Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 110 of 320
Found at i:35681431 original size:13 final size:13
Alignment explanation
Indices: 35681413--35681450 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
35681403 AAAAAAGACA
*
35681413 GACACGGCCGTGC
1 GACACGGTCGTGC
35681426 GACACGGTCGTGC
1 GACACGGTCGTGC
35681439 GACACGGTCGTG
1 GACACGGTCGTG
35681451 TGCACCAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.32, G:0.39, T:0.13
Consensus pattern (13 bp):
GACACGGTCGTGC
Found at i:35690501 original size:51 final size:50
Alignment explanation
Indices: 35690424--35690601 Score: 191
Period size: 52 Copynumber: 3.5 Consensus size: 50
35690414 CGGATACTCG
* *
35690424 GTGG-CTTGCACATAGTACCACCCTTGTAGTCAAAGCAACCTTCTTCACAAA
1 GTGGCCTT-CACATAGTACCACACTTGT-GACAAAGCAACCTTCTTCACAAA
* * * *
35690475 GTGGCCTTCACATAGTACTACACTTGTGACCAAAGCTATCTTTCTTCAAAAA
1 GTGGCCTTCACATAGTACCACACTTGTGA-CAAAGC-AACCTTCTTCACAAA
* * * * *
35690527 GTGGCCTTC-CTATAGTACCACACTTGCGACCAAGCTATC-TCTTCTCAAA
1 GTGGCCTTCAC-ATAGTACCACACTTGTGACAAAGCAACCTTCTTCACAAA
35690576 GTGGCCTTCACATAGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
35690602 AGTTACTAGT
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
49 32 0.30
50 2 0.02
51 33 0.31
52 40 0.37
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (50 bp):
GTGGCCTTCACATAGTACCACACTTGTGACAAAGCAACCTTCTTCACAAA
Found at i:35690542 original size:52 final size:51
Alignment explanation
Indices: 35690463--35690601 Score: 196
Period size: 52 Copynumber: 2.7 Consensus size: 51
35690453 TCAAAGCAAC
* *
35690463 CTTCTTCACAAAGTGGCCTTCACATAGTACTACACTTGTGACCAAAGCTATCT
1 CTTCTTCA-AAAGTGGCCTTCACATAGTACCACACTTGCGACC-AAGCTATCT
35690516 -TTCTTCAAAAAGTGGCCTTC-CTATAGTACCACACTTGCGACCAAGCTATCT
1 CTTCTTC-AAAAGTGGCCTTCAC-ATAGTACCACACTTGCGACCAAGCTATCT
35690567 CTTC-TC-AAAGTGGCCTTCACATAGTACCACACTTG
1 CTTCTTCAAAAGTGGCCTTCACATAGTACCACACTTG
35690602 AGTTACTAGT
Statistics
Matches: 80, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
49 27 0.34
50 1 0.01
51 12 0.15
52 39 0.49
53 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (51 bp):
CTTCTTCAAAAGTGGCCTTCACATAGTACCACACTTGCGACCAAGCTATCT
Found at i:35693069 original size:19 final size:19
Alignment explanation
Indices: 35693047--35693091 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
35693037 GCAATATTCC
35693047 GATTTTCATGCCATATCAA
1 GATTTTCATGCCATATCAA
*
35693066 GATTTTCATGCCATGTCAA
1 GATTTTCATGCCATATCAA
35693085 GAGTTTT
1 GA-TTTT
35693092 ATGTCCGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (19 bp):
GATTTTCATGCCATATCAA
Found at i:35693954 original size:20 final size:20
Alignment explanation
Indices: 35693929--35693968 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35693919 TGTATCCATA
*
35693929 AAATTTCAAAATTTTTCATT
1 AAATTTCAAAACTTTTCATT
* *
35693949 AAATTTTACAACTTTTCATT
1 AAATTTCAAAACTTTTCATT
35693969 TTATTCCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATTTCAAAACTTTTCATT
Found at i:35695032 original size:27 final size:27
Alignment explanation
Indices: 35694967--35695032 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
35694957 AAAACACCAG
*
35694967 CTCGCCAGGCCCTCTAAGGAACCCCAA
1 CTCGCCAGGCCTTCTAAGGAACCCCAA
* * *
35694994 CTTGCCAAGCCTTCT-AGAGAACCCTAA
1 CTCGCCAGGCCTTCTAAG-GAACCCCAA
*
35695021 CTCGTCAGGCCT
1 CTCGCCAGGCCT
35695033 ACTGGCAAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
26 2 0.06
27 29 0.94
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.18
Consensus pattern (27 bp):
CTCGCCAGGCCTTCTAAGGAACCCCAA
Found at i:35697072 original size:22 final size:22
Alignment explanation
Indices: 35697042--35697089 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
35697032 GTGATGCAGA
*
35697042 CCGTGTGTCACACACGGTCTAC
1 CCGTATGTCACACACGGTCTAC
35697064 CCGTATGTCACACACGGTCTAC
1 CCGTATGTCACACACGGTCTAC
35697086 CCGT
1 CCGT
35697090 GTGGCCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.23
Consensus pattern (22 bp):
CCGTATGTCACACACGGTCTAC
Found at i:35698450 original size:31 final size:31
Alignment explanation
Indices: 35698414--35698507 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
35698404 TAATAACAAT
35698414 AAAACATTTATCACATAATATCAAAACATTA
1 AAAACATTTATCACATAATATCAAAACATTA
* * *
35698445 AAAACA--TATAAC-TCATA--ATAACA--A
1 AAAACATTTATCACATAATATCAAAACATTA
35698469 GAAAACATTTATCACATAATATCAAAACATTA
1 -AAAACATTTATCACATAATATCAAAACATTA
35698501 AAAACAT
1 AAAACAT
35698508 GCTACAACAC
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
24 1 0.02
25 6 0.12
26 5 0.10
27 5 0.10
28 8 0.16
29 5 0.10
30 5 0.10
31 13 0.27
32 1 0.02
ACGTcount: A:0.57, C:0.16, G:0.01, T:0.26
Consensus pattern (31 bp):
AAAACATTTATCACATAATATCAAAACATTA
Found at i:35698459 original size:56 final size:56
Alignment explanation
Indices: 35698394--35698507 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
35698384 ACCAATAAGT
*
35698394 ATATAACTCATAATAACAATAAAACATTTATCACATAATATCAAAACATTAAAAAC
1 ATATAACTCATAATAACAAGAAAACATTTATCACATAATATCAAAACATTAAAAAC
35698450 ATATAACTCATAATAACAAGAAAACATTTATCACATAATATCAAAACATTAAAAAC
1 ATATAACTCATAATAACAAGAAAACATTTATCACATAATATCAAAACATTAAAAAC
35698506 AT
1 AT
35698508 GCTACAACAC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.57, C:0.16, G:0.01, T:0.26
Consensus pattern (56 bp):
ATATAACTCATAATAACAAGAAAACATTTATCACATAATATCAAAACATTAAAAAC
Found at i:35707527 original size:46 final size:46
Alignment explanation
Indices: 35707459--35707595 Score: 202
Period size: 46 Copynumber: 3.0 Consensus size: 46
35707449 TATATATACA
* * * * *
35707459 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCACACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
35707505 CATCTCACACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCACACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
*
35707551 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCACACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
35707596 ATACACTTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCACACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:35707638 original size:22 final size:22
Alignment explanation
Indices: 35707612--35707686 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
35707602 TTCCACGTTC
35707612 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
35707634 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGGCCTT
35707658 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
35707681 ATCACA
1 ATCACA
35707687 CATATGCATG
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.30
23 11 0.28
24 11 0.28
25 6 0.15
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:35707660 original size:47 final size:47
Alignment explanation
Indices: 35707569--35707712 Score: 209
Period size: 47 Copynumber: 3.1 Consensus size: 47
35707559 ACACATTTCG
* * * * * *
35707569 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCA-TGTCCACATTCATCA
*
35707616 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTCCACATTCATCA
35707663 CATTGGCCATTCGGCCTTATCACACATATGCATGTCCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTCCACATTCATCA
35707710 CAT
1 CAT
35707713 AAAATCCTAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
46 1 0.01
47 87 0.99
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATATGCATGTCCACATTCATCA
Found at i:35707710 original size:25 final size:25
Alignment explanation
Indices: 35707634--35707711 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 25
35707624 ATTCGGCCTT
*
35707634 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTCCACATTC
** *
35707659 AT--CACAT-TGGCCAT-TCGGCCTT-
1 ATCACACATAT-G-CATGTCCACATTC
35707681 ATCACACATATGCATGTCCACATTC
1 ATCACACATATGCATGTCCACATTC
35707706 ATCACA
1 ATCACA
35707712 TAAAATCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 14
0.65 0.12 0.23
Matches are distributed among these distances:
22 3 0.08
23 13 0.33
24 14 0.36
25 9 0.23
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.29
Consensus pattern (25 bp):
ATCACACATATGCATGTCCACATTC
Found at i:35707713 original size:23 final size:23
Alignment explanation
Indices: 35707638--35707713 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
35707628 GGCCTTATCA
*
35707638 CACATATGCATGTTCACATTCAT
1 CACATATGCATGTCCACATTCAT
*
35707661 CACAT-TGGCCAT-TCGGC-CTTATCA-
1 CACATAT-G-CATGTC--CACAT-TCAT
35707685 CACATATGCATGTCCACATTCAT
1 CACATATGCATGTCCACATTCAT
35707708 CACATA
1 CACATA
35707714 AAATCCTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 18
0.66 0.05 0.29
Matches are distributed among these distances:
22 5 0.12
23 18 0.44
24 13 0.32
25 5 0.12
ACGTcount: A:0.29, C:0.30, G:0.11, T:0.30
Consensus pattern (23 bp):
CACATATGCATGTCCACATTCAT
Found at i:35711393 original size:28 final size:28
Alignment explanation
Indices: 35711352--35711508 Score: 97
Period size: 28 Copynumber: 5.5 Consensus size: 28
35711342 GAAACACACT
* * * *
35711352 TCGCATACACAGTGCCCACTGACTGATT
1 TCGCACACATAGTGCCCACTGACAGATC
* * * *
35711380 TCGCACACATAGTGCTCGA-TTAAAGAAC
1 TCGCACACATAGTGC-CCACTGACAGATC
* *
35711408 TCGCACACATAGTGCCTCAATTACCA-ATC
1 TCGCACACATAGTGCC-CACTGA-CAGATC
* * *
35711437 TCGCACACATAGTGCTCGATTGA-AGAAC
1 TCGCACACATAGTGC-CCACTGACAGATC
*
35711465 TCGCACACATAGTGCCTCAACT-ACTGATC
1 TCGCACACATAGTGCC-C-ACTGACAGATC
*
35711494 TGGCACACATAGTGC
1 TCGCACACATAGTGC
35711509 TCGGTTGGAG
Statistics
Matches: 100, Mismatches: 20, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
27 3 0.03
28 51 0.51
29 44 0.44
30 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TCGCACACATAGTGCCCACTGACAGATC
Found at i:35711440 original size:29 final size:29
Alignment explanation
Indices: 35711380--35711508 Score: 124
Period size: 29 Copynumber: 4.5 Consensus size: 29
35711370 CTGACTGATT
* *
35711380 TCGCACACATAGTG-CTCGATTA-AAGAAC
1 TCGCACACATAGTGCCTCAATTACAA-ATC
*
35711408 TCGCACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTGCCTCAATTACAAATC
*
35711437 TCGCACACATAGTG-CTCGATTGA-AGAA-C
1 TCGCACACATAGTGCCTCAATT-ACA-AATC
* **
35711465 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCCTCAATTACAAATC
*
35711494 TGGCACACATAGTGC
1 TCGCACACATAGTGC
35711509 TCGGTTGGAG
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
28 37 0.44
29 46 0.55
30 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (29 bp):
TCGCACACATAGTGCCTCAATTACAAATC
Found at i:35711447 original size:57 final size:57
Alignment explanation
Indices: 35711380--35711540 Score: 241
Period size: 57 Copynumber: 2.8 Consensus size: 57
35711370 CTGACTGATT
* *
35711380 TCGCACACATAGTGCTCGATTAAAGAACTCGCACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
**
35711437 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
* * * * *
35711494 TGGCACACATAGTGCTCGGTTGGAGAACTTGCACACACAGTGCCTCA
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCA
35711541 TAATTCCAGC
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 95 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (57 bp):
TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
Found at i:35711618 original size:40 final size:40
Alignment explanation
Indices: 35711568--35711861 Score: 457
Period size: 40 Copynumber: 7.4 Consensus size: 40
35711558 CCTTCGAGGT
*
35711568 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCAGAAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
* * *
35711608 TTAGTCCGGATATATCACTAGTACGAATGCTCTTTGGAAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
*
35711648 TTAGCCCAGATATATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
*
35711688 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
* * * *
35711728 TTAGCTCGGATACATCACTAGCACGAATGCTCTTTGAAAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
35711768 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGG-AC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
*
35711807 TTAGCCCGGATACATCACTAGCACGAATGCTCTTC-GAGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGA-AC
*
35711847 TTAGCCCTGATATAT
1 TTAGCCCGGATATAT
35711862 ATAACTCTCA
Statistics
Matches: 230, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
38 1 0.00
39 36 0.16
40 193 0.84
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (40 bp):
TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
Found at i:35713410 original size:46 final size:46
Alignment explanation
Indices: 35713342--35713478 Score: 202
Period size: 46 Copynumber: 3.0 Consensus size: 46
35713332 TATATATACA
* * * * *
35713342 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCACACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
35713388 CATCTCACACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCACACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
*
35713434 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCACACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
35713479 ATACACTTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCACACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:35713523 original size:47 final size:47
Alignment explanation
Indices: 35713452--35713689 Score: 361
Period size: 47 Copynumber: 5.1 Consensus size: 47
35713442 ACACATTTCG
* * * * * * *
35713452 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCA-TGTTCACATTCATCA
* *
35713499 CATTGGCCATTCTGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
*
35713546 CATTGGCCATTCGACCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
35713593 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
*
35713640 CATTGGCCATTCGGCCTTATCACACATATGCATGTCCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
35713687 CAT
1 CAT
35713690 AAAATCCTAA
Statistics
Matches: 178, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 1 0.01
47 177 0.99
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
Found at i:35713593 original size:25 final size:25
Alignment explanation
Indices: 35713517--35713641 Score: 76
Period size: 24 Copynumber: 5.2 Consensus size: 25
35713507 ATTCTGCCTT
*
35713517 ATCACATATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
*
35713542 AT--CACAT-TGGCCA--TTCGACCTT-
1 ATCACACATAT-G-CATGTTC-ACATTC
35713564 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
* *
35713589 AT--CACAT-TGGCCA--TTCGGCCTT-
1 ATCACACATAT-G-CATGTTC-ACATTC
35713611 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
35713636 ATCACA
1 ATCACA
35713642 TTGGCCATTC
Statistics
Matches: 75, Mismatches: 7, Indels: 36
0.64 0.06 0.31
Matches are distributed among these distances:
22 12 0.16
23 22 0.29
24 23 0.31
25 18 0.24
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (25 bp):
ATCACACATATGCATGTTCACATTC
Found at i:35713616 original size:22 final size:22
Alignment explanation
Indices: 35713589--35713663 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
35713579 GTTCACATTC
35713589 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
35713611 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGGCCTT
35713635 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
35713658 ATCACA
1 ATCACA
35713664 CATATGCATG
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.30
23 11 0.28
24 11 0.28
25 6 0.15
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:35716705 original size:55 final size:53
Alignment explanation
Indices: 35716550--35716694 Score: 182
Period size: 53 Copynumber: 2.7 Consensus size: 53
35716540 TTCCTTTTTA
* *
35716550 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCTTTGCCTTATG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCTTTGCCTTATG
* * * *
35716603 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCTTTGCCTTAT-G
** * *
35716657 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATG
1 -AACTCACCAATGCCATGTCTTGACATGGTCTTACATG
35716695 ATTTCCTTGC
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 48 0.61
54 1 0.01
55 30 0.38
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (53 bp):
AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGTATCTTTGCCTTATG
Found at i:35718464 original size:20 final size:20
Alignment explanation
Indices: 35718439--35718481 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
35718429 ATCTTGCTAA
35718439 AAATTCAAAGAAAAAGAAAG
1 AAATTCAAAGAAAAAGAAAG
35718459 AAATTCAAAGAAAAAGAAAG
1 AAATTCAAAGAAAAAGAAAG
35718479 AAA
1 AAA
35718482 ATAAACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.72, C:0.05, G:0.14, T:0.09
Consensus pattern (20 bp):
AAATTCAAAGAAAAAGAAAG
Found at i:35719426 original size:43 final size:43
Alignment explanation
Indices: 35719279--35719437 Score: 164
Period size: 43 Copynumber: 3.7 Consensus size: 43
35719269 TGTGTTATCG
* *
35719279 TGTAAGACCACGTCTGGGAC-GTTGGCATTGACT-TATGATTTACG
1 TGTAAGACCACGTCTGGGACAG-TGGCATTGA-TATTTGA-TTACA
* * * *
35719323 TGTAAGACCACGTCTGAGACATTGGCA-TCATATTTGATTTCA
1 TGTAAGACCACGTCTGGGACAGTGGCATTGATATTTGATTACA
** * *
35719365 TGTAAGACCTTGTTTGGGACAGTGACATTGATATTTGATTACA
1 TGTAAGACCACGTCTGGGACAGTGGCATTGATATTTGATTACA
35719408 TGTAAGACCACGTCTGGGAC-GTTGGCATTG
1 TGTAAGACCACGTCTGGGACAG-TGGCATTG
35719438 TAGAAGCTTT
Statistics
Matches: 93, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
42 26 0.28
43 43 0.46
44 24 0.26
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACAGTGGCATTGATATTTGATTACA
Found at i:35740403 original size:13 final size:12
Alignment explanation
Indices: 35740387--35740411 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35740377 AAAAAAAAGG
35740387 AAAAAAAATTGC
1 AAAAAAAATTGC
35740399 AAAAAAAATTGC
1 AAAAAAAATTGC
35740411 A
1 A
35740412 TACGGTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGC
Found at i:35742665 original size:23 final size:24
Alignment explanation
Indices: 35742621--35742672 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
35742611 TAAGTGATAA
*
35742621 AAAAAGAGAGAGTGATTCAAAA-G
1 AAAAAGAAAGAGTGATTCAAAATG
*
35742644 AAAAAGAAACGAGTGA-TGAAAATG
1 AAAAAGAAA-GAGTGATTCAAAATG
35742668 AAAAA
1 AAAAA
35742673 AAGAATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.62, C:0.04, G:0.23, T:0.12
Consensus pattern (24 bp):
AAAAAGAAAGAGTGATTCAAAATG
Found at i:35748413 original size:21 final size:19
Alignment explanation
Indices: 35748387--35748434 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
35748377 TCTTTTTGGA
*
35748387 TTTCTTTTTCTTTTTCAATCT
1 TTTCTTTTT-TCTTTCAAT-T
35748408 TTTCTTCTTTTCTTTCAATT
1 TTTCTT-TTTTCTTTCAATT
*
35748428 TCTCTTT
1 TTTCTTT
35748435 CTCGCTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 6 0.25
21 14 0.58
22 3 0.12
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTCTTTTTTCTTTCAATT
Found at i:35750828 original size:22 final size:22
Alignment explanation
Indices: 35750800--35750843 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
35750790 TTTTGAACCA
35750800 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
35750822 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
35750844 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:35753563 original size:24 final size:24
Alignment explanation
Indices: 35753536--35753615 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
35753526 CCATTGAGCG
35753536 AGAAAAAGAGAAAGAGATTGAAAA
1 AGAAAAAGAGAAAGAGATTGAAAA
** * * **
35753560 AGAAATCGAAAAAGTGAGAGAAAA
1 AGAAAAAGAGAAAGAGATTGAAAA
* *
35753584 AGAAAATGAAGAAAAGAAAATTGAAAA
1 AGAAAAAG-AG-AAAG-AGATTGAAAA
35753611 AGAAA
1 AGAAA
35753616 TTGAGAATGA
Statistics
Matches: 40, Mismatches: 13, Indels: 3
0.71 0.23 0.05
Matches are distributed among these distances:
24 24 0.60
25 1 0.03
26 4 0.10
27 11 0.28
ACGTcount: A:0.68, C:0.01, G:0.23, T:0.09
Consensus pattern (24 bp):
AGAAAAAGAGAAAGAGATTGAAAA
Found at i:35753616 original size:12 final size:12
Alignment explanation
Indices: 35753546--35753644 Score: 59
Period size: 12 Copynumber: 8.6 Consensus size: 12
35753536 AGAAAAAGAG
*
35753546 AAAGAGATTGAA
1 AAAGAAATTGAA
*
35753558 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
35753570 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
35753582 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
35753596 AAAGAAAATTGAA
1 AAAG-AAATTGAA
35753609 AAAGAAATTG--
1 AAAGAAATTGAA
35753619 --AG-AA-TGAA
1 AAAGAAATTGAA
35753627 AAA-AAATTGAA
1 AAAGAAATTGAA
35753638 AAAGAAA
1 AAAGAAA
35753645 AAGCGAAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 2 0.03
10 3 0.05
11 7 0.11
12 33 0.50
13 6 0.09
14 6 0.09
15 5 0.08
ACGTcount: A:0.67, C:0.01, G:0.20, T:0.12
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:35753633 original size:17 final size:18
Alignment explanation
Indices: 35753599--35753647 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
35753589 ATGAAGAAAA
35753599 GAAAATTGAAAAAGAAATT
1 GAAAA-TGAAAAAGAAATT
*
35753618 GAGAATGAAAAA-AAATT
1 GAAAATGAAAAAGAAATT
*
35753635 GAAAAAGAAAAAG
1 GAAAATGAAAAAG
35753648 CGAAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 15 0.58
18 7 0.27
19 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
GAAAATGAAAAAGAAATT
Found at i:35753642 original size:29 final size:27
Alignment explanation
Indices: 35753579--35753645 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 27
35753569 AAAAGTGAGA
35753579 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAGAAAATT
*
35753606 GAAAAAGAAATTGAGAATGAAAA-AAAATT
1 GAAAAAGAAAAT--GAA-GAAAAGAAAATT
35753635 GAAAAAGAAAA
1 GAAAAAGAAAA
35753646 AGCGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 11 0.31
29 19 0.54
30 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAGAAAATT
Found at i:35753699 original size:33 final size:33
Alignment explanation
Indices: 35753662--35753724 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35753652 AAAAGAAATT
35753662 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
35753695 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
35753725 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:35759457 original size:30 final size:30
Alignment explanation
Indices: 35759371--35759468 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
35759361 TTAAACTAAA
* *
35759371 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
35759401 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
35759431 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
35759461 ATGAGCTA
1 ATGAGCTA
35759469 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:35767072 original size:33 final size:33
Alignment explanation
Indices: 35767034--35767096 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35767024 GATTACTCAC
35767034 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
35767067 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
35767097 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:35767123 original size:21 final size:21
Alignment explanation
Indices: 35767094--35767149 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
35767084 CAAGCTCTCT
*
35767094 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
35767115 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
35767136 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
35767150 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:35767142 original size:14 final size:14
Alignment explanation
Indices: 35767093--35767149 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
35767083 TCAAGCTCTC
35767093 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
35767106 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
35767120 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
35767134 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
35767148 TT
1 TT
35767150 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:35767209 original size:18 final size:18
Alignment explanation
Indices: 35767111--35767214 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
35767101 TCTTTTTTCG
35767111 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
35767130 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
35767150 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
35767168 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
35767186 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
35767204 CTTTTTGTTTT
1 CTTTTTCTTTT
35767215 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:35767231 original size:6 final size:6
Alignment explanation
Indices: 35767111--35767218 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
35767101 TCTTTTTTCG
* * * **
35767111 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
35767162 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
35767210 -GTTTT CTTT
1 CTTTTT CTTT
35767219 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:35768307 original size:29 final size:27
Alignment explanation
Indices: 35768252--35768312 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 27
35768242 TGAAACTTGA
*
35768252 TTTTTTTTGCTCACCTTTTTTTTCTTTT
1 TTTTTTTTGCTCA-CTTTTTTTACTTTT
35768280 CTTTTTTTTGCTCGA-TTTTTTTCACTTTT
1 -TTTTTTTTGCTC-ACTTTTTTT-ACTTTT
35768309 TTTT
1 TTTT
35768313 GAATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 11 0.38
29 17 0.59
30 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (27 bp):
TTTTTTTTGCTCACTTTTTTTACTTTT
Found at i:35768349 original size:11 final size:12
Alignment explanation
Indices: 35768295--35768351 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
35768285 TTTTGCTCGA
*
35768295 TTTTTTTC-ACT
1 TTTTTTTCAAAT
* *
35768306 TTTTTTTGAATT
1 TTTTTTTCAAAT
35768318 TTTTTTCAATCAAAT
1 TTTTTT---TCAAAT
35768333 TTTTTTTCAAAT
1 TTTTTTTCAAAT
35768345 TTTTTTT
1 TTTTTTT
35768352 ATTTTTTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 7 0.18
12 21 0.55
15 10 0.26
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:35771828 original size:33 final size:33
Alignment explanation
Indices: 35771790--35771852 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35771780 GATTACTCAC
35771790 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
35771823 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
35771853 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:35771879 original size:21 final size:21
Alignment explanation
Indices: 35771850--35771905 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
35771840 CAAGCTCTCT
*
35771850 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
35771871 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
35771892 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
35771906 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:35771898 original size:14 final size:14
Alignment explanation
Indices: 35771849--35771905 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
35771839 TCAAGCTCTC
35771849 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
35771862 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
35771876 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
35771890 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
35771904 TT
1 TT
35771906 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:35771965 original size:18 final size:18
Alignment explanation
Indices: 35771867--35771970 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
35771857 TCTTTTTTCG
35771867 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
35771886 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
35771906 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
35771924 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
35771942 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
35771960 CTTTTTGTTTT
1 CTTTTTCTTTT
35771971 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:35771987 original size:6 final size:6
Alignment explanation
Indices: 35771867--35771974 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
35771857 TCTTTTTTCG
* * * **
35771867 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
35771918 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
35771966 -GTTTT CTTT
1 CTTTTT CTTT
35771975 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:35773061 original size:29 final size:27
Alignment explanation
Indices: 35773006--35773066 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 27
35772996 TTAAACTTGA
*
35773006 TTTTTTTTGCTCACCTTTTTTTTCTTTT
1 TTTTTTTTGCTCA-CTTTTTTTACTTTT
35773034 CTTTTTTTTGCTCGA-TTTTTTTCACTTTT
1 -TTTTTTTTGCTC-ACTTTTTTT-ACTTTT
35773063 TTTT
1 TTTT
35773067 GAATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 11 0.38
29 17 0.59
30 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (27 bp):
TTTTTTTTGCTCACTTTTTTTACTTTT
Found at i:35776579 original size:33 final size:33
Alignment explanation
Indices: 35776541--35776603 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35776531 GATTACTCAC
35776541 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
35776574 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
35776604 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:35776630 original size:21 final size:21
Alignment explanation
Indices: 35776601--35776656 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
35776591 CAAGCTCTCT
*
35776601 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
35776622 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
35776643 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
35776657 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:35776649 original size:14 final size:14
Alignment explanation
Indices: 35776600--35776656 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
35776590 TCAAGCTCTC
35776600 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
35776613 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
35776627 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
35776641 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
35776655 TT
1 TT
35776657 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:35776716 original size:18 final size:18
Alignment explanation
Indices: 35776618--35776721 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
35776608 TCTTTTTTCG
35776618 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
35776637 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
35776657 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
35776675 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
35776693 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
35776711 CTTTTTGTTTT
1 CTTTTTCTTTT
35776722 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:35776738 original size:6 final size:6
Alignment explanation
Indices: 35776618--35776725 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
35776608 TCTTTTTTCG
* * * **
35776618 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
35776669 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
35776717 -GTTTT CTTT
1 CTTTTT CTTT
35776726 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:35777816 original size:30 final size:28
Alignment explanation
Indices: 35777759--35777820 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 28
35777749 TGAAACTTGA
*
35777759 TTTTTTTTGCTCACCTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCA-CTTTTTTTACTTTT-T
35777789 TTTTTTTTGCTCGA-TTTTTTTCACTTTTT
1 TTTTTTTTGCTC-ACTTTTTTT-ACTTTTT
35777818 TTT
1 TTT
35777821 GAATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 11 0.38
30 17 0.59
31 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (28 bp):
TTTTTTTTGCTCACTTTTTTTACTTTTT
Found at i:35777857 original size:12 final size:13
Alignment explanation
Indices: 35777813--35777862 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
35777803 TTTTTTTCAC
* *
35777813 TTTTTTTTGAATT
1 TTTTTTTTCAAAT
35777826 TTTTTTTCAATCAAAT
1 TTTTTTT---TCAAAT
35777842 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
35777855 TTTTTTTT
1 TTTTTTTT
35777863 ATTTTTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 21 0.66
16 11 0.34
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:35791125 original size:6 final size:6
Alignment explanation
Indices: 35791095--35791202 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
35791085 AAAGAAATTG
* ** *
35791095 AAAG-A AAACAA AAAGAA AACA-AA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
35791142 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
35791193 AAAGAA AAAG
1 AAAGAA AAAG
35791203 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:35791184 original size:14 final size:13
Alignment explanation
Indices: 35791163--35791200 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
35791153 AAAAGTGAGA
35791163 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
35791175 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
35791190 GAAAAAGAAAA
1 GAAAAAGAAAA
35791201 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:35791214 original size:21 final size:21
Alignment explanation
Indices: 35791107--35791214 Score: 51
Period size: 24 Copynumber: 4.9 Consensus size: 21
35791097 AGAAAACAAA
*
35791107 AAGAAAACAAAAAAGAAAAAG
1 AAGAAAAGAAAAAAGAAAAAG
**
35791128 AAATTGCAAAAG-AAAAAGAAATCG
1 -AA--G-AAAAGAAAAAAGAAAAAG
*
35791152 AA-AAAGTGAGAGAAAAAGAAAATG
1 AAGAAA---AGA-AAAAAGAAAAAG
**
35791176 AAGAAAAGAAAATTGAAAAAG
1 AAGAAAAGAAAAAAGAAAAAG
*
35791197 AA-AAAGCGAAAAAAGAAA
1 AAGAAA-AGAAAAAAGAAA
35791215 TTGAAAGAGA
Statistics
Matches: 65, Mismatches: 11, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
19 3 0.05
20 3 0.05
21 20 0.31
22 7 0.11
23 2 0.03
24 23 0.35
25 7 0.11
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (21 bp):
AAGAAAAGAAAAAAGAAAAAG
Found at i:35791254 original size:33 final size:33
Alignment explanation
Indices: 35791217--35791279 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35791207 AAAAGAAATT
35791217 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
35791250 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
35791280 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:35795371 original size:52 final size:51
Alignment explanation
Indices: 35795307--35795438 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 51
35795297 ATGAACAAAT
* * *
35795307 GAGTTACTTAATGCATAACTTAATTTAATGATGAAAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACTTAATTTAATGATGAAAAC-TTAACTAACATGA
* * * * *
35795359 GAGTTACATAATGCATGTCATCATTT-ATGATGCAAACTTAACTTACATGA
1 GAGTTACATAATGCATGACTTAATTTAATGATGAAAACTTAACTAACATGA
* *
35795409 GAGTTACATAATGCATGACTTTATTAAATG
1 GAGTTACATAATGCATGACTTAATTTAATG
35795439 CAAAACACAT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
50 33 0.49
51 13 0.19
52 21 0.31
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (51 bp):
GAGTTACATAATGCATGACTTAATTTAATGATGAAAACTTAACTAACATGA
Found at i:35802023 original size:15 final size:15
Alignment explanation
Indices: 35802005--35802040 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
35801995 AAAAAAATCG
35802005 AAAAAAAAATTGAAA
1 AAAAAAAAATTGAAA
**
35802020 AAAAAAATTTTGAAA
1 AAAAAAAAATTGAAA
35802035 AAAAAA
1 AAAAAA
35802041 TTGTATACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (15 bp):
AAAAAAAAATTGAAA
Found at i:35802028 original size:13 final size:13
Alignment explanation
Indices: 35801981--35802040 Score: 63
Period size: 12 Copynumber: 4.6 Consensus size: 13
35801971 TTGTAGATTC
35801981 AAAAAAAAA--GA
1 AAAAAAAAATTGA
*
35801992 AATAAAAAAATCG-
1 AA-AAAAAAATTGA
35802005 AAAAAAAAATTGA
1 AAAAAAAAATTGA
35802018 AAAAAAAAATTTTGA
1 AAAAAAAAA--TTGA
35802033 AAAAAAAA
1 AAAAAAAA
35802041 TTGTATACGG
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
11 2 0.05
12 16 0.38
13 11 0.26
14 1 0.02
15 12 0.29
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:35802035 original size:14 final size:14
Alignment explanation
Indices: 35802004--35802042 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
35801994 TAAAAAAATC
35802004 GAAAAAAAAA--TT
1 GAAAAAAAAATTTT
35802016 GAAAAAAAAAATTTT
1 G-AAAAAAAAATTTT
35802031 GAAAAAAAAATT
1 GAAAAAAAAATT
35802043 GTATACGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 9 0.38
14 11 0.46
15 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (14 bp):
GAAAAAAAAATTTT
Found at i:35805516 original size:30 final size:29
Alignment explanation
Indices: 35805417--35805518 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 29
35805407 CGAGTTTAAA
* *
35805417 CTAAAATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
35805446 CTAAATTGAGCTGAGGCTAAACTCCTAAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
*
35805475 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
35805505 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
35805519 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
29 26 0.47
30 29 0.53
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:35807952 original size:48 final size:48
Alignment explanation
Indices: 35807897--35808002 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
35807887 TTGTCTTTTC
*
35807897 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
35807945 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
35807993 TTTCTTTTTC
1 TTTCTTTTTC
35808003 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:35808194 original size:27 final size:26
Alignment explanation
Indices: 35808147--35808224 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 26
35808137 ACATTTCTTG
*
35808147 TCTTTCCTT-TCTT-CTTATTTCTTTT
1 TCTTTTCTTCTCTTGCTT-TTTCTTTT
35808172 TCTTTTTCTTCTCTTGCTTTTTCTTTT
1 TC-TTTTCTTCTCTTGCTTTTTCTTTT
* *
35808199 TCTTTTCTTTTCTTTGTTTTTTCTTT
1 TCTTTTCTTCTC-TTGCTTTTTCTTT
35808225 ACAAGAATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.04
26 15 0.33
27 26 0.57
28 3 0.07
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.76
Consensus pattern (26 bp):
TCTTTTCTTCTCTTGCTTTTTCTTTT
Found at i:35808219 original size:21 final size:21
Alignment explanation
Indices: 35808154--35808224 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
35808144 TTGTCTTTCC
*
35808154 TTTCTTCTTATTTCTTTTTCTT
1 TTTCTT-TTCTTTCTTTTTCTT
* *
35808176 TTTCTTCTCTTGCTTTTTCTT
1 TTTCTTTTCTTTCTTTTTCTT
*
35808197 TTTCTTTTCTTTTCTTTGT-TT
1 TTTCTTTTC-TTTCTTTTTCTT
35808218 TTTCTTT
1 TTTCTTT
35808225 ACAAGAATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 29 0.69
22 13 0.31
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTCTTTTCTTTCTTTTTCTT
Found at i:35808224 original size:16 final size:16
Alignment explanation
Indices: 35808140--35808224 Score: 57
Period size: 16 Copynumber: 5.1 Consensus size: 16
35808130 CTCATCAACA
* *
35808140 TTTCTTGTCTTTCCTT
1 TTTCTTTTCTTTTCTT
35808156 TCTTCTTATTTCTTTTTCTT
1 T-TTC-T-TTTC-TTTTCTT
* *
35808176 TTTCTTCTC-TTGCTT
1 TTTCTTTTCTTTTCTT
35808191 TTTCTTTTTCTTTTC-T
1 TTTC-TTTTCTTTTCTT
*
35808207 TTTCTTTGTTTTTTCTT
1 TTTCTTT-TCTTTTCTT
35808224 T
1 T
35808225 ACAAGAATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
15 12 0.22
16 16 0.30
17 11 0.20
18 2 0.04
19 6 0.11
20 7 0.13
ACGTcount: A:0.01, C:0.20, G:0.04, T:0.75
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTT
Found at i:35809205 original size:11 final size:11
Alignment explanation
Indices: 35809177--35809245 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 11
35809167 TTGAATTTCG
35809177 ATTTTTTTGTGA
1 ATTTTTTT-TGA
*
35809189 CTTTTTTTTTGA
1 -ATTTTTTTTGA
*
35809201 ATTTTTTTTTCA
1 A-TTTTTTTTGA
35809213 ATCAATTTTTTTCGA
1 AT---TTTTTTT-GA
35809228 ATTTTTTTTG-
1 ATTTTTTTTGA
35809238 ATTTTTTT
1 ATTTTTTT
35809246 GTTACTCCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
10 8 0.17
11 2 0.04
12 20 0.43
13 7 0.15
14 7 0.15
15 3 0.06
ACGTcount: A:0.16, C:0.06, G:0.07, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:35811019 original size:30 final size:29
Alignment explanation
Indices: 35810920--35811021 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 29
35810910 CGAGTTTAAA
* *
35810920 CTAAAATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
35810949 CTAAATTGAGCTGAGGCTAAACTCCTAAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
*
35810978 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
35811008 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
35811022 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
29 26 0.47
30 29 0.53
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:35818119 original size:12 final size:13
Alignment explanation
Indices: 35818090--35818122 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
35818080 TATACAAGTT
35818090 AAAAAAAAATTCG
1 AAAAAAAAATTCG
35818103 AAAAAAAAATAT-G
1 AAAAAAAAAT-TCG
35818116 AAAAAAA
1 AAAAAAA
35818123 GGTGTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:35819041 original size:9 final size:10
Alignment explanation
Indices: 35819034--35819090 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
35819024 AAGAGAAAAC
35819034 AAAGAAAAGA
1 AAAGAAAAGA
35819044 AAAGAAAAAGTA
1 AAAG-AAAAG-A
*
35819056 AAAGAAGA-A
1 AAAGAAAAGA
35819065 AAAGAAAACGA
1 AAAGAAAA-GA
35819076 AATA-AAAAGA
1 AA-AGAAAAGA
35819086 AAAGA
1 AAAGA
35819091 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:35819058 original size:6 final size:5
Alignment explanation
Indices: 35819034--35819090 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
35819024 AAGAGAAAAC
*
35819034 AAAGA AAAGA AAAGAA AAAGTA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
35819081 AAAGA AAAGA
1 AAAGA AAAGA
35819091 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:35819065 original size:15 final size:14
Alignment explanation
Indices: 35819034--35819090 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
35819024 AAGAGAAAAC
35819034 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
35819050 AAAGTAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
35819065 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
35819081 AAAGAAAAGA
1 AAAGAAAAGA
35819091 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:35819170 original size:11 final size:12
Alignment explanation
Indices: 35819138--35819168 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35819128 TTAAGAGAAC
35819138 TTGAAAAAGCCT
1 TTGAAAAAGCCT
35819150 TTGAAAAAGCCT
1 TTGAAAAAGCCT
35819162 TTGAAAA
1 TTGAAAA
35819169 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:35819205 original size:30 final size:31
Alignment explanation
Indices: 35819171--35819252 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
35819161 TTTGAAAAGC
*
35819171 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* * *
35819201 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* *
35819231 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAAAGAAAAAGAAAT
35819253 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
Found at i:35819225 original size:24 final size:24
Alignment explanation
Indices: 35819176--35819245 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
35819166 AAAGCAAAAA
*
35819176 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
35819200 GAAAAAGAGAACGAAAA-GAAATTT
1 GAAAAAGAAAAAGAAAATGAAA-TT
* ** *
35819224 GAGAGTGAAAAAGAAGATGAAA
1 GAAAAAGAAAAAGAAAATGAAA
35819246 AAGAAATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 28 0.80
25 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:35820973 original size:12 final size:12
Alignment explanation
Indices: 35820921--35820988 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 12
35820911 TTGGAGTAAC
35820921 AAAAAAA-TC-A
1 AAAAAAATTCAA
35820931 AAAAAAATTCGAA
1 AAAAAAATTC-AA
*
35820944 AAAAAATTGATTGAAA
1 AAAAAA---ATT-CAA
35820960 AAAAAAATTCAA
1 AAAAAAATTCAA
* *
35820972 AAAAAAAGTGAA
1 AAAAAAATTCAA
35820984 AAAAA
1 AAAAA
35820989 TCGAGCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.15
11 2 0.04
12 17 0.36
13 10 0.21
16 11 0.23
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:35822084 original size:17 final size:18
Alignment explanation
Indices: 35822052--35822085 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35822042 AAAAGAGAGT
*
35822052 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
35822070 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
35822086 GGAGTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:35825806 original size:30 final size:30
Alignment explanation
Indices: 35825772--35825868 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
35825762 AGCTCACTCC
35825772 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
35825802 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
35825832 CAGCTCAACTTTAGCTCACGAACTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
35825862 TAGCTCA
1 TAGCTCA
35825869 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:35827672 original size:20 final size:20
Alignment explanation
Indices: 35827625--35827672 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
35827615 AGTAAGCTCG
35827625 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
35827645 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
35827665 GTTGAGCT
1 GTTGAGCT
35827673 GGACGGTCTC
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:35828055 original size:20 final size:20
Alignment explanation
Indices: 35827999--35828055 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
35827989 AGCTCCGTTT
* *
35827999 AGCTCATATCCAGCTCACTCG
1 AGCTCA-ATTCAGCTCACTCA
* *
35828020 AGCTCAAGTCAACTCACTCA
1 AGCTCAATTCAGCTCACTCA
35828040 AGCTCAATTCAGCTCA
1 AGCTCAATTCAGCTCA
35828056 ATCTTAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 24 0.80
21 6 0.20
ACGTcount: A:0.30, C:0.35, G:0.12, T:0.23
Consensus pattern (20 bp):
AGCTCAATTCAGCTCACTCA
Found at i:35830746 original size:48 final size:47
Alignment explanation
Indices: 35830667--35830772 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
35830657 GAGTGTCATG
*
35830667 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
35830715 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
35830763 GAAAAAGAAA
1 GAAAAAGAAA
35830773 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:35832489 original size:20 final size:20
Alignment explanation
Indices: 35832433--35832489 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
35832423 AGCTCCGTTT
* *
35832433 AGCTCATTTCCAGCTCACTCG
1 AGCTCAATT-CAGCTCACTCA
* *
35832454 AGCTCAAGTCAACTCACTCA
1 AGCTCAATTCAGCTCACTCA
35832474 AGCTCAATTCAGCTCA
1 AGCTCAATTCAGCTCA
35832490 ATCTTAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.28, C:0.35, G:0.12, T:0.25
Consensus pattern (20 bp):
AGCTCAATTCAGCTCACTCA
Found at i:35844015 original size:23 final size:22
Alignment explanation
Indices: 35843963--35844015 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
35843953 TCCACGTCTT
*
35843963 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
35843985 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
35844008 TTTCTTTT
1 TTTCTTTT
35844016 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:35847350 original size:10 final size:10
Alignment explanation
Indices: 35847335--35847396 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
35847325 TTTGAACCGT
*
35847335 TACCAATTCG
1 TACCAATTCA
*
35847345 TACCAAATACCA
1 TACC-AAT-TCA
*
35847357 TACCATTTCA
1 TACCAATTCA
35847367 TACCAATTCCA
1 TACCAATT-CA
*
35847378 TACCATTTCA
1 TACCAATTCA
35847388 TACCAATTC
1 TACCAATTC
35847397 CCAAATACCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 23 0.55
11 14 0.33
12 5 0.12
ACGTcount: A:0.35, C:0.32, G:0.02, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:35847380 original size:21 final size:21
Alignment explanation
Indices: 35847335--35847397 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
35847325 TTTGAACCGT
* * *
35847335 TACCAATTCGTACCAAATACCA
1 TACCATTTCATACC-AATTCCA
35847357 TACCATTTCATACCAATTCCA
1 TACCATTTCATACCAATTCCA
35847378 TACCATTTCATACCAATTCC
1 TACCATTTCATACCAATTCC
35847398 CAAATACCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 26 0.68
22 12 0.32
ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:35847730 original size:11 final size:11
Alignment explanation
Indices: 35847714--35847755 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
35847704 GGAGTTCGAC
35847714 AAAAAAAAA-G
1 AAAAAAAAATG
*
35847724 AAAAAAAAATT
1 AAAAAAAAATG
*
35847735 AAAAAAAATTG
1 AAAAAAAAATG
35847746 AAAAAAAAAT
1 AAAAAAAAAT
35847756 TACATACGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:35847739 original size:12 final size:11
Alignment explanation
Indices: 35847714--35847757 Score: 56
Period size: 10 Copynumber: 4.1 Consensus size: 11
35847704 GGAGTTCGAC
*
35847714 AAAAAAAAA-G
1 AAAAAAAAATT
35847724 AAAAAAAAATT
1 AAAAAAAAATT
35847735 -AAAAAAAATT
1 AAAAAAAAATT
35847745 GAAAAAAAAATT
1 -AAAAAAAAATT
35847757 A
1 A
35847758 CATACGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 19 0.63
11 1 0.03
12 10 0.33
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:35847739 original size:22 final size:22
Alignment explanation
Indices: 35847714--35847757 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35847704 GGAGTTCGAC
35847714 AAAAAAAAAGAAAAAAAAATTA
1 AAAAAAAAAGAAAAAAAAATTA
**
35847736 AAAAAAATTGAAAAAAAAATTA
1 AAAAAAAAAGAAAAAAAAATTA
35847758 CATACGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (22 bp):
AAAAAAAAAGAAAAAAAAATTA
Found at i:35848556 original size:15 final size:15
Alignment explanation
Indices: 35848524--35848557 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35848514 GTTCAATGAA
*
35848524 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
35848539 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
35848554 GAGG
1 GAGG
35848558 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:35852253 original size:121 final size:124
Alignment explanation
Indices: 35852028--35852276 Score: 312
Period size: 121 Copynumber: 2.0 Consensus size: 124
35852018 AACCCCAAAG
*
35852028 AAAATTCTGCACTCAACAAATCTGAAATTTGATAGAAAAAATAATAATAAGATGTTTTTACAAAG
1 AAAATTCTGCACTCAACAAATCTGAAATTTGATAG---AAATAATAATAAGATGTTTGTACAAAG
* * *
35852093 GGTGGCTGGCCAATGCTTATATAGGCCTCCAACAAATCCTAATCTCACAAGTAACTAATAAA
63 GGTGGCCGGCCAATGCTTAAATAGGCCTCCAACAAATCCTAATCTAACAAGTAACTAATAAA
* ** *
35852155 AAAATTCTGCTCTCAACAAATCTGAAATTT-A-AG-AATAATTCTAAG-TGTTATGTACAAGGGG
1 AAAATTCTGCACTCAACAAATCTGAAATTTGATAGAAATAATAATAAGATGTT-TGTACAAAGGG
**
35852216 TGGCCGGCC-ATGCCTTTAAATAGGCCT-CAAGTAATCCTAATCTAACAAGTAACTAATAAA
65 TGGCCGGCCAATG-C-TTAAATAGGCCTCCAACAAATCCTAATCTAACAAGTAACTAATAAA
35852276 A
1 A
35852277 TTAAACCTAA
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
120 7 0.06
121 59 0.54
122 11 0.10
125 2 0.02
126 1 0.01
127 29 0.27
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (124 bp):
AAAATTCTGCACTCAACAAATCTGAAATTTGATAGAAATAATAATAAGATGTTTGTACAAAGGGT
GGCCGGCCAATGCTTAAATAGGCCTCCAACAAATCCTAATCTAACAAGTAACTAATAAA
Found at i:35854325 original size:20 final size:20
Alignment explanation
Indices: 35854302--35854348 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
35854292 AGGTTAAGAT
*
35854302 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
35854322 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
35854342 TGAGCTG
1 TGAGCTG
35854349 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:35855002 original size:13 final size:13
Alignment explanation
Indices: 35854984--35855008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35854974 TAACCTACAA
35854984 AATTAAATAACAT
1 AATTAAATAACAT
35854997 AATTAAATAACA
1 AATTAAATAACA
35855009 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:35855256 original size:21 final size:21
Alignment explanation
Indices: 35855232--35855271 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35855222 GAAAAAGGAA
*
35855232 TGAGCTGAAACGAGCTAAATT
1 TGAGCTCAAACGAGCTAAATT
35855253 TGAGCTCAAACGAGCTAAA
1 TGAGCTCAAACGAGCTAAA
35855272 ACGAGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (21 bp):
TGAGCTCAAACGAGCTAAATT
Found at i:35857298 original size:30 final size:30
Alignment explanation
Indices: 35857264--35857360 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
35857254 AGCTCACTCC
35857264 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
35857294 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
35857324 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
35857354 TAGCTCA
1 TAGCTCA
35857361 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:35859099 original size:13 final size:12
Alignment explanation
Indices: 35859081--35859118 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
35859071 AAAGGAGAAG
35859081 AAATTCAGAAAAA
1 AAATTC-GAAAAA
35859094 AAATTC-AAAAA
1 AAATTCGAAAAA
35859105 AAA-TCGAAAAA
1 AAATTCGAAAAA
35859116 AAA
1 AAA
35859119 GGAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.08
11 16 0.67
13 6 0.25
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (12 bp):
AAATTCGAAAAA
Found at i:35859105 original size:10 final size:11
Alignment explanation
Indices: 35859088--35859138 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 11
35859078 AAGAAATTCA
35859088 GAAAAAAAATTC
1 GAAAAAAAA-TC
35859100 -AAAAAAAATC
1 GAAAAAAAATC
*
35859110 GAAAAAAAA-G
1 GAAAAAAAATC
*
35859120 GAAAAAAAA-G
1 GAAAAAAAATC
35859130 GAAAAAAAA
1 GAAAAAAAA
35859139 AAGTGACAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 21 0.57
11 16 0.43
ACGTcount: A:0.78, C:0.04, G:0.12, T:0.06
Consensus pattern (11 bp):
GAAAAAAAATC
Found at i:35859139 original size:11 final size:10
Alignment explanation
Indices: 35859100--35859138 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
35859090 AAAAAAATTC
*
35859100 AAAAAAAATCG
1 AAAAAAAA-GG
35859111 AAAAAAAAGG
1 AAAAAAAAGG
35859121 AAAAAAAAGG
1 AAAAAAAAGG
35859131 AAAAAAAA
1 AAAAAAAA
35859139 AAGTGACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:35859149 original size:13 final size:12
Alignment explanation
Indices: 35859111--35859152 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 12
35859101 AAAAAAATCG
35859111 AAAAAAAAGG--
1 AAAAAAAAGGAA
35859121 AAAAAAAAGGAA
1 AAAAAAAAGGAA
35859133 AAAAAAAAGTGACA
1 AAAAAAAAG-GA-A
35859147 AAAAAA
1 AAAAAA
35859153 TCGAGTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.36
12 9 0.32
13 2 0.07
14 7 0.25
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGGAA
Found at i:35859150 original size:45 final size:45
Alignment explanation
Indices: 35859101--35859191 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 45
35859091 AAAAAATTCA
*
35859101 AAAAAAATCGA-AAAAAAAGGAAAAA-AAAGGAAAAAAAAAAGTGAC
1 AAAAAAATCGATAAAAAAAAGAAAAAGAAA--AAAAAAAAAAGTGAC
*
35859146 AAAAAAATCGAGTTAAAAAAAAGAAAAAGAAAAAAAACAAAAGTGA
1 AAAAAAATCGA--TAAAAAAAAGAAAAAGAAAAAAAAAAAAAGTGA
35859192 AAAGTCTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
45 11 0.28
47 13 0.32
48 13 0.32
49 3 0.08
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (45 bp):
AAAAAAATCGATAAAAAAAAGAAAAAGAAAAAAAAAAAAAGTGAC
Found at i:35860094 original size:5 final size:5
Alignment explanation
Indices: 35860084--35860145 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
35860074 AAGAGAAAAC
* *
35860084 AAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAGA AAAGA AAA-GA
35860131 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
35860146 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.04
5 35 0.73
6 10 0.21
7 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:35860114 original size:26 final size:26
Alignment explanation
Indices: 35860084--35860145 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
35860074 AAGAGAAAAC
35860084 AAAGAAAAGAAAAGAAAAAGAAA-AA
1 AAAGAAAAGAAAAGAAAAAGAAATAA
* * *
35860109 GCAAGAGAAGAAAAGAAAATGAAATAA
1 -AAAGAAAAGAAAAGAAAAAGAAATAA
35860136 AAAGAAAAGA
1 AAAGAAAAGA
35860146 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (26 bp):
AAAGAAAAGAAAAGAAAAAGAAATAA
Found at i:35860146 original size:31 final size:30
Alignment explanation
Indices: 35860072--35860147 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
35860062 TACATTCTTG
* *
35860072 TAAAGAGAAAACA-AAGAAAAGAAAAGAAA
1 TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
35860101 -AAGAAA-AAGCAAGAGAAGAAAAGAAAATGAAA
1 TAA-AAAGAA--AAGAGAAGAAAAGAAAA-GAAA
35860133 TAAAAAGAAAAGAGA
1 TAAAAAGAAAAGAGA
35860148 GGCAAGAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
28 4 0.11
29 2 0.05
30 3 0.08
31 18 0.47
32 7 0.18
33 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.04
Consensus pattern (30 bp):
TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
Found at i:35860225 original size:11 final size:12
Alignment explanation
Indices: 35860193--35860223 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35860183 TTGAGAGAAC
35860193 TTGAAAAAGCCT
1 TTGAAAAAGCCT
35860205 TTGAAAAAGCCT
1 TTGAAAAAGCCT
35860217 TTGAAAA
1 TTGAAAA
35860224 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:35862504 original size:29 final size:30
Alignment explanation
Indices: 35862403--35862498 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
35862393 AGCTCACTCC
35862403 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * *
35862433 TAGCTCAACTTCAGCTTA-GAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
35862462 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
35862492 TAGCTCA
1 TAGCTCA
35862499 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
29 24 0.47
30 27 0.53
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:35865951 original size:19 final size:20
Alignment explanation
Indices: 35865927--35865967 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
35865917 AATCTCATTT
35865927 TCTTTTCTTTGTTT-TTCTC
1 TCTTTTCTTTGTTTCTTCTC
35865946 TCTTTTCTTTGTTTCTTCTC
1 TCTTTTCTTTGTTTCTTCTC
35865966 TC
1 TC
35865968 GATTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTTCTTTGTTTCTTCTC
Found at i:35875706 original size:22 final size:22
Alignment explanation
Indices: 35875652--35875717 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
35875642 GGTATTTGGG
* *
35875652 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
*
35875673 AATTCGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
35875695 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
35875718 TCAAAAGGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 18 0.49
22 14 0.38
23 5 0.14
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:35877156 original size:29 final size:29
Alignment explanation
Indices: 35877090--35877146 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
35877080 GATTCAAAGA
*
35877090 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
35877119 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
35877147 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:35882643 original size:17 final size:18
Alignment explanation
Indices: 35882621--35882661 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
35882611 CGTTTCTTTT
35882621 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
35882638 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
35882656 T-TTTTG
1 TCTTTTG
35882662 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:35882645 original size:24 final size:25
Alignment explanation
Indices: 35882590--35882645 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
35882580 ACAAACAAAT
* *
35882590 TCTTTTTTCATTTTCATCACTCGTT
1 TCTTTTTTCATTTTAATCACTCGTC
35882615 TC-TTTTTC-TTTTGAATCACTC-TC
1 TCTTTTTTCATTTT-AATCACTCGTC
35882638 TCTTTTTT
1 TCTTTTTT
35882646 ATCACTCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 7 0.26
24 18 0.67
25 2 0.07
ACGTcount: A:0.11, C:0.23, G:0.04, T:0.62
Consensus pattern (25 bp):
TCTTTTTTCATTTTAATCACTCGTC
Found at i:35884872 original size:15 final size:15
Alignment explanation
Indices: 35884852--35884880 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35884842 CTAGACCGTA
35884852 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
35884867 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
35884881 CAACTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TGCAATTTTTTTTTT
Found at i:35884877 original size:12 final size:13
Alignment explanation
Indices: 35884860--35884892 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
35884850 TATGCAATTT
35884860 TTTTTTTTGCAA-
1 TTTTTTTTGCAAC
*
35884872 TTTTTTTTTCAAC
1 TTTTTTTTGCAAC
35884885 TTTTTTTT
1 TTTTTTTT
35884893 TGAAGCTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTTTTTGCAAC
Found at i:35884877 original size:13 final size:14
Alignment explanation
Indices: 35884859--35884894 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
35884849 GTATGCAATT
35884859 TTTTTTTTTGCAA-
1 TTTTTTTTTGCAAC
35884872 TTTTTTTTT-CAAC
1 TTTTTTTTTGCAAC
35884885 TTTTTTTTTG
1 TTTTTTTTTG
35884895 AAGCTACGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.11, C:0.08, G:0.06, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTGCAAC
Found at i:35888524 original size:30 final size:28
Alignment explanation
Indices: 35888471--35888526 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
35888461 TTCTTCCACG
* *
35888471 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
35888499 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
35888527 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:35888638 original size:12 final size:12
Alignment explanation
Indices: 35888621--35888654 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35888611 TGTTCTTTTT
*
35888621 CTTTTTCAATGG
1 CTTTTTCAATGA
35888633 CTTTTTCAATGA
1 CTTTTTCAATGA
*
35888645 CTTTCTCAAT
1 CTTTTTCAAT
35888655 CTCTTTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.50
Consensus pattern (12 bp):
CTTTTTCAATGA
Found at i:35889603 original size:13 final size:12
Alignment explanation
Indices: 35889567--35889599 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
35889557 TCAGATTTTG
35889567 TTTTTTTTTGAA
1 TTTTTTTTTGAA
35889579 TTTTTTTTTGAA
1 TTTTTTTTTGAA
35889591 TTTTTTTTT
1 TTTTTTTTT
35889600 TGAAACTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:35894417 original size:20 final size:20
Alignment explanation
Indices: 35894371--35894417 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
35894361 AGCTCGTTTC
*
35894371 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
35894391 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
35894411 CAGCTCA
1 CAGCTCA
35894418 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:35895863 original size:29 final size:29
Alignment explanation
Indices: 35895797--35895853 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
35895787 GATTCAAAGA
*
35895797 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
35895826 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
35895854 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:35898765 original size:10 final size:10
Alignment explanation
Indices: 35898750--35898811 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
35898740 TTTGAACCAT
*
35898750 TACCAATTCG
1 TACCAATTCA
*
35898760 TACCAAATACCA
1 TACC-AAT-TCA
*
35898772 TACCATTTCA
1 TACCAATTCA
35898782 TACCAATTCCA
1 TACCAATT-CA
* *
35898793 TACCATTTCG
1 TACCAATTCA
35898803 TACCAATTC
1 TACCAATTC
35898812 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Done.