGCTTCTCTATCTTCTTCTACGAAAGAGTCGAGCAAAAGGTTGAATA
65 TGGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATA
* * * *
903883 AGTTTTTTAGATTATGAACTT-TTGCTTGCTCTTTAGATGAGTTCTTCTTATTACAAACTCCTTC
1 AGTTCTTCAGATTATGAACTTCTT-CTTCCTCTTCAGATGAGTTCTTCTTATTACAAACTCCTTC
* ** *
903947 TGGAAATATTGATGCTGCTATATCTCCTTCTATGATAGAGTCGATCAAAAGGTTGAATA
65 TGGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATA
*
904006 AGTTCTTCAGATTATGTACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACAAACTATTACA
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTC----T------TATTACA
* * * *
904071 AACTCCTTCTGAAAATATTGATGCTGCTCTATCT-TTTTTGGCGATGGAGTCGAGCAAAAGGTTG
56 AACTCCTTCTGGAAATATTGATGCTGCTCTATCTCCTTCT-GCGATAGAGTCGAGCAAAAGGTTG
904135 AATA
120 AATA
* *
904139 AGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGATGAG---TTCTTATTACAAACTTCTTCT
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACAAACTCCTTCT
* * * *
904201 GGAAATGTTGATGTTGCTATATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAATA
66 GGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATA
* * *
904259 AGTTCTTCAGATTATGAACTTCTTCTT-CTCTTTAGATGAGTTCTTCTTATTACGAACTTCTTCT
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACAAACTCCTTCT
* *
904323 AGAAATGTTGAT
66 GGAAATATTGAT
904335 CCATCGAGTG
Statistics
Matches: 490, Mismatches: 66, Indels: 41
0.82 0.11 0.07
Matches are distributed among these distances:
119 12 0.02
120 88 0.18
121 3 0.01
122 31 0.06
123 123 0.25
124 114 0.23
125 9 0.02
126 1 0.00
127 1 0.00
130 3 0.01
132 3 0.01
133 102 0.21
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (123 bp):
AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACAAACTCCTTCT
GGAAATATTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATA
Found at i:904169 original size:133 final size:133
Alignment explanation
Indices: 903931--904316 Score: 523
Period size: 133 Copynumber: 3.0 Consensus size: 133
903921 GAGTTCTTCT
** *
903931 TATTACAAACTCCTTCTGGAAATATTGATGCTGCTATATCTCCTTCTATGATAGAGTCGATCAAA
1 TATTACAAACTCCTTCTGGAAATATTGATGCTGCTATATCTCCTTCTGCGATAGAGTCGAGCAAA
*
903996 AGGTTGAATAAGTTCTTCAGATTATGTACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACA
66 AGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACA
904061 AAC
131 AAC
* * * * *
904064 TATTACAAACTCCTTCTGAAAATATTGATGCTGCTCTATCT-TTTTTGGCGATGGAGTCGAGCAA
1 TATTACAAACTCCTTCTGGAAATATTGATGCTGCTATATCTCCTTCT-GCGATAGAGTCGAGCAA
*
904128 AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGATGAG---TTCTTATTAC
65 AAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
904190 AAAC
130 AAAC
* * *
904194 ---T------T-CTTCTGGAAATGTTGATGTTGCTATATCTCCTTCTGCGATAGAATCGAGCAAA
1 TATTACAAACTCCTTCTGGAAATATTGATGCTGCTATATCTCCTTCTGCGATAGAGTCGAGCAAA
* *
904249 AGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTT-CTCTTTAGATGAGTTCTTCTTATTACG
66 AGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACA
904313 AAC
131 AAC
904316 T
1 T
904317 TCTTCTAGAA
Statistics
Matches: 226, Mismatches: 21, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
119 12 0.05
120 77 0.34
121 4 0.02
122 13 0.06
127 1 0.00
130 14 0.06
132 3 0.01
133 102 0.45
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (133 bp):
TATTACAAACTCCTTCTGGAAATATTGATGCTGCTATATCTCCTTCTGCGATAGAGTCGAGCAAA
AGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACA
AAC
Found at i:904261 original size:120 final size:120
Alignment explanation
Indices: 904064--904334 Score: 375
Period size: 120 Copynumber: 2.2 Consensus size: 120
904054 TATTACAAAC
* * * * * * * *
904064 TATTACAAACTCCTTCTGAAAATATTGATGCTGCTCTATCTTTTTTGGCGATGGAGTCGAGCAAA
1 TATTACAAACTTCTTCTGGAAATGTTGATGCTGCTATATCTCTTCTGGCGATAGAATCGAGCAAA
*
904129 AGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGATGAG-TTCT
66 AGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTT-CTCTTCAGATGAGTTTCT
*
904184 TATTACAAACTTCTTCTGGAAATGTTGATGTTGCTATATCTCCTTCT-GCGATAGAATCGAGCAA
1 TATTACAAACTTCTTCTGGAAATGTTGATGCTGCTATATCT-CTTCTGGCGATAGAATCGAGCAA
*
904248 AAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCTCTTTAGATGAGTTCTTCT
65 AAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCTCTTCAGATGAG-T-TTCT
* *
904306 TATTACGAACTTCTTCTAGAAATGTTGAT
1 TATTACAAACTTCTTCTGGAAATGTTGAT
904335 CCATCGAGTG
Statistics
Matches: 134, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
119 12 0.09
120 88 0.66
121 3 0.02
122 31 0.23
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (120 bp):
TATTACAAACTTCTTCTGGAAATGTTGATGCTGCTATATCTCTTCTGGCGATAGAATCGAGCAAA
AGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCTCTTCAGATGAGTTTCT
Found at i:904286 original size:256 final size:255
Alignment explanation
Indices: 903700--904317 Score: 788
Period size: 256 Copynumber: 2.5 Consensus size: 255
903690 AACTCTCTAA
* ** * *
903700 TGGAAATGTTGATGCTGCTCTATCTCCTTCTGTGATAGAGTTAAGTAAAAGGTTGAATAAGTCCT
1 TGGAAATGTTGATGCTGCTATATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAATAAGTTCT
* * * * *
903765 TTATATTACGAACTTC-T-TT-TTCCTCTTCAGATGAGTTATTC---TT---A-TTTACGAACTC
66 TCAGATTATGAACTTCTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACAACTTTACAAACTC
* *
903820 CTTCTGGAAATATTGATGCTTCTCTATCTTCTTCTACGAAAGAGTCGAGCAAAAGGTTGAATAAG
131 CTTCTGAAAATATTGATGCTGCTCTATCTTCTTCTACGAAAGAGTCGAGCAAAAGGTTGAATAAG
* * * *
903885 TTTTTTAGATTATGAACTTTTGCTTGCTCTTTAGATGAGTTCTTCTTATTACAAACTCCTTC
196 TTCTTCAGATTATGAACTTTTGCTTCCTCTTCAGATGAG-T-TTCTTATTACAAACTCCTTC
* * *
903947 TGGAAATATTGATGCTGCTATATCTCCTTCTATGATAGAGTCGATCAAAAGGTTGAATAAGTTCT
1 TGGAAATGTTGATGCTGCTATATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAATAAGTTCT
*
904012 TCAGATTATG---TACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACAAACTATTACAAAC
66 TCAGATTATGAACTTCTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC-AACT-TTACAAAC
* * **
904074 TCCTTCTGAAAATATTGATGCTGCTCTATCTT-TTTTGGCGATGGAGTCGAGCAAAAGGTTGAAT
129 TCCTTCTGAAAATATTGATGCTGCTCTATCTTCTTCT-ACGAAAGAGTCGAGCAAAAGGTTGAAT
* *
904138 AAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGATGAG-TTCTTATTACAAACTTCTTC
193 AAGTTCTTCAGATTATGAACTTTTGCTTCCTCTTCAGATGAGTTTCTTATTACAAACTCCTTC
* * *
904200 TGGAAATGTTGATGTTGCTATATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCT
1 TGGAAATGTTGATGCTGCTATATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAATAAGTTCT
904265 TCAGATTATGAACTTCTTCTTC-T-CT-TT-AGATGAGTTCTTCTTATTACGAACTT
66 TCAGATTATGAACTTCTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC-AACTT
904318 CTTCTAGAAA
Statistics
Matches: 321, Mismatches: 34, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
244 2 0.01
245 1 0.00
246 2 0.01
247 85 0.26
250 2 0.01
251 1 0.00
252 24 0.07
253 90 0.28
254 3 0.01
255 5 0.02
256 106 0.33
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (255 bp):
TGGAAATGTTGATGCTGCTATATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAATAAGTTCT
TCAGATTATGAACTTCTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACAACTTTACAAACTC
CTTCTGAAAATATTGATGCTGCTCTATCTTCTTCTACGAAAGAGTCGAGCAAAAGGTTGAATAAG
TTCTTCAGATTATGAACTTTTGCTTCCTCTTCAGATGAGTTTCTTATTACAAACTCCTTC
Found at i:928422 original size:17 final size:17
Alignment explanation
Indices: 928400--928441 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
928390 GTGCTTCAAC
928400 TTTCTTT-CTTTCTTTCT
1 TTTCTTTGCTTT-TTTCT
928417 TTTCTTTGCTTTTTTCT
1 TTTCTTTGCTTTTTTCT
928434 TCTTCTTT
1 T-TTCTTT
928442 TTGAGTGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTCTTTGCTTTTTTCT
Found at i:937556 original size:351 final size:351
Alignment explanation
Indices: 936913--937615 Score: 1201
Period size: 351 Copynumber: 2.0 Consensus size: 351
936903 AGTATCTTAA
*
936913 AGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGTTTCTTTAA
1 AGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTAA
*
936978 GGGGTGGTATAAAGGACTTTGACCCACTAGTTATAAGAACTAGGAACCATAAGTATCAAGGGAAA
66 GGGGTGGTATAAAGGACTTTGACCCACTAGTTATAAGAACTAGGAACCAAAAGTATCAAGGGAAA
* * * *
937043 AGGGGTTGACGCCACAAGTATAAAAATACTTGATAAGTCGATAAAAGTCATCAGGACTTAAGAAA
131 AGGGGTTGACACCACAAGTATAAAAATACTTAATAAGTCGATAAAAGTCACCAAGACTTAAGAAA
* * * **
937108 AGAGAATAATCTCACTTTAATTAATCAAAAGGTCTGATTACAAATGAAATGTGCTTTCCTATTTA
196 AGAGAATAATCTCACTTTAATTAATCAAAACGTCTGATTACAAATGAAATATGATGGCCTATTTA
* * * *
937173 TAGTTTTCAAAGTGTTTAGGCTGAATAAACACTTGATGGTTTGGCCAAGATTGAAACCCCTTTGA
261 TAGTTTTCAAAGGGTTTAGGCCGAATAAACACTTGATGGTTCGGCAAAGATTGAAACCCCTTTGA
937238 AAATACATGATTTTTAATGAAAATAC
326 AAATACATGATTTTTAATGAAAATAC
937264 AGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTAA
1 AGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTAA
* *
937329 GGGGTGGTATAAAGGA-TATTGACCCACTAGTTATAAGTACTAGGAACCAAAAGTATCAAGGGGA
66 GGGGTGGTATAAAGGACT-TTGACCCACTAGTTATAAGAACTAGGAACCAAAAGTATCAAGGGAA
937393 AAGGGGTTGACACCACAAGTATAAAAATACTTAATAAGTCGATAAAAGTCACCAAGACTTAAGAA
130 AAGGGGTTGACACCACAAGTATAAAAATACTTAATAAGTCGATAAAAGTCACCAAGACTTAAGAA
*
937458 AAGAGAATAATCTCACTTTAATTAATCAAAACGTTTGATTACAAATGAAATATGATGGCCTATTT
195 AAGAGAATAATCTCACTTTAATTAATCAAAACGTCTGATTACAAATGAAATATGATGGCCTATTT
*
937523 ATAGTTTTCAAAGGGTTTAGGCCGAATAAACACTTGATGGTTCGGCAAAGGTTGAAACCCCTTTG
260 ATAGTTTTCAAAGGGTTTAGGCCGAATAAACACTTGATGGTTCGGCAAAGATTGAAACCCCTTTG
* *
937588 AAAATACATGATTTTTGATGAAACTAC
325 AAAATACATGATTTTTAATGAAAATAC
937615 A
1 A
937616 TGATTAAAAT
Statistics
Matches: 330, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
350 1 0.00
351 329 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (351 bp):
AGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTAA
GGGGTGGTATAAAGGACTTTGACCCACTAGTTATAAGAACTAGGAACCAAAAGTATCAAGGGAAA
AGGGGTTGACACCACAAGTATAAAAATACTTAATAAGTCGATAAAAGTCACCAAGACTTAAGAAA
AGAGAATAATCTCACTTTAATTAATCAAAACGTCTGATTACAAATGAAATATGATGGCCTATTTA
TAGTTTTCAAAGGGTTTAGGCCGAATAAACACTTGATGGTTCGGCAAAGATTGAAACCCCTTTGA
AAATACATGATTTTTAATGAAAATAC
Found at i:939739 original size:35 final size:37
Alignment explanation
Indices: 939672--939751 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
939662 ATACTATTTC
*
939672 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
939709 CATCACCATAGTTCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
939744 CATCACCA
1 CATCACCA
939752 AACTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:940231 original size:14 final size:15
Alignment explanation
Indices: 940197--940243 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
940187 ATTTTGGAGT
940197 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
940212 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
940226 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
940243 G
1 G
940244 TGAAGCAAGT
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:944591 original size:35 final size:37
Alignment explanation
Indices: 944518--944596 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 37
944508 TACTATTTCT
*
944518 ATCACCATAATCCATCTTCCATTATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
* *
944555 ATCACCATAGTCCATC-ACCA-TATCTCGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
944590 ATCACCA
1 ATCACCA
944597 AACTCTCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.37, G:0.04, T:0.29
Consensus pattern (37 bp):
ATCACCATAATCCATCTACCATTATCACGCCTATATC
Found at i:950067 original size:36 final size:36
Alignment explanation
Indices: 950002--950098 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
949992 GTTGGTGATA
*
950002 ATATAGGCGTGAT-ATGGTGATGGAATATGGTAATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTAATG
*
950037 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTAATG
950073 ATATAGGCGTGATAATGGTGATGGAC
1 ATATAGGCGTGATAATGGTGATGGAC
950099 AGATTGTATC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 13 0.22
36 46 0.78
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGACTATGGTAATG
Found at i:953468 original size:15 final size:15
Alignment explanation
Indices: 953435--953472 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
953425 CACTTTTCTT
953435 TTTCTTTTGATTTTC
1 TTTCTTTTGATTTTC
**
953450 -TTCTTTTTCTTTTC
1 TTTCTTTTGATTTTC
953464 TTTCTTTTG
1 TTTCTTTTG
953473 CACTCCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTCTTTTGATTTTC
Found at i:953992 original size:13 final size:12
Alignment explanation
Indices: 953935--954020 Score: 58
Period size: 11 Copynumber: 7.2 Consensus size: 12
953925 ATATAGGCGT
953935 GATATGGTGATG
1 GATATGGTGATG
*
953947 GAATATAGTGAT-
1 G-ATATGGTGATG
953959 GATATAGGTG-T-
1 GATAT-GGTGATG
953970 GATAATGGTGATG
1 GAT-ATGGTGATG
953983 GACTATGGTGAT-
1 GA-TATGGTGATG
*
953995 GATATAGGCG-T-
1 GATAT-GGTGATG
954006 GATAATGGTGATG
1 GAT-ATGGTGATG
954019 GA
1 GA
954021 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 22 0.37
12 16 0.27
13 21 0.35
14 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:953994 original size:36 final size:36
Alignment explanation
Indices: 953925--954021 Score: 160
Period size: 36 Copynumber: 2.7 Consensus size: 36
953915 GTTGGTAATA
*
953925 ATATAGGCGTGAT-ATGGTGATGGAATATAGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATAGTGATG
* *
953960 ATATAGGTGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATAGTGATG
953996 ATATAGGCGTGATAATGGTGATGGAC
1 ATATAGGCGTGATAATGGTGATGGAC
954022 AGATTGTATC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 12 0.21
36 45 0.79
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.31
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGACTATAGTGATG
Found at i:960650 original size:9 final size:9
Alignment explanation
Indices: 960636--960670 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
960626 ATTATTTTTC
960636 AAAAAACAA
1 AAAAAACAA
960645 AAAAAACAAAA
1 AAAAAAC--AA
960656 AAAAAACAA
1 AAAAAACAA
960665 AAAAAA
1 AAAAAA
960671 AAGCTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 15 0.62
11 9 0.38
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:960660 original size:12 final size:11
Alignment explanation
Indices: 960643--960672 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
960633 TTCAAAAAAC
960643 AAAAAAAACAA
1 AAAAAAAACAA
960654 AAAAAAAACAA
1 AAAAAAAACAA
960665 AAAAAAAA
1 AAAAAAAA
960673 GCTAAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:965371 original size:1 final size:1
Alignment explanation
Indices: 965367--965408 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
965357 ATTATTTTTC
* * *
965367 AAAAAAACAAAAAAAAAAACAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
965409 GCTAAATAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:965382 original size:12 final size:12
Alignment explanation
Indices: 965367--965408 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
965357 ATTATTTTTC
965367 AAAAAAACAAAA
1 AAAAAAACAAAA
965379 AAAAAAACAAAA
1 AAAAAAACAAAA
965391 AAAAAAACAAAA
1 AAAAAAACAAAA
965403 AAAAAA
1 AAAAAA
965409 GCTAAATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:970100 original size:11 final size:11
Alignment explanation
Indices: 970086--970122 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
970076 ATTATTTTTC
970086 AAAAAAAC-AA
1 AAAAAAACAAA
970096 AAAAAAACAAA
1 AAAAAAACAAA
970107 AAAAAAACAAA
1 AAAAAAACAAA
970118 AAAAA
1 AAAAA
970123 GAAGCTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:970101 original size:10 final size:10
Alignment explanation
Indices: 970086--970122 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
970076 ATTATTTTTC
970086 AAAAAAACAA
1 AAAAAAACAA
970096 AAAAAAACAAA
1 AAAAAAAC-AA
970107 AAAAAAACAA
1 AAAAAAACAA
970117 AAAAAA
1 AAAAAA
970123 GAAGCTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:980196 original size:24 final size:25
Alignment explanation
Indices: 980150--980204 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
980140 ACAATTAGGC
*
980150 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
980174 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
980199 CA-TTGA
1 CACTTGA
980205 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:984083 original size:22 final size:21
Alignment explanation
Indices: 984049--984089 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
984039 TTTTCACATC
* *
984049 TTTACTTAGCTTTATATTATG
1 TTTACATAGCTTTAGATTATG
984070 TTTACATATGCTTTAGATTA
1 TTTACATA-GCTTTAGATTA
984090 ATTTATTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (21 bp):
TTTACATAGCTTTAGATTATG
Found at i:985054 original size:19 final size:20
Alignment explanation
Indices: 985030--985072 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
985020 AGCATTTATC
*
985030 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
985049 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
985069 TTCA
1 TTCA
985073 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:985525 original size:22 final size:21
Alignment explanation
Indices: 985484--985538 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
985474 CTATCCTTTC
*
985484 TTTATTTTATTATTCTTATTA
1 TTTATTTTATTATTCATATTA
985505 TTTATTTTCATTACTT-ATATTA
1 TTTATTTT-ATTA-TTCATATTA
**
985527 TTTCCTTTATTA
1 TTTATTTTATTA
985539 AGTCCATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 12 0.41
22 15 0.52
23 2 0.07
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATTTTATTATTCATATTA
Found at i:989459 original size:13 final size:11
Alignment explanation
Indices: 989418--989502 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 11
989408 TACAATCTTC
989418 CATCACCATTAT
1 CATCACCA-TAT
989430 CA-CACCTATAT
1 CATCACC-ATAT
989441 CATCACCATAGT
1 CATCACCATA-T
989453 CCATCACCATTAT
1 -CATCACCA-TAT
*
989466 CA-CGCCTATAT
1 CATCACC-ATAT
989477 CATCACCATATT
1 CATCACCATA-T
989489 CCATCACCATAT
1 -CATCACCATAT
989501 CA
1 CA
989503 CGACTATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 25 0.40
12 16 0.26
13 19 0.31
14 2 0.03
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:989463 original size:36 final size:36
Alignment explanation
Indices: 989416--989519 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
989406 GATACAATCT
989416 TCCATCACCATTATCACACCTATATCATCACCATAG
1 TCCATCACCATTATCACACCTATATCATCACCATAG
* *
989452 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACACCTATATCATCACCATAG
*
989488 TCCATCACCA-TATCACGA-CTATATTATCACCA
1 TCCATCACCATTATCAC-ACCTATATCATCACCA
989520 ACTTCTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACACCTATATCATCACCATAG
Found at i:990089 original size:22 final size:21
Alignment explanation
Indices: 990059--990099 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
990049 CATCTCCATT
*
990059 TCATCATCAACACTATCAACA
1 TCATCATCAACACCATCAACA
*
990080 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
990100 TTCTGCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.34, G:0.02, T:0.22
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:991173 original size:21 final size:22
Alignment explanation
Indices: 991147--991199 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
991137 TATAACCTCT
991147 TTTTTTCTTTCTCTTTTTTT-C
1 TTTTTTCTTTCTCTTTTTTTCC
991168 TTTTTTCTTTCTCTTTTTTTCC
1 TTTTTTCTTTCTCTTTTTTTCC
*
991190 CTTTTTCTTT
1 TTTTTTCTTT
991200 TTTCTATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTTCTTTCTCTTTTTTTCC
Found at i:991188 original size:14 final size:14
Alignment explanation
Indices: 991143--991170 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
991133 TCTTTATAAC
991143 CTCTTTTTTTCTTT
1 CTCTTTTTTTCTTT
991157 CTCTTTTTTTCTTT
1 CTCTTTTTTTCTTT
991171 TTTCTTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTCTTTTTTTCTTT
Found at i:991193 original size:10 final size:10
Alignment explanation
Indices: 991149--991195 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
991139 TAACCTCTTT
991149 TTTTCTTTCTC
1 TTTT-TTTCTC
*
991160 TTTTTTTCTT
1 TTTTTTTCTC
991170 TTTTCTTTCTC
1 TTTT-TTTCTC
*
991181 TTTTTTTCCC
1 TTTTTTTCTC
991191 TTTTT
1 TTTTT
991196 CTTTTTTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 19 0.59
11 13 0.41
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:997651 original size:9 final size:9
Alignment explanation
Indices: 997640--997669 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
997630 AAAAATCATA
997640 AAAAAAG-C
1 AAAAAAGCC
997648 AAAAAAGCC
1 AAAAAAGCC
997657 AAAAAAGCC
1 AAAAAAGCC
997666 AAAA
1 AAAA
997670 TTTCAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.73, C:0.17, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAGCC
Found at i:999780 original size:15 final size:15
Alignment explanation
Indices: 999762--999812 Score: 68
Period size: 14 Copynumber: 3.4 Consensus size: 15
999752 AAATTTTGGC
999762 TTTTTTGGCTTTTTT
1 TTTTTTGGCTTTTTT
*
999777 TTTTTT-GTTTTTTT
1 TTTTTTGGCTTTTTT
*
999791 TTTTTTGCCTTTTTT
1 TTTTTTGGCTTTTTT
999806 TGTTTTT
1 T-TTTTT
999813 TTGAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.42
15 13 0.42
16 5 0.16
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (15 bp):
TTTTTTGGCTTTTTT
Found at i:999795 original size:13 final size:13
Alignment explanation
Indices: 999771--999795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
999761 CTTTTTTGGC
999771 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
999784 TTTTTTTTTTTT
1 TTTTTTTTTTTT
999796 TGCCTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:1002522 original size:809 final size:808
Alignment explanation
Indices: 1000965--1003974 Score: 5384
Period size: 809 Copynumber: 3.7 Consensus size: 808
1000955 TGCATGTATC
*
1000965 ACGCATTGAAAGATATTCAAGAATTTTTCCAAAATTATTGTACACCGATAACCCCCTCAAAAATG
1 ACGCATTGAAAGACATTCAAGAATTTTTCCAAAATTATTGTACACCGATAACCCCCTCAAAAATG
1001030 TTGCTCAAGTTGATCCAGTGTTTTCTAGGTTTTCTGGTTTGGTTCTTTTTTTTTCTTTGACTCTT
66 TTGCTCAAGTTGATCCAGTGTTTTCTAGGTTTTCTGGTTTGGTTCTTTTTTTTTCTTTGACTCTT
1001095 AGTGCATTAGGTTCTTTTGTTTTTCCTTTTTATTGTTCTTTTGCATTATCTAACACATTA-ACTT
131 AGTGCATTAGGTTCTTTTGTTTTTCCTTTTTATTGTTCTTTTGCATTATCTAACACATTATA-TT
1001159 TCTTGTGTTAGTAGGATTAAAGAGTTTGCATACTTCTTCCTCCCTTGCATTCCCGTTCTCTTGGA
195 TCTTGTGTTAGTAGGATTAAAGAGTTTGCATACTTCTTCCTCCCTTGCATTCCCGTTCTCTTGGA
*
1001224 CTCTAACCCTTGTTTGGCCTCTTAGAACTTTTAGGTTTTCTTATTGCCTATTCTAGTAATCAAAC
260 CTCTAACCCTTGTTTGGCCTCTTAGAACTTTTAGGTTTTCTTATCGCCTATTCTAGTAATCAAAC
* * *
1001289 TCCGATACGAACTGTGGAAGACTAATTGGTAAAGTGAGTTTTAAAGAGTACAAGATTGGCTTACT
325 TCCGATACGAACTGTGGAAGACTACTTGCTAAAGTGAGTTTTAAAGAGTACAAGATTAGCTTACT
1001354 TGCCTCTCGTTGTGTTACTTTCTTGGAGTGACTTATGAGGTTTTTTTGTTTTGTTGAATTTTCTT
390 TGCCTCTCGTTGTGTTACTTTCTTGGAGTGACTTATGAGG-TTTTTTGTTTTGTTGAATTTTCTT
1001419 TCTTTTATTTTTATTTTACTTTAAAATTTTCTTTTGAGTGTTATGATTTCAGGATGGGCGACAAT
454 TCTTTTATTTTTATTTTACTTTAAAATTTTCTTTTGAGTGTTATGATTTCAGGATGGGCGACAAT
* *
1001484 TAAAATAAGACACTTACGACTATCTTAGCCGCAGTTGCCCGACTCACGACTCAAGTTGAAAGATT
519 TAAAACAAGACACTTACGACTATCTTAGCCGCACTTGCCCGACTCACGACTCAAGTTGAAAGATT
1001549 TGATGAAATCAAATCTAAAGGAGGAATTTCGTGTTGAAAATTTCCAGATTGCAACTTCATATATT
584 TGATGAAATCAAATCTAAAGGAGGAATTTCGTGTTGAAAATTTCCAGATTGCAACTTCATATATT
1001614 GAATATCATTTCACACAAAAAATCAAAATTTTTGGAGATCAAGAACACCTTCAAACAAAGCGATC
649 GAATATCATTTCACACAAAAAATCAAAATTTTTGGAGATCAAGAACACCTTCAAACAAAGCGATC
1001679 ATGAAAAATAGATTGTTTGAGGACTCACCGTTCAACAGAGTCTACTAGATACTACTGAAGGTATT
714 ATGAAAAATAGATTGTTTGAGGACTCACCGTTCAACAGAGTCTACTAGATACTACTGAAGGTATT
1001744 TGGTTCTGAAATTTTACAGATGGTTTCTTG
779 TGGTTCTGAAATTTTACAGATGGTTTCTTG
1001774 ACGCATTGAAAGACATTCAAGAATTTTTCCAAAATTATTGTACACCGATAACCCCCTCAAAAATG
1 ACGCATTGAAAGACATTCAAGAATTTTTCCAAAATTATTGTACACCGATAACCCCCTCAAAAATG
*
1001839 TTGCTCAAGTTGATCCAGTGTTTTCTAGGTTTTCTGGTTTGGTTCTTTTTTTTTCTTTGACTCAT
66 TTGCTCAAGTTGATCCAGTGTTTTCTAGGTTTTCTGGTTTGGTTCTTTTTTTTTCTTTGACTCTT
*
1001904 AGTGCATTAGGTTCTTTTGTTTTTCCTTTTTATTGTTCTTTTGCATTATCTAACACATTATCTTT
131 AGTGCATTAGGTTCTTTTGTTTTTCCTTTTTATTGTTCTTTTGCATTATCTAACACATTATATTT
*
1001969 CTTATGTTAGTAGGATTAAAGAGTTTGCATACTTCTTCCTCCCTTGCATTCCCGTTCTCTTGGAC
196 CTTGTGTTAGTAGGATTAAAGAGTTTGCATACTTCTTCCTCCCTTGCATTCCCGTTCTCTTGGAC
1002034 TCTAACCCTTGTTTGGCCTCTTAGAACTTTTAGGTTTTCTTATCGCCTATTCTAGTAATCAAACT
261 TCTAACCCTTGTTTGGCCTCTTAGAACTTTTAGGTTTTCTTATCGCCTATTCTAGTAATCAAACT
*
1002099 CCGATACGAACTGTGGAAGACTACTTGCTAAAGTGAGTTTTAAAGAGTACAAGATTAGTTTACTT
326 CCGATACGAACTGTGGAAGACTACTTGCTAAAGTGAGTTTTAAAGAGTACAAGATTAGCTTACTT
1002164 GCCTCTCGTTGTGTTACTTTCTTGGAGTGACTTATGAGGTTTTTTTGTTTTGTTGAATTTTCTTT
391 GCCTCTCGTTGTGTTACTTTCTTGGAGTGACTTATGAGG-TTTTTTGTTTTGTTGAATTTTCTTT
*
1002229 CTTTTATTTTTATTTTACTTTAAAATTTTCTTTGGAGTGTTATGATTTCAGGATGGGCGACAATT
455 CTTTTATTTTTATTTTACTTTAAAATTTTCTTTTGAGTGTTATGATTTCAGGATGGGCGACAATT
1002294 AAAACAAGACACTTACGACTATCTTAGCCGCACTTGCCCGACTCACGACTCAAGTTGAAAGATTT
520 AAAACAAGACACTTACGACTATCTTAGCCGCACTTGCCCGACTCACGACTCAAGTTGAAAGATTT
* *
1002359 GATGAAATCAAATTTAAAGGAGGAATTTCGTGTTGAAAATTTCCAGATTGCAACTTCATATGTTG
585 GATGAAATCAAATCTAAAGGAGGAATTTCGTGTTGAAAATTTCCAGATTGCAACTTCATATATTG
* *
1002424 AATATCATTTCACACAAACAATCAAAATTTTTAGAGATCAAGAACACCTTCAAACAAAGCGATCA
650 AATATCATTTCACACAAAAAATCAAAATTTTTGGAGATCAAGAACACCTTCAAACAAAGCGATCA
* *
1002489 TGAAACACAGATTGTTTGAGGACTCACCGTTCAACAGAGTCTACTAGATACTACTGAAGGTATTT
715 TGAAAAATAGATTGTTTGAGGACTCACCGTTCAACAGAGTCTACTAGATACTACTGAAGGTATTT
1002554 GGTTCTGAAATTTTACAGATGGTTTCTTG
780 GGTTCTGAAATTTTACAGATGGTTTCTTG
1002583 ACGCATTGAAAGACATTCAAGAATTTTTCCAAAATTATTGTACACCGATAACCCCCTCAAAAATG
1 ACGCATTGAAAGACATTCAAGAATTTTTCCAAAATTATTGTACACCGATAACCCCCTCAAAAATG
1002648 TTGCTCAAGTTGATCCAGTGTTTTCTAGGTTTTCTGGTTTGGTTCTTTTTTTTTTCTTTGACTCT
66 TTGCTCAAGTTGATCCAGTGTTTTCTAGGTTTTCTGGTTTGGTTC-TTTTTTTTTCTTTGACTCT
1002713 TAGTGCATTAGGTTCTTTTGTTTTTCCTTTTTATTGTTCTTTTGCATTATCTAACACATTATATT
130 TAGTGCATTAGGTTCTTTTGTTTTTCCTTTTTATTGTTCTTTTGCATTATCTAACACATTATATT
*
1002778 TCTTGTGTTAGTAGGATTAAAGAGTTTGCATACTTCTTCCTCCCTTGCATTCCTGTTCTCTTGGA
195 TCTTGTGTTAGTAGGATTAAAGAGTTTGCATACTTCTTCCTCCCTTGCATTCCCGTTCTCTTGGA
1002843 CTCTAACCCTTGTTTGGCCTCTTAGAACTTTTAGGTTTTCTTATCGCCTATTCTAGTAATCAAAC
260 CTCTAACCCTTGTTTGGCCTCTTAGAACTTTTAGGTTTTCTTATCGCCTATTCTAGTAATCAAAC
* *
1002908 TCCGAT----AC----GAAGACTACTTGGTAAAGTGAGTTTTAAAGAGTACAAGATTGGCTTACT
325 TCCGATACGAACTGTGGAAGACTACTTGCTAAAGTGAGTTTTAAAGAGTACAAGATTAGCTTACT
*
1002965 TGTCTCTCGTTGTGTTACTTTCTTGGAGTGACTTATGAGGTTTTTTGTTTTGTTGAATTTTCTTT
390 TGCCTCTCGTTGTGTTACTTTCTTGGAGTGACTTATGAGGTTTTTTGTTTTGTTGAATTTTCTTT
1003030 CTTTTATTTTTATTTTACTTTAAAATTTTCTTTTGAGTGTTATGATTTCAGGATGGGCGACAATT
455 CTTTTATTTTTATTTTACTTTAAAATTTTCTTTTGAGTGTTATGATTTCAGGATGGGCGACAATT
1003095 AAAACAAGACACTTACGACTATCTTAGCCGCACTTGCCCGACTCACGACTCAAGTTGAAAGATTT
520 AAAACAAGACACTTACGACTATCTTAGCCGCACTTGCCCGACTCACGACTCAAGTTGAAAGATTT
* *
1003160 GATGAAATCAAATCTAAAGGAGGAATTTCGTGTTGAAAATTTCTAGTTTGCAACTTCATATATTG
585 GATGAAATCAAATCTAAAGGAGGAATTTCGTGTTGAAAATTTCCAGATTGCAACTTCATATATTG
* *
1003225 AATATCGTTTCACACAAAAAATCAAAATTTTTGGAGCTCAAGAACACCTTCAAACAAAGCGATCA
650 AATATCATTTCACACAAAAAATCAAAATTTTTGGAGATCAAGAACACCTTCAAACAAAGCGATCA
** * * *
1003290 CAAAAAATAGATTATTTGAGGACTCACCGTTCAACAGAGTCTACTGGATACTACTAAAGGTATTT
715 TGAAAAATAGATTGTTTGAGGACTCACCGTTCAACAGAGTCTACTAGATACTACTGAAGGTATTT
*
1003355 GGTTTTGAAATTTTACA-AGTGGTTTCTTG
780 GGTTCTGAAATTTTACAGA-TGGTTTCTTG
* * * *
1003384 ACGCATTGAAAGACATTCAAGAATTTTTCCAAAATTATTGGACATCGGTAACCCCCTCAAAAACG
1 ACGCATTGAAAGACATTCAAGAATTTTTCCAAAATTATTGTACACCGATAACCCCCTCAAAAATG
*
1003449 TTGCTCAAGTTGATCCAGTGTTTTCTTGGTTTTCTGGTTTGGTTC--TTTTTTTCTTTGACTCTT
66 TTGCTCAAGTTGATCCAGTGTTTTCTAGGTTTTCTGGTTTGGTTCTTTTTTTTTCTTTGACTCTT
* *
1003512 AGTGTATTAGGTTCTTTTGTTTTTCCTTTTTATTGCTCTTTTGCATTATCTAACACATTATATTT
131 AGTGCATTAGGTTCTTTTGTTTTTCCTTTTTATTGTTCTTTTGCATTATCTAACACATTATATTT
* * * *
1003577 CTTGTGTTAGTAGGATTAAAGAGTTCGCATATTTCTTCCTCCCTTGCATTCTCGTTCTCTTGGAG
196 CTTGTGTTAGTAGGATTAAAGAGTTTGCATACTTCTTCCTCCCTTGCATTCCCGTTCTCTTGGAC
*
1003642 TCTAACCCTTGTTTGGCCTCTTAGAACTTTTAGGTTTTCTAATCGCCT-TTGCTAGTAATCAAAC
261 TCTAACCCTTGTTTGGCCTCTTAGAACTTTTAGGTTTTCTTATCGCCTATT-CTAGTAATCAAAC
*
1003706 TCCGATACGAACTGTGGAATACTACTTAGC-AAAGT-ATGTTTTAAAGAGTACAAGATTAGCTTA
325 TCCGATACGAACTGTGGAAGACTACTT-GCTAAAGTGA-GTTTTAAAGAGTACAAGATTAGCTTA
* *
1003769 CTTGCCTCTCGTTGTGTTACTTTCTTGGAGTGACTTATGAGGTTTCTTGTTTTGTTGAGTTTTCT
388 CTTGCCTCTCGTTGTGTTACTTTCTTGGAGTGACTTATGAGGTTTTTTGTTTTGTTGAATTTTCT
* *
1003834 TTCTTTTATTTTTATTTTACTTTAAAATTTTCTTTTGAGTTTTATGATTTCAGGATGGGCGATAA
453 TTCTTTTATTTTTATTTTACTTTAAAATTTTCTTTTGAGTGTTATGATTTCAGGATGGGCGACAA
* *
1003899 TAAAAACAAGACACTTACGACTATCTTAGCCGCACTTGCCCGACTCATGACTCAAGTTGAAAGAT
518 TTAAAACAAGACACTTACGACTATCTTAGCCGCACTTGCCCGACTCACGACTCAAGTTGAAAGAT
1003964 TTGATGAAATC
583 TTGATGAAATC
1003975 GTGAGAGAAC
Statistics
Matches: 2121, Mismatches: 66, Indels: 31
0.96 0.03 0.01
Matches are distributed among these distances:
797 2 0.00
798 207 0.10
800 1 0.00
801 465 0.22
802 87 0.04
805 1 0.00
806 241 0.11
807 1 0.00
809 900 0.42
810 216 0.10
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (808 bp):
ACGCATTGAAAGACATTCAAGAATTTTTCCAAAATTATTGTACACCGATAACCCCCTCAAAAATG
TTGCTCAAGTTGATCCAGTGTTTTCTAGGTTTTCTGGTTTGGTTCTTTTTTTTTCTTTGACTCTT
AGTGCATTAGGTTCTTTTGTTTTTCCTTTTTATTGTTCTTTTGCATTATCTAACACATTATATTT
CTTGTGTTAGTAGGATTAAAGAGTTTGCATACTTCTTCCTCCCTTGCATTCCCGTTCTCTTGGAC
TCTAACCCTTGTTTGGCCTCTTAGAACTTTTAGGTTTTCTTATCGCCTATTCTAGTAATCAAACT
CCGATACGAACTGTGGAAGACTACTTGCTAAAGTGAGTTTTAAAGAGTACAAGATTAGCTTACTT
GCCTCTCGTTGTGTTACTTTCTTGGAGTGACTTATGAGGTTTTTTGTTTTGTTGAATTTTCTTTC
TTTTATTTTTATTTTACTTTAAAATTTTCTTTTGAGTGTTATGATTTCAGGATGGGCGACAATTA
AAACAAGACACTTACGACTATCTTAGCCGCACTTGCCCGACTCACGACTCAAGTTGAAAGATTTG
ATGAAATCAAATCTAAAGGAGGAATTTCGTGTTGAAAATTTCCAGATTGCAACTTCATATATTGA
ATATCATTTCACACAAAAAATCAAAATTTTTGGAGATCAAGAACACCTTCAAACAAAGCGATCAT
GAAAAATAGATTGTTTGAGGACTCACCGTTCAACAGAGTCTACTAGATACTACTGAAGGTATTTG
GTTCTGAAATTTTACAGATGGTTTCTTG
Found at i:1010196 original size:13 final size:13
Alignment explanation
Indices: 1010174--1010203 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1010164 ACTAAACACC
1010174 TTTC-ACATACCT
1 TTTCAACATACCT
1010186 TTTCAACATACCT
1 TTTCAACATACCT
1010199 TTTCA
1 TTTCA
1010204 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1013373 original size:11 final size:12
Alignment explanation
Indices: 1013338--1013371 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1013328 AAGCAACAAC
1013338 AAAGAAGAAAAGA
1 AAAGAA-AAAAGA
1013351 AAAGAAAAAAGA
1 AAAGAAAAAAGA
1013363 AAAGAAAAA
1 AAAGAAAAA
1013372 GACTTCTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAGA
Found at i:1013429 original size:14 final size:15
Alignment explanation
Indices: 1013395--1013441 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1013385 AATTTGGAGT
1013395 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
1013410 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
1013424 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
1013441 G
1 G
1013442 TGAAGCAAGT
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:1020615 original size:11 final size:13
Alignment explanation
Indices: 1020583--1020612 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1020573 TGGCCAAAGA
1020583 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1020596 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1020608 TGAAA
1 TGAAA
1020613 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1023699 original size:20 final size:20
Alignment explanation
Indices: 1023674--1023729 Score: 96
Period size: 20 Copynumber: 2.8 Consensus size: 20
1023664 ATCTTCATTT
1023674 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
1023694 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
1023714 AAAT-ATTGTATTTTCA
1 AAATCA-TGTATTTTCA
1023730 AAGGGGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.43
Consensus pattern (20 bp):
AAATCATGTATTTTCATCAA
Found at i:1028742 original size:11 final size:13
Alignment explanation
Indices: 1028710--1028739 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1028700 TGGCCAAAGA
1028710 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1028723 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1028735 TGAAA
1 TGAAA
1028740 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1032672 original size:33 final size:33
Alignment explanation
Indices: 1032593--1032696 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
1032583 ATACAATCTG
* *
1032593 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
1032629 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1032662 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1032695 TC
1 TC
1032697 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:1037141 original size:33 final size:33
Alignment explanation
Indices: 1037062--1037165 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
1037052 ATACAATCTG
* *
1037062 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
1037098 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1037131 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1037164 TC
1 TC
1037166 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:1038480 original size:19 final size:20
Alignment explanation
Indices: 1038443--1038493 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1038433 GAAACCCCTT
1038443 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
1038463 TGAAAATACATG-TTTTTAA
1 TGAAAATACATGATTTTTAA
*
1038482 TGAAGATACATG
1 TGAAAATACATG
1038494 CTATTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1039640 original size:21 final size:21
Alignment explanation
Indices: 1039601--1039640 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1039591 GTGCATTCTT
* * *
1039601 ATTAGCTCATAGACTTTATAC
1 ATTAGCTCACACACATTATAC
1039622 ATTAGCTCACACACATTAT
1 ATTAGCTCACACACATTAT
1039641 GAGATGATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (21 bp):
ATTAGCTCACACACATTATAC
Found at i:1044452 original size:33 final size:33
Alignment explanation
Indices: 1044373--1044476 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
1044363 ATACAATCTG
* *
1044373 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
1044409 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1044442 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1044475 TC
1 TC
1044477 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:1049118 original size:19 final size:21
Alignment explanation
Indices: 1049075--1049126 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
1049065 GAAACCCCTT
1049075 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
*
1049096 TGAAAATACATTA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
1049115 TGAAGATACATG
1 TGAAAATACATG
1049127 CTCTTGACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:1050843 original size:36 final size:36
Alignment explanation
Indices: 1050796--1050900 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
1050786 ATACAAATTT
1050796 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
1050832 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * * *
1050868 TCCACCACCATTATCACTCCCATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
1050901 ACTTATAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.29, C:0.38, G:0.04, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1051370 original size:12 final size:12
Alignment explanation
Indices: 1051353--1051396 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1051343 AGTGCAAAAG
1051353 AAAGAAAAGAAA
1 AAAGAAAAGAAA
1051365 AAAGAAAA-AAA
1 AAAGAAAAGAAA
** *
1051376 AATCAAAAGCAA
1 AAAGAAAAGAAA
1051388 AAAGAAAAG
1 AAAGAAAAG
1051397 TGAAGCAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:1055298 original size:23 final size:23
Alignment explanation
Indices: 1055270--1055373 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
1055260 ACAAATTGTC
1055270 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCC-ATAT
*
1055293 CATCACCA-TAGTCCATCTCCAT-T
1 CATCACCATTA-T-CATCGCCATAT
* *
1055316 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCGCCATA-T
*
1055341 CCATCACCATTATCA-CGCCTTTAT
1 -CATCACCATTATCATCGCC-ATAT
1055365 CATCACCAT
1 CATCACCAT
1055374 AGTCCATCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 22
0.70 0.07 0.24
Matches are distributed among these distances:
22 7 0.11
23 28 0.44
24 9 0.14
25 13 0.20
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.30
Consensus pattern (23 bp):
CATCACCATTATCATCGCCATAT
Found at i:1055315 original size:36 final size:36
Alignment explanation
Indices: 1055267--1055444 Score: 275
Period size: 36 Copynumber: 4.9 Consensus size: 36
1055257 GATACAAATT
1055267 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
1055303 GTCCATCTCCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
1055339 GTCCATCACCATTATCACGCCTTTATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
1055375 GTCCATCTCCATTATCATGCCTATATCGTCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
1055411 TTCCACCACCATTATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
1055445 ACTTATAAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 128 1.00
ACGTcount: A:0.28, C:0.37, G:0.06, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1055347 original size:13 final size:11
Alignment explanation
Indices: 1055270--1055411 Score: 58
Period size: 11 Copynumber: 12.0 Consensus size: 11
1055260 ACAAATTGTC
1055270 CATCACCATTAT
1 CATCACCA-TAT
*
1055282 CA-CGCCTATAT
1 CATCACC-ATAT
1055293 CATCACCATAGT
1 CATCACCATA-T
*
1055305 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1055318 CA-CGCCTATAT
1 CATCACC-ATAT
1055329 CATCACCATAGT
1 CATCACCATA-T
1055341 CCATCACCATTAT
1 -CATCACCA-TAT
* *
1055354 CA-CGCCTTTAT
1 CATCACC-ATAT
1055365 CATCACCATAGT
1 CATCACCATA-T
*
1055377 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1055390 CATGC-CTATAT
1 CAT-CACCATAT
*
1055401 CGTCACCATAT
1 CATCACCATAT
1055412 TCCACCACCA
Statistics
Matches: 100, Mismatches: 13, Indels: 35
0.68 0.09 0.24
Matches are distributed among these distances:
10 1 0.01
11 42 0.42
12 25 0.25
13 26 0.26
14 6 0.06
ACGTcount: A:0.28, C:0.35, G:0.06, T:0.31
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1058566 original size:23 final size:23
Alignment explanation
Indices: 1058538--1058641 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
1058528 ACAAATTTTC
1058538 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCC-ATAT
*
1058561 CATCACCA-TAGTCCATCTCCAT-T
1 CATCACCATTA-T-CATCGCCATAT
* *
1058584 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCGCCATA-T
*
1058609 CCATCACCATTATCA-CGCCTTTAT
1 -CATCACCATTATCATCGCC-ATAT
1058633 CATCACCAT
1 CATCACCAT
1058642 AGTCCATCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 22
0.70 0.07 0.24
Matches are distributed among these distances:
22 7 0.11
23 28 0.44
24 9 0.14
25 13 0.20
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.30
Consensus pattern (23 bp):
CATCACCATTATCATCGCCATAT
Found at i:1058583 original size:36 final size:36
Alignment explanation
Indices: 1058536--1058712 Score: 282
Period size: 36 Copynumber: 4.9 Consensus size: 36
1058526 ATACAAATTT
1058536 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1058572 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1058608 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
1058644 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
1058680 TCCACCACCATTATCACGCCCATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
1058713 ACTTATAAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 129 1.00
ACGTcount: A:0.28, C:0.37, G:0.05, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1058615 original size:13 final size:11
Alignment explanation
Indices: 1058538--1058679 Score: 58
Period size: 11 Copynumber: 12.0 Consensus size: 11
1058528 ACAAATTTTC
1058538 CATCACCATTAT
1 CATCACCA-TAT
*
1058550 CA-CGCCTATAT
1 CATCACC-ATAT
1058561 CATCACCATAGT
1 CATCACCATA-T
*
1058573 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1058586 CA-CGCCTATAT
1 CATCACC-ATAT
1058597 CATCACCATAGT
1 CATCACCATA-T
1058609 CCATCACCATTAT
1 -CATCACCA-TAT
* *
1058622 CA-CGCCTTTAT
1 CATCACC-ATAT
1058633 CATCACCATAGT
1 CATCACCATA-T
*
1058645 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1058658 CA-CGCCTATAT
1 CATCACC-ATAT
*
1058669 CGTCACCATAT
1 CATCACCATAT
1058680 TCCACCACCA
Statistics
Matches: 100, Mismatches: 13, Indels: 35
0.68 0.09 0.24
Matches are distributed among these distances:
11 43 0.43
12 26 0.26
13 25 0.25
14 6 0.06
ACGTcount: A:0.28, C:0.36, G:0.06, T:0.30
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1059192 original size:22 final size:22
Alignment explanation
Indices: 1059159--1059204 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
1059149 TTTGGAGTGC
*
1059159 AAAAAAAGAAAAG-AAAAAGAA
1 AAAAAAACAAAAGCAAAAAGAA
1059180 AAAAAAATCAAAAGCAAAAAGAA
1 AAAAAAA-CAAAAGCAAAAAGAA
1059203 AA
1 AA
1059205 GTTAAGCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 5 0.23
23 10 0.45
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (22 bp):
AAAAAAACAAAAGCAAAAAGAA
Found at i:1063150 original size:23 final size:23
Alignment explanation
Indices: 1063122--1063225 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
1063112 ACAAATTTTC
1063122 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCC-ATAT
*
1063145 CATCACCA-TAGTCCATCTCCAT-T
1 CATCACCATTA-T-CATCGCCATAT
* *
1063168 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCGCCATA-T
*
1063193 CCATCACCATTATCA-CGCCTTTAT
1 -CATCACCATTATCATCGCC-ATAT
1063217 CATCACCAT
1 CATCACCAT
1063226 AGTCCATCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 22
0.70 0.07 0.24
Matches are distributed among these distances:
22 7 0.11
23 28 0.44
24 9 0.14
25 13 0.20
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.30
Consensus pattern (23 bp):
CATCACCATTATCATCGCCATAT
Found at i:1063167 original size:36 final size:36
Alignment explanation
Indices: 1063120--1063296 Score: 282
Period size: 36 Copynumber: 4.9 Consensus size: 36
1063110 ATACAAATTT
1063120 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1063156 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1063192 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
1063228 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
1063264 TCCACCACCATTATCACGCCCATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
1063297 ACTTATAAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 129 1.00
ACGTcount: A:0.28, C:0.37, G:0.05, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1063199 original size:13 final size:11
Alignment explanation
Indices: 1063122--1063263 Score: 58
Period size: 11 Copynumber: 12.0 Consensus size: 11
1063112 ACAAATTTTC
1063122 CATCACCATTAT
1 CATCACCA-TAT
*
1063134 CA-CGCCTATAT
1 CATCACC-ATAT
1063145 CATCACCATAGT
1 CATCACCATA-T
*
1063157 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1063170 CA-CGCCTATAT
1 CATCACC-ATAT
1063181 CATCACCATAGT
1 CATCACCATA-T
1063193 CCATCACCATTAT
1 -CATCACCA-TAT
* *
1063206 CA-CGCCTTTAT
1 CATCACC-ATAT
1063217 CATCACCATAGT
1 CATCACCATA-T
*
1063229 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1063242 CA-CGCCTATAT
1 CATCACC-ATAT
*
1063253 CGTCACCATAT
1 CATCACCATAT
1063264 TCCACCACCA
Statistics
Matches: 100, Mismatches: 13, Indels: 35
0.68 0.09 0.24
Matches are distributed among these distances:
11 43 0.43
12 26 0.26
13 25 0.25
14 6 0.06
ACGTcount: A:0.28, C:0.36, G:0.06, T:0.30
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1065159 original size:16 final size:16
Alignment explanation
Indices: 1065138--1065170 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1065128 TTCTGCCACC
1065138 TATGTTAGGATGCAAA
1 TATGTTAGGATGCAAA
1065154 TATGTTAGGATGCAAA
1 TATGTTAGGATGCAAA
1065170 T
1 T
1065171 GAGCTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (16 bp):
TATGTTAGGATGCAAA
Found at i:1068668 original size:16 final size:16
Alignment explanation
Indices: 1068647--1068679 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1068637 TTCTGCCACC
1068647 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
*
1068663 TATGTTAGGATGCAAA
1 TATGTTAGAATGCAAA
1068679 T
1 T
1068680 GAGCTAACTA
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:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:1069544 original size:23 final size:22
Alignment explanation
Indices: 1069492--1069545 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1069482 AGATGTAATA
* *
1069492 TATGTATATGATATAACTATGT
1 TATGTATATGAAATAACTATAT
1069514 TATAGTATATGAAATAA-TCATCAT
1 TAT-GTATATGAAATAACT-AT-AT
1069538 TATGTATA
1 TATGTATA
1069546 AATATAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.15
23 19 0.70
24 4 0.15
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (22 bp):
TATGTATATGAAATAACTATAT
Found at i:1078176 original size:13 final size:13
Alignment explanation
Indices: 1078158--1078219 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
1078148 AGATACTATT
1078158 TCCATCACCATAA
1 TCCATCACCATAA
* *
1078171 TCCATCTTCCATTA
1 TCCATC-ACCATAA
1078185 T-CA-CACC-TATA
1 TCCATCACCATA-A
*
1078196 T-CATCACCATAG
1 TCCATCACCATAA
1078208 TCCATCACCATA
1 TCCATCACCATA
1078220 TCACGCCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 6 0.15
13 20 0.51
14 6 0.15
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.29
Consensus pattern (13 bp):
TCCATCACCATAA
Found at i:1078229 original size:35 final size:37
Alignment explanation
Indices: 1078160--1078239 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
1078150 ATACTATTTC
*
1078160 CATCACCATAATCCATCTTCCATTATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
* *
1078197 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
1078232 CATCACCA
1 CATCACCA
1078240 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:1078703 original size:14 final size:15
Alignment explanation
Indices: 1078669--1078715 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1078659 AATTTGGAGT
1078669 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
1078684 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
1078698 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
1078715 G
1 G
1078716 TGAAGCAAGT
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:1081788 original size:24 final size:24
Alignment explanation
Indices: 1081761--1081812 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1081751 TTCTTTTTCT
*
1081761 TTTTGTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
1081785 TTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
1081809 TTTT
1 TTTT
1081813 TCTTTGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.08, C:0.13, G:0.21, T:0.58
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTTGAC
Found at i:1082576 original size:21 final size:21
Alignment explanation
Indices: 1082537--1082576 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1082527 AAGGAAGATT
*
1082537 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
1082558 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
1082577 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Done.