Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 26
Found at i:2486013 original size:30 final size:28
Alignment explanation
Indices: 2485991--2486045 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2485981 CGGTGATTGA
*
2485991 TATATTTACCGATCTAACACCGGTCAGAT
1 TATATTTTCCGATCTAACACCGGT-AGAT
* *
2486020 TATATTTTCTGATCTAACACCCGTAG
1 TATATTTTCCGATCTAACACCGGTAG
2486046 CAGTAAAGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (28 bp):
TATATTTTCCGATCTAACACCGGTAGAT
Found at i:2487599 original size:35 final size:34
Alignment explanation
Indices: 2487514--2487600 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2487504 ATTTGGTATT
*
2487514 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
2487548 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
2487586 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2487601 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:2489878 original size:111 final size:111
Alignment explanation
Indices: 2489741--2490073 Score: 585
Period size: 111 Copynumber: 3.0 Consensus size: 111
2489731 ATTACAAAAA
2489741 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
2489806 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGATATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
2489852 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
2489917 AATTAAAACGTTCAAATGTTACCATATCAGCAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
2489963 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCTACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
2490028 AATTAAAACGTTAAAATGTTACTGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
2490074 ATGATTTCTA
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 210 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:2490201 original size:12 final size:10
Alignment explanation
Indices: 2490188--2490228 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
2490178 TTTAAAAAGA
*
2490188 GAGAGTATTT
1 GAGAGAATTT
2490198 GAGAGAAATTT
1 GAGAG-AATTT
2490209 G-GAGAATTT
1 GAGAGAATTT
2490218 GAGAGAATTT
1 GAGAGAATTT
2490228 G
1 G
2490229 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 6 0.21
10 17 0.61
11 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:2490410 original size:50 final size:50
Alignment explanation
Indices: 2490350--2490474 Score: 130
Period size: 49 Copynumber: 2.5 Consensus size: 50
2490340 AGATACACAG
*
2490350 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGTCAAATCACC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
** * ** * *
2490400 GTAT-GTCGCGGGGCA-GGGGCGTGCTATATTCATGTGGCGCCAAATCAGC
1 GTATAG-CGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
*
2490449 GTATAGCGC-GATTCAGGGGGCACGCT
1 GTATAGCGCGGA-TCAGGGGGCGCGCT
2490475 TTACTGCTAC
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
48 1 0.02
49 38 0.64
50 20 0.34
ACGTcount: A:0.20, C:0.26, G:0.35, T:0.19
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:2494895 original size:23 final size:23
Alignment explanation
Indices: 2494868--2494913 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2494858 GACATAGTTG
2494868 GGTCGGGTGAG-CGGGTCAAGTCA
1 GGTCGGGTG-GTCGGGTCAAGTCA
*
2494891 GGTCGGGTGGTCGGGTCAGGTCA
1 GGTCGGGTGGTCGGGTCAAGTCA
2494914 AACCTGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.13, C:0.17, G:0.50, T:0.20
Consensus pattern (23 bp):
GGTCGGGTGGTCGGGTCAAGTCA
Found at i:2501814 original size:7 final size:7
Alignment explanation
Indices: 2501802--2501841 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
2501792 CGATCAACGG
2501802 CGGTCAA
1 CGGTCAA
2501809 CGGTCAA
1 CGGTCAA
2501816 CGGTCAA
1 CGGTCAA
2501823 CGGCGGTCAA
1 ---CGGTCAA
2501833 CGGTCAA
1 CGGTCAA
2501840 CG
1 CG
2501842 ACGGTCAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 23 0.77
10 7 0.23
ACGTcount: A:0.25, C:0.30, G:0.33, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:2501815 original size:17 final size:17
Alignment explanation
Indices: 2501808--2501851 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
2501798 ACGGCGGTCA
2501808 ACGGTCAACGGTCAACG
1 ACGGTCAACGGTCAACG
*
2501825 GCGGTCAACGGTCAACG
1 ACGGTCAACGGTCAACG
2501842 ACGGTCAACG
1 ACGGTCAACG
2501852 ATCACGATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.27, C:0.30, G:0.32, T:0.11
Consensus pattern (17 bp):
ACGGTCAACGGTCAACG
Found at i:2501829 original size:10 final size:10
Alignment explanation
Indices: 2501784--2501851 Score: 61
Period size: 10 Copynumber: 6.7 Consensus size: 10
2501774 AAAGTCAACA
2501784 GTCAACGGCG
1 GTCAACGGCG
*
2501794 ATCAACGGCG
1 GTCAACGGCG
2501804 GTCAACGGTCAACG
1 GTCAACGG----CG
2501818 GTCAACGGCG
1 GTCAACGGCG
2501828 GTCAA---CG
1 GTCAACGGCG
*
2501835 GTCAACGACG
1 GTCAACGGCG
2501845 GTCAACG
1 GTCAACG
2501852 ATCACGATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
7 7 0.14
10 32 0.65
14 10 0.20
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.12
Consensus pattern (10 bp):
GTCAACGGCG
Found at i:2506925 original size:11 final size:11
Alignment explanation
Indices: 2506909--2506934 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2506899 CAATTACAAA
2506909 ATATTTAAAAT
1 ATATTTAAAAT
2506920 ATATTTAAAAT
1 ATATTTAAAAT
2506931 ATAT
1 ATAT
2506935 GATAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTTAAAAT
Found at i:2511369 original size:483 final size:484
Alignment explanation
Indices: 2510430--2511400 Score: 1818
Period size: 483 Copynumber: 2.0 Consensus size: 484
2510420 GTTGCAGGAA
2510430 ATCCATTTTACAACTTGGCATCATGTCCTGTTAAATAAAGGTTTTTACGAGTGTTAGACACGTCT
1 ATCCATTTTACAACTTGGCATCATGTCCTGTTAAATAAAGGTTTTTACGAGTGTTAGACACGTCT
* * *
2510495 GACACAGACATGCTCTAAGGTGACAAACTCTGAACTGCACAGCAAAGAACATGAAGAGAACAAAA
66 GACACAGACATGCTCAAACGTGACAAACTATGAACTGCACAGCAAAGAACATGAAGAGAACAAAA
* *
2510560 AGGTAAAATGATCAAACCGCCTGAACAAGCCCAAACATGACAGGACATGCGATTTGCACTTTTTC
131 AGGTAAAATGATCAAAACGCCAGAACAAGCCCAAACATGACAGGACATGCGATTTGCACTTTTTC
*
2510625 CCTTGAATATGGAGTCAACAATGAACAAAATGTTAAATCCTAAGGAACTCAAATGCTTAAAATCA
196 CCTTGAATATGGAGTCAACAATGAAAAAAATGTTAAATCCTAAGGAACTCAAATGCTTAAAATCA
2510690 ATAAAGAAAACAAAGAAAACAGAAAGTGAAACAATAATGGATAGTTAAATACTGGAGAAACCGCG
261 ATAAAGAAAACAAAGAAAACAGAAAGTGAAACAATAATGGATAGTTAAATACTGGAGAAACCGCG
*
2510755 AAGTATCAACGTAAATATGTTACAGGATTGAGAACGATAGAGAAAGAAAGAAAGCAAAGATGGTT
326 AAGTATCAACGTAAATATGTTACAGGATTGAGAACGATAAAGAAAGAAAGAAAGCAAAGATGGTT
2510820 CAAAATGAGATAACTATGAGAAGACATTTACTATTGAATAATTCATAGCAGATAGTTTAAGGTCT
391 CAAAATGAGATAACTATGAGAAGACATTTACTATTGAATAATTCATAGCAGATAGTTTAAGGTCT
2510885 CTTCTAAAACTTTCAACTTGAGCTATTTG
456 CTTCTAAAACTTTCAACTTGAGCTATTTG
2510914 ATCCATTTTACAACTTGGCATCATGTCCTGTT-AATAAAGGTTTTTACGAGTGTTAGACACGTCT
1 ATCCATTTTACAACTTGGCATCATGTCCTGTTAAATAAAGGTTTTTACGAGTGTTAGACACGTCT
*
2510978 GACATAGACATGCTCAAACGTGACAAACTATGAACTGCACAGCAAAGAACATGAAGAGAACAAAA
66 GACACAGACATGCTCAAACGTGACAAACTATGAACTGCACAGCAAAGAACATGAAGAGAACAAAA
* * *
2511043 AGGTAAAATGATCAAAACGCCAGAACAAGCCCCAACATGACAGGACATGTGATTTGCATTTTTTC
131 AGGTAAAATGATCAAAACGCCAGAACAAGCCCAAACATGACAGGACATGCGATTTGCACTTTTTC
2511108 CCTTGAATATGGAGTCAACAATGAAAAAAATGTTAAATCCTAAGGAACTCAAATGCTTAAAATCA
196 CCTTGAATATGGAGTCAACAATGAAAAAAATGTTAAATCCTAAGGAACTCAAATGCTTAAAATCA
2511173 ATAAAGAAAACAAAGAAAACAGAAAGTGAAACAATAATGGATAGTTAAATACTGGAGAAACCGCG
261 ATAAAGAAAACAAAGAAAACAGAAAGTGAAACAATAATGGATAGTTAAATACTGGAGAAACCGCG
2511238 AAGTATCAACGTAAATATGTTACAGGATTGAGAACGATAAAGAAAGAAAGAAAGCAAAGATGGTT
326 AAGTATCAACGTAAATATGTTACAGGATTGAGAACGATAAAGAAAGAAAGAAAGCAAAGATGGTT
*
2511303 CAAAATGAGATAACTATGAGAAGACATTTACTATTGAATAATTCATAGCAGATTGTTTAAGGTCT
391 CAAAATGAGATAACTATGAGAAGACATTTACTATTGAATAATTCATAGCAGATAGTTTAAGGTCT
*
2511368 CTTCTAAAACTTTCAGCTTGAGCTATTTG
456 CTTCTAAAACTTTCAACTTGAGCTATTTG
2511397 ATCC
1 ATCC
2511401 TAAAGAATTT
Statistics
Matches: 474, Mismatches: 13, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
483 442 0.93
484 32 0.07
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (484 bp):
ATCCATTTTACAACTTGGCATCATGTCCTGTTAAATAAAGGTTTTTACGAGTGTTAGACACGTCT
GACACAGACATGCTCAAACGTGACAAACTATGAACTGCACAGCAAAGAACATGAAGAGAACAAAA
AGGTAAAATGATCAAAACGCCAGAACAAGCCCAAACATGACAGGACATGCGATTTGCACTTTTTC
CCTTGAATATGGAGTCAACAATGAAAAAAATGTTAAATCCTAAGGAACTCAAATGCTTAAAATCA
ATAAAGAAAACAAAGAAAACAGAAAGTGAAACAATAATGGATAGTTAAATACTGGAGAAACCGCG
AAGTATCAACGTAAATATGTTACAGGATTGAGAACGATAAAGAAAGAAAGAAAGCAAAGATGGTT
CAAAATGAGATAACTATGAGAAGACATTTACTATTGAATAATTCATAGCAGATAGTTTAAGGTCT
CTTCTAAAACTTTCAACTTGAGCTATTTG
Found at i:2514322 original size:6 final size:6
Alignment explanation
Indices: 2514311--2514335 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2514301 TTCTCATTGG
2514311 TCCATT TCCATT TCCATT TCCATT T
1 TCCATT TCCATT TCCATT TCCATT T
2514336 AACTGGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TCCATT
Found at i:2519259 original size:6 final size:6
Alignment explanation
Indices: 2519235--2519272 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
2519225 AAAATGGTAA
2519235 AATTTC ACA-TTC TAATTTC AATTTC AATTTC AATTTC A
1 AATTTC A-ATTTC -AATTTC AATTTC AATTTC AATTTC A
2519273 TCCCTCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (6 bp):
AATTTC
Found at i:2520026 original size:13 final size:13
Alignment explanation
Indices: 2520008--2520033 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2519998 AATGAATATA
2520008 ATATTCATTTAAT
1 ATATTCATTTAAT
2520021 ATATTCATTTAAT
1 ATATTCATTTAAT
2520034 GAGAAATGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTCATTTAAT
Found at i:2523501 original size:2 final size:2
Alignment explanation
Indices: 2523494--2523530 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2523484 AGGAGACTTT
2523494 TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2523531 AAGCTATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2524683 original size:81 final size:80
Alignment explanation
Indices: 2524566--2525268 Score: 987
Period size: 80 Copynumber: 8.7 Consensus size: 80
2524556 TCAAAATTGT
* * * * * *
2524566 TTAATTGTTCATCTAACTGTCATAATTGATATCTTTCTGTCAAATACACAACTAGGCCATTATTC
1 TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCC-TTATTC
2524631 TTTTACTCAACGGTAC
65 TTTTACTCAACGGTAC
* *
2524647 TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCTTATTCT
1 TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTTATTCT
2524712 TTTACTCAACGGTAC
66 TTTACTCAACGGTAC
* *
2524727 TTAA-CGGTTCATGTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTTATTC
1 TTAATC-GTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTTATTC
*
2524791 TTTTACTCAACGATAC
65 TTTTACTCAACGGTAC
*
2524807 TTAATCGTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCATTATTC
1 TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCC-TTATTC
2524872 TTTTACTCAACGGTAC
65 TTTTACTCAACGGTAC
* * * * *
2524888 TTAA-CAGTTCATTTAACTGACATAATTGATACATTTCTGTTAAATGCACAGCTAGGCCTTATTC
1 TTAATC-GTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTTATTC
*
2524952 CTTTACTCAACGGTAC
65 TTTTACTCAACGGTAC
*
2524968 TTAATCGTTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGCTAGGCCATTATTC
1 TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCC-TTATTC
2525033 TTTTACTCAACGGTAC
65 TTTTACTCAACGGTAC
* * * * * * * **
2525049 TTAACCGTTCATCTAACTGACATAATTGACATCTTTCTATCAAATGTATAGTTATACCATTATTC
1 TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCC-TTATTC
* *
2525114 TTTTACTTAAAGGTAC
65 TTTTACTCAACGGTAC
* * * * *
2525130 TGAACCGTTCATCTAACTGGCATAATTGACATCTTTCTATCAAATGCACAGTTAGGCCTTATTCT
1 TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTTATTCT
2525195 TTTACTCAACGGTAC
66 TTTACTCAACGGTAC
* * * *
2525210 TTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATACACAGTTAGGCCT
1 TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCT
2525269 CAAAGGCACT
Statistics
Matches: 566, Mismatches: 50, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
79 1 0.00
80 296 0.52
81 269 0.48
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (80 bp):
TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTTATTCT
TTTACTCAACGGTAC
Found at i:2524872 original size:161 final size:160
Alignment explanation
Indices: 2524572--2525268 Score: 1016
Period size: 161 Copynumber: 4.3 Consensus size: 160
2524562 TTGTTTAATT
* * * * *
2524572 GTTCATCTAACTGTCATAATTGATATCTTTCTGTCAAATACACAACTAGGCCATTATTCTTTTAC
1 GTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCC-TTATTCTTTTAC
* *
2524637 TCAACGGTACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAG
65 TCAACGGTACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAG
*
2524702 GCCTTATTCTTTTACTCAACGGTACTTAACG
130 GCCTTATTCTTTTACTCAACGGTACTTAACC
* * *
2524733 GTTCATGTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTTATTCTTTTACT
1 GTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTTATTCTTTTACT
* *
2524798 CAACGATACTTAATCGTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG
66 CAACGGTACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG
*
2524863 CCATTATTCTTTTACTCAACGGTACTTAACA
131 CC-TTATTCTTTTACTCAACGGTACTTAACC
* * * * *
2524894 GTTCATTTAACTGACATAATTGATACATTTCTGTTAAATGCACAGCTAGGCCTTATTCCTTTACT
1 GTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTTATTCTTTTACT
*
2524959 CAACGGTACTTAATCGTTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGCTAGG
66 CAACGGTACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG
2525024 CCATTATTCTTTTACTCAACGGTACTTAACC
131 CC-TTATTCTTTTACTCAACGGTACTTAACC
* * * * * **
2525055 GTTCATCTAACTGACATAATTGACATCTTTCTATCAAATGTATAGTTATACCATTATTCTTTTAC
1 GTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCC-TTATTCTTTTAC
* * * * * * *
2525120 TTAAAGGTACTGAACCGTTCATCTAACTGGCATAATTGACATCTTTCTATCAAATGCACAGTTAG
65 TCAACGGTACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAG
2525185 GCCTTATTCTTTTACTCAACGGTACTTAACC
130 GCCTTATTCTTTTACTCAACGGTACTTAACC
* * * *
2525216 GTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATACACAGTTAGGCCT
1 GTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCT
2525269 CAAAGGCACT
Statistics
Matches: 486, Mismatches: 48, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
160 77 0.16
161 336 0.69
162 73 0.15
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (160 bp):
GTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTTATTCTTTTACT
CAACGGTACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG
CCTTATTCTTTTACTCAACGGTACTTAACC
Found at i:2525308 original size:68 final size:68
Alignment explanation
Indices: 2525199--2525340 Score: 203
Period size: 68 Copynumber: 2.1 Consensus size: 68
2525189 TATTCTTTTA
* * * *
2525199 CTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATACACAGTTA
1 CTCAAAGGCACTTAACCGTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATACACAATTA
2525264 GGC
66 GGC
* * * *
2525267 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAATTA
1 CTCAAAGGCACTTAACCGTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATACACAATTA
*
2525332 TGC
66 GGC
2525335 CTCAAA
1 CTCAAA
2525341 TCTTTTAACT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (68 bp):
CTCAAAGGCACTTAACCGTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATACACAATTA
GGC
Found at i:2525620 original size:59 final size:57
Alignment explanation
Indices: 2525557--2525774 Score: 271
Period size: 59 Copynumber: 3.8 Consensus size: 57
2525547 TTCCCATATA
* * * *
2525557 AAAATTCTTACACTTAATATGAATTACTTATCATTTTAGCACACAAGGTGCCCAATACT
1 AAAATTCATACACTTAGTATGAATTTCTTAT-ATTTTAGCACACAA-GTGCCCTATACT
2525616 AAAATTCATACACTTAGTATGAATTTCTTAATATTTTAGCACACGAAGTGCCCTATA-T
1 AAAATTCATACACTTAGTATGAATTTCTT-ATATTTTAGCACAC-AAGTGCCCTATACT
* * * *
2525674 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGTACACAAAGTGCCCTATACG
1 -AAAATTCATACACTTAGTATGAATTTCTT-ATATTTTAGCACAC-AAGTGCCCTATACT
*
2525734 GAAATTCATACACTTAGTATGAATTTCTTA-ATTTT-GCACAC
1 AAAATTCATACACTTAGTATGAATTTCTTATATTTTAGCACAC
2525775 TTAGTGTCAT
Statistics
Matches: 145, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
56 5 0.03
57 5 0.03
58 2 0.01
59 129 0.89
60 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (57 bp):
AAAATTCATACACTTAGTATGAATTTCTTATATTTTAGCACACAAGTGCCCTATACT
Found at i:2526454 original size:31 final size:31
Alignment explanation
Indices: 2526419--2526603 Score: 271
Period size: 31 Copynumber: 6.0 Consensus size: 31
2526409 CCCGAAGGTC
* *
2526419 CAGTCCATATATTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
* *
2526450 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
*
2526481 CAGTCCATATGTCCCGAAGAACACAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
* * *
2526512 CAGTCCATATGTTCCGATGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
*
2526543 CGGTCCATATGTCCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
* *
2526574 CAGTCCAAATATCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
2526604 CCCTCGACTC
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 138 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:2526779 original size:22 final size:22
Alignment explanation
Indices: 2526753--2526819 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
2526743 GTAAACATCT
*
2526753 ATCTCATATCATATAACATGTA
1 ATCTCATATCATATAACATATA
*
2526775 ATCTCATATGCATGTAATCATATA
1 ATCTCATAT-CATATAA-CATATA
* * *
2526799 A-ATCGTATCATATAACTTATA
1 ATCTCATATCATATAACATATA
2526820 TCATTTCTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
21 5 0.14
22 15 0.41
23 11 0.30
24 6 0.16
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (22 bp):
ATCTCATATCATATAACATATA
Found at i:2527282 original size:20 final size:20
Alignment explanation
Indices: 2527253--2527328 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
2527243 ATTTAAGGTA
2527253 TGTATCGGTACACTCCATAG
1 TGTATCGGTACACTCCATAG
* * *
2527273 TGTATTGGTACATTCCTTAACTGG
1 TGTATCGGTACACTCC---A-TAG
*
2527297 TGTATTGGTACACTACC-TA-
1 TGTATCGGTACACT-CCATAG
2527316 TGTATCGGTACAC
1 TGTATCGGTACAC
2527329 AAATTACATT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
19 12 0.27
20 15 0.33
23 1 0.02
24 15 0.33
25 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
TGTATCGGTACACTCCATAG
Found at i:2530796 original size:31 final size:31
Alignment explanation
Indices: 2530773--2530942 Score: 259
Period size: 31 Copynumber: 5.5 Consensus size: 31
2530763 CATATATTCT
*
2530773 GAAGAACATAGGTAATCAGTCCATATGTTCC
1 GAAGAACATAGGTAATCAGTCCATATGTCCC
* *
2530804 GAATAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAATCAGTCCATATGTCCC
* *
2530835 GAAGAACATAGGTAATAAGTCCATATGTTCC
1 GAAGAACATAGGTAATCAGTCCATATGTCCC
* *
2530866 GAAGAACATAGGTAAACAGTTCATATGTCCC
1 GAAGAACATAGGTAATCAGTCCATATGTCCC
* *
2530897 GAAAAACATAGGTAATCAGTCTATATGTCCC
1 GAAGAACATAGGTAATCAGTCCATATGTCCC
2530928 GAAGAACATAGGTAA
1 GAAGAACATAGGTAA
2530943 CCTCGACTCT
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 123 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (31 bp):
GAAGAACATAGGTAATCAGTCCATATGTCCC
Found at i:2530858 original size:62 final size:62
Alignment explanation
Indices: 2530773--2530942 Score: 286
Period size: 62 Copynumber: 2.7 Consensus size: 62
2530763 CATATATTCT
*
2530773 GAAGAACATAGGTAATCAGTCCATATGTTCCGAATAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAATCAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCC
* *
2530835 GAAGAACATAGGTAATAAGTCCATATGTTCCGAAGAACATAGGTAAACAGTTCATATGTCCC
1 GAAGAACATAGGTAATCAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCC
* * *
2530897 GAAAAACATAGGTAATCAGTCTATATGTCCCGAAGAACATAGGTAA
1 GAAGAACATAGGTAATCAGTCCATATGTTCCGAAGAACATAGGTAA
2530943 CCTCGACTCT
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 101 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (62 bp):
GAAGAACATAGGTAATCAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:2530923 original size:93 final size:93
Alignment explanation
Indices: 2530761--2530942 Score: 292
Period size: 93 Copynumber: 2.0 Consensus size: 93
2530751 GAAGGACCAA
* * * *
2530761 TCCATATATTCTGAAGAACATAGGTAATCAGTCCATATGTTCCGAATAACATAGGTAAACAGTCC
1 TCCATATATTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAAAACATAGGTAAACAGTCC
2530826 ATATGTCCCGAAGAACATAGGTAATAAG
66 ATATGTCCCGAAGAACATAGGTAATAAG
* * * *
2530854 TCCATATGTTCCGAAGAACATAGGTAAACAGTTCATATGTCCCGAAAAACATAGGTAATCAGTCT
1 TCCATATATTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAAAACATAGGTAAACAGTCC
2530919 ATATGTCCCGAAGAACATAGGTAA
66 ATATGTCCCGAAGAACATAGGTAA
2530943 CCTCGACTCT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 81 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (93 bp):
TCCATATATTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAAAACATAGGTAAACAGTCC
ATATGTCCCGAAGAACATAGGTAATAAG
Found at i:2535061 original size:21 final size:21
Alignment explanation
Indices: 2535035--2535130 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
2535025 AAATCTCCTT
*
2535035 AAGGACCACATATATATTCTA
1 AAGGACCACATATATGTTCTA
*
2535056 AAGGACCA-A-ATATGTGTCTCG
1 AAGGACCACATATATGT-TCT-A
* *
2535077 AATGACCACATATATGTTCCA
1 AAGGACCACATATATGTTCTA
** * *
2535098 AAGGATTACATATATGTCCTG
1 AAGGACCACATATATGTTCTA
2535119 AAGGACCACATA
1 AAGGACCACATA
2535131 GAACCCTCAA
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
19 5 0.09
20 4 0.07
21 40 0.69
22 3 0.05
23 6 0.10
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (21 bp):
AAGGACCACATATATGTTCTA
Found at i:2535126 original size:42 final size:42
Alignment explanation
Indices: 2535030--2535130 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
2535020 CATAGAAATC
* * *
2535030 TCCTTAAGGACCACATATATATTCTAAAGGACCAAATATGTG
1 TCCTGAAGGACCACATATATATTCCAAAGGACCAAATATATG
* * ** *
2535072 T-CTCGAATGACCACATATATGTTCCAAAGGATTACATATATG
1 TCCT-GAAGGACCACATATATATTCCAAAGGACCAAATATATG
2535114 TCCTGAAGGACCACATA
1 TCCTGAAGGACCACATA
2535131 GAACCCTCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
41 2 0.04
42 44 0.92
43 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (42 bp):
TCCTGAAGGACCACATATATATTCCAAAGGACCAAATATATG
Found at i:2540442 original size:18 final size:20
Alignment explanation
Indices: 2540421--2540467 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
2540411 ACCTGACCCG
2540421 AAATAATATATTTA-TTAA-
1 AAATAATATATTTATTTAAT
* *
2540439 AAATATTATTTTTATTTAAT
1 AAATAATATATTTATTTAAT
2540459 AAA-AATATA
1 AAATAATATA
2540468 GATTTAATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 12 0.52
19 8 0.35
20 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAATATATTTATTTAAT
Found at i:2540472 original size:23 final size:22
Alignment explanation
Indices: 2540429--2540472 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2540419 CGAAATAATA
* *
2540429 TATTTATTAAAAATATTATTTT
1 TATTTAATAAAAATATGATTTT
2540451 TATTTAATAAAAATATAGATTT
1 TATTTAATAAAAATAT-GATTT
2540473 AATTGGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTTAATAAAAATATGATTTT
Found at i:2542055 original size:2 final size:2
Alignment explanation
Indices: 2541996--2542042 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2541986 TTAAATAGAT
2541996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2542038 TA TA T
1 TA TA T
2542043 GACAATAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2546273 original size:20 final size:21
Alignment explanation
Indices: 2546236--2546274 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2546226 TGATTTCAAA
2546236 AATTTACTTTTCAGAAAATTT
1 AATTTACTTTTCAGAAAATTT
2546257 AATTTA-TTTTACA-AAAAT
1 AATTTACTTTT-CAGAAAAT
2546275 CATTTATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (21 bp):
AATTTACTTTTCAGAAAATTT
Found at i:2548915 original size:3 final size:3
Alignment explanation
Indices: 2548907--2548952 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
2548897 CTACAAAATG
2548907 TAA TAA TAA TTAA TAA TAA TAA -AA GTAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
2548953 ATATATCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2550131 original size:26 final size:26
Alignment explanation
Indices: 2550095--2550152 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
2550085 TGCATTCCTT
2550095 ATTTTTCCTTTATTTTCTTATATCTC
1 ATTTTTCCTTTATTTTCTTATATCTC
2550121 ATTTTTCCTTTATTTTCTTATATCTC
1 ATTTTTCCTTTATTTTCTTATATCTC
2550147 ATTTTT
1 ATTTTT
2550153 TTAATAACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.16, C:0.17, G:0.00, T:0.67
Consensus pattern (26 bp):
ATTTTTCCTTTATTTTCTTATATCTC
Found at i:2550201 original size:22 final size:23
Alignment explanation
Indices: 2550161--2550203 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2550151 TTTTAATAAC
*
2550161 TCTACCTTTATTACACGTTTTTA
1 TCTACCTTTATGACACGTTTTTA
2550184 TCTACCTTT-TGACACGTTTT
1 TCTACCTTTATGACACGTTTT
2550204 CAGTTGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.19, C:0.23, G:0.07, T:0.51
Consensus pattern (23 bp):
TCTACCTTTATGACACGTTTTTA
Found at i:2552834 original size:60 final size:60
Alignment explanation
Indices: 2552741--2552904 Score: 159
Period size: 60 Copynumber: 2.8 Consensus size: 60
2552731 TATTATTAAT
* * ** * * ** *
2552741 TAAATTGGTCCCTAAACTTTTTAATTTTATAATTTCCTCCCCAAGCTATGACTCTCATTC
1 TAAATTAGTCCCTAAACTTTTAAACATTATAATTTCATCCACAAAATATGACACTCATTC
* * * *
2552801 TAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCATAAAATATGACACTCTTTC
1 TAAATTAGTCCCTAAACTTTTAAACATTATAATTTCATCCACAAAATATGACACTCATTC
* * ** *
2552861 TAAATTAGTCCCCAAGCTTTTGGATATTATAATTTCATCC-CAAA
1 TAAATTAGTCCCTAAACTTTTAAACATTATAATTTCATCCACAAA
2552905 TTCATCCAAA
Statistics
Matches: 83, Mismatches: 21, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
59 3 0.04
60 80 0.96
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
TAAATTAGTCCCTAAACTTTTAAACATTATAATTTCATCCACAAAATATGACACTCATTC
Found at i:2553132 original size:60 final size:60
Alignment explanation
Indices: 2553029--2553141 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
2553019 TTATACATAC
*
2553029 AGTTTGGGATGAAATTGGAATGTTTAAAAAGTTTGGGGACTAATTTAGAATGAAGCTTAT
1 AGTTTGGGATGAAATTGGAATGTTTAAAAAGTTTGAGGACTAATTTAGAATGAAGCTTAT
* *
2553089 AGTTTGGGGATGAAATTGGAATG-TTCAAAAGTTTGAGGTCTAATTTAGAATGA
1 AGTTT-GGGATGAAATTGGAATGTTTAAAAAGTTTGAGGACTAATTTAGAATGA
2553142 TTATCATAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
60 32 0.65
61 17 0.35
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (60 bp):
AGTTTGGGATGAAATTGGAATGTTTAAAAAGTTTGAGGACTAATTTAGAATGAAGCTTAT
Found at i:2553151 original size:60 final size:60
Alignment explanation
Indices: 2553029--2553182 Score: 177
Period size: 60 Copynumber: 2.6 Consensus size: 60
2553019 TTATACATAC
* * *
2553029 AGTTTGGGATGAAATTGGAATGTTTAAAAAGTTTGGGGACTAATTTAGAATGAAGCTTAT
1 AGTTTGGGATGAAATTGGAATGTTTAAAAAGTTTGAGGACTAATTTAGAATGAAGATCAT
* * **
2553089 AGTTTGGGGATGAAATTGGAATG-TTCAAAAGTTTGAGGTCTAATTTAGAATGATTATCAT
1 AGTTT-GGGATGAAATTGGAATGTTTAAAAAGTTTGAGGACTAATTTAGAATGAAGATCAT
* ** *
2553149 AGTTTAGGGATGCAATTATAATATTT-AAAAGTTT
1 AGTTT-GGGATGAAATTGGAATGTTTAAAAAGTTT
2553183 ATGAATCATT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
60 61 0.76
61 19 0.24
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (60 bp):
AGTTTGGGATGAAATTGGAATGTTTAAAAAGTTTGAGGACTAATTTAGAATGAAGATCAT
Found at i:2560507 original size:71 final size:72
Alignment explanation
Indices: 2560383--2560519 Score: 224
Period size: 71 Copynumber: 1.9 Consensus size: 72
2560373 TTTTAAGTTT
* *
2560383 AATAATTAAAAAATATTTTTAAATATATTTTTTATTTAAAATACTTTAAAATATGATAATTTAGT
1 AATAATTAAAAAATATTTTTAAATATATTTTTTATTTAAAATAATTTAAAATATGATAATTCAGT
2560448 GGGCTCC
66 GGGCTCC
*
2560455 AATAATTAAAAAATATTTTTAAATATA-TTTTTATTTAAAA-AATTTGAAAATATTATAATTCAG
1 AATAATTAAAAAATATTTTTAAATATATTTTTTATTTAAAATAATTT-AAAATATGATAATTCAG
2560518 TG
65 TG
2560520 AAAAAATAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
70 4 0.07
71 30 0.49
72 27 0.44
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (72 bp):
AATAATTAAAAAATATTTTTAAATATATTTTTTATTTAAAATAATTTAAAATATGATAATTCAGT
GGGCTCC
Found at i:2566964 original size:3 final size:3
Alignment explanation
Indices: 2566956--2566988 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2566946 TTCAAAACAA
2566956 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2566989 TTACCTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2567825 original size:31 final size:31
Alignment explanation
Indices: 2567787--2567859 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
2567777 AATTTTGAAA
* *
2567787 ATTATAAAATAGTAATTATATTTATTAAGTT
1 ATTATAAAATAGTAATTATATTTATCAAATT
* * *
2567818 ATTATAAAATATTTATTGTATTTATCAAATT
1 ATTATAAAATAGTAATTATATTTATCAAATT
*
2567849 AATATAAAATA
1 ATTATAAAATA
2567860 TCCATATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (31 bp):
ATTATAAAATAGTAATTATATTTATCAAATT
Found at i:2567928 original size:32 final size:31
Alignment explanation
Indices: 2567892--2567965 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 31
2567882 ATAAAATTAG
*
2567892 ATAAATTTAAAGATTATTTTATTAAAAAAATA
1 ATAAATTTAAAGATTAATTTA-TAAAAAAATA
** * **
2567924 ATAAATTTAGTGATTAATTTATAATAATTTA
1 ATAAATTTAAAGATTAATTTATAAAAAAATA
2567955 ATAAATTTAAA
1 ATAAATTTAAA
2567966 AGGTCATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 16 0.47
32 18 0.53
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (31 bp):
ATAAATTTAAAGATTAATTTATAAAAAAATA
Found at i:2571536 original size:16 final size:17
Alignment explanation
Indices: 2571515--2571546 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2571505 TAATATTGAA
2571515 ACTTGAACT-AAAAAAG
1 ACTTGAACTCAAAAAAG
2571531 ACTTGAACTCAAAAAA
1 ACTTGAACTCAAAAAA
2571547 AAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (17 bp):
ACTTGAACTCAAAAAAG
Found at i:2585014 original size:15 final size:16
Alignment explanation
Indices: 2584988--2585020 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2584978 GATTTGTTTG
2584988 TTTCACAAAAAATATT
1 TTTCACAAAAAATATT
2585004 TTTCA-AAAAAATATT
1 TTTCACAAAAAATATT
2585019 TT
1 TT
2585021 AATAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTCACAAAAAATATT
Found at i:2591065 original size:13 final size:13
Alignment explanation
Indices: 2591047--2591071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2591037 TTATATAATA
2591047 CTAAAAAAATTAT
1 CTAAAAAAATTAT
2591060 CTAAAAAAATTA
1 CTAAAAAAATTA
2591072 AATTTACAGC
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):
CTAAAAAAATTAT
Found at i:2593246 original size:9 final size:10
Alignment explanation
Indices: 2593223--2593261 Score: 55
Period size: 9 Copynumber: 4.1 Consensus size: 10
2593213 TTAAATTTAA
2593223 TTATAAATAT
1 TTATAAATAT
2593233 TTATAAAT-T
1 TTATAAATAT
*
2593242 TTATAAGTAT
1 TTATAAATAT
2593252 TTAT-AATAT
1 TTATAAATAT
2593261 T
1 T
2593262 ATGATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (10 bp):
TTATAAATAT
Found at i:2593381 original size:51 final size:52
Alignment explanation
Indices: 2593325--2593445 Score: 156
Period size: 55 Copynumber: 2.3 Consensus size: 52
2593315 GAGTTGAAGG
* *
2593325 ATTTGATTTA-TACTTGAA-AATTAATCTATTAATTGTTAAAAATTTTGAGTT
1 ATTTGAGTTACTA-TTGAAGAATTAATCTATTAATTGTTAAAAATTATGAGTT
*
2593376 ATTTGAGTTACTATTTAAGTCGAATTAATCTATTAATTGTTAAAAATTATGAGTT
1 ATTTGAGTTACTATTGAA---GAATTAATCTATTAATTGTTAAAAATTATGAGTT
*
2593431 ATTCGAGTTACTATT
1 ATTTGAGTTACTATT
2593446 TAAGCCATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
51 13 0.21
52 2 0.03
55 46 0.75
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.47
Consensus pattern (52 bp):
ATTTGAGTTACTATTGAAGAATTAATCTATTAATTGTTAAAAATTATGAGTT
Found at i:2593403 original size:55 final size:55
Alignment explanation
Indices: 2593343--2593449 Score: 196
Period size: 55 Copynumber: 1.9 Consensus size: 55
2593333 TATACTTGAA
* *
2593343 AATTAATCTATTAATTGTTAAAAATTTTGAGTTATTTGAGTTACTATTTAAGTCG
1 AATTAATCTATTAATTGTTAAAAATTATGAGTTATTCGAGTTACTATTTAAGTCG
2593398 AATTAATCTATTAATTGTTAAAAATTATGAGTTATTCGAGTTACTATTTAAG
1 AATTAATCTATTAATTGTTAAAAATTATGAGTTATTCGAGTTACTATTTAAG
2593450 CCATTCGAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (55 bp):
AATTAATCTATTAATTGTTAAAAATTATGAGTTATTCGAGTTACTATTTAAGTCG
Found at i:2594429 original size:2 final size:2
Alignment explanation
Indices: 2594424--2594457 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2594414 ACAAATAACT
2594424 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2594458 TTCTTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2594445 original size:15 final size:15
Alignment explanation
Indices: 2594425--2594454 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2594415 CAAATAACTT
2594425 ATATATATATATATA
1 ATATATATATATATA
2594440 ATATATATATATATA
1 ATATATATATATATA
2594455 TATTTCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:2594446 original size:17 final size:17
Alignment explanation
Indices: 2594424--2594456 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2594414 ACAAATAACT
2594424 TATATATATATATATAA
1 TATATATATATATATAA
2594441 TATATATATATATATA
1 TATATATATATATATA
2594457 TTTCTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:2601187 original size:23 final size:24
Alignment explanation
Indices: 2601159--2601219 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
2601149 ATTTTTTTTA
*
2601159 ATTATTATTATTTATTTATTTACTAT
1 ATTATTTTTATTTATTTA--TACTAT
**
2601185 ATTCCTTTT-TTTATTTATACTAT
1 ATTATTTTTATTTATTTATACTAT
2601208 ATTATTTTTATT
1 ATTATTTTTATT
2601220 ATATATATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 13 0.45
24 2 0.07
25 8 0.28
26 6 0.21
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTATTTTTATTTATTTATACTAT
Found at i:2601221 original size:23 final size:23
Alignment explanation
Indices: 2601159--2601240 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 23
2601149 ATTTTTTTTA
*
2601159 ATTATTATTATTTATTTATTTACTAT
1 ATTATTTTTA-TTATTTA--TACTAT
*
2601185 ATTCCTTTTT-TTATTTATACTAT
1 ATT-ATTTTTATTATTTATACTAT
*
2601208 ATTATTTTTATTATATATATCTTAT
1 ATTATTTTTATTATTTATA-C-TAT
*
2601233 ATCATTTT
1 ATTATTTT
2601241 ATATATATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
22 5 0.11
23 17 0.36
24 1 0.02
25 17 0.36
26 3 0.06
27 4 0.09
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTATTTTTATTATTTATACTAT
Found at i:2601232 original size:20 final size:20
Alignment explanation
Indices: 2601140--2601227 Score: 64
Period size: 18 Copynumber: 4.5 Consensus size: 20
2601130 ATTTCGTCCC
2601140 ATAC-ATATTATTTTT-TTT
1 ATACTATATTATTTTTATTT
2601158 A-A-T-TATTATTATTTATTT
1 ATACTATATTATT-TTTATTT
*
2601176 ATTTACTATATTCCTTTTTTTATTT
1 A--TACTATA-T--TATTTTTATTT
2601201 ATACTATATTATTTTTA-TT
1 ATACTATATTATTTTTATTT
2601220 ATA-TATAT
1 ATACTATAT
2601228 CTTATATCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 22
0.70 0.02 0.27
Matches are distributed among these distances:
16 7 0.12
17 4 0.07
18 10 0.18
19 5 0.09
20 7 0.12
21 1 0.02
22 2 0.04
23 9 0.16
24 1 0.02
25 8 0.14
26 3 0.05
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (20 bp):
ATACTATATTATTTTTATTT
Found at i:2601239 original size:25 final size:24
Alignment explanation
Indices: 2601169--2601250 Score: 68
Period size: 23 Copynumber: 3.6 Consensus size: 24
2601159 ATTATTATTA
* *
2601169 TTTATT-TATTTA-CTATATTCCTT
1 TTTATTATATATATCTATA-TCATT
* *
2601192 TTT-TTATTTATA-CTATATTATT
1 TTTATTATATATATCTATATCATT
2601214 TTTATTATATATATCTTATATCA-T
1 TTTATTATATATATC-TATATCATT
2601238 TTTA-TATATATAT
1 TTTATTATATATAT
2601251 GTGTACATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
22 8 0.16
23 29 0.59
24 6 0.12
25 6 0.12
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTATTATATATATCTATATCATT
Found at i:2601330 original size:21 final size:20
Alignment explanation
Indices: 2601304--2601369 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
2601294 TTCTTAATAT
2601304 TATATTTTATACGGTTTTATA
1 TATATTTTATAC-GTTTTATA
*
2601325 TATA-TTT-T-C--TTAATA
1 TATATTTTATACGTTTTATA
2601340 TTATATTTTATACGTTTTTATA
1 -TATATTTTATACG-TTTTATA
2601362 TATATTTT
1 TATATTTT
2601370 GTTTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
15 5 0.14
16 4 0.11
17 3 0.08
18 2 0.06
19 2 0.06
20 3 0.08
21 12 0.33
22 5 0.14
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (20 bp):
TATATTTTATACGTTTTATA
Found at i:2601338 original size:37 final size:37
Alignment explanation
Indices: 2601287--2601369 Score: 150
Period size: 37 Copynumber: 2.3 Consensus size: 37
2601277 ATTTACTATG
2601287 TATATA-TTTCTTAATATTATATTTTATACGGTTTTA
1 TATATATTTTCTTAATATTATATTTTATACGGTTTTA
*
2601323 TATATATTTTCTTAATATTATATTTTATACGTTTTTA
1 TATATATTTTCTTAATATTATATTTTATACGGTTTTA
2601360 TATATATTTT
1 TATATATTTT
2601370 GTTTTTTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 6 0.13
37 39 0.87
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (37 bp):
TATATATTTTCTTAATATTATATTTTATACGGTTTTA
Found at i:2601423 original size:11 final size:10
Alignment explanation
Indices: 2601383--2601470 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 10
2601373 TTTTTAAACA
2601383 TTTTATTCATT
1 TTTTATT-ATT
*
2601394 TTGT-TTA-T
1 TTTTATTATT
2601402 TTTTATTATT
1 TTTTATTATT
2601412 TTTTATTAATT
1 TTTTATT-ATT
* *
2601423 TTTTA-CATG
1 TTTTATTATT
*
2601432 TTTTGTTATT
1 TTTTATTATT
*
2601442 TTCTATT-TT
1 TTTTATTATT
*
2601451 TTCTTGTT-TT
1 TT-TTATTATT
*
2601461 ATTTATTATT
1 TTTTATTATT
2601471 CTCACGTTTG
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
8 4 0.07
9 18 0.31
10 25 0.43
11 11 0.19
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (10 bp):
TTTTATTATT
Found at i:2601466 original size:26 final size:27
Alignment explanation
Indices: 2601420--2601472 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
2601410 TTTTTTATTA
2601420 ATTTTTTACATGTTTTGTTATT-TTCT
1 ATTTTTTACATGTTTTGTTATTATTCT
* *
2601446 ATTTTTT-CTTGTTTTATTTATTATTCT
1 ATTTTTTACATGTTTT-GTTATTATTCT
2601473 CACGTTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.15, C:0.08, G:0.06, T:0.72
Consensus pattern (27 bp):
ATTTTTTACATGTTTTGTTATTATTCT
Found at i:2602251 original size:23 final size:23
Alignment explanation
Indices: 2602194--2602275 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
2602184 TATTTTTTTA
*
2602194 ATTATTATTATTTATTTATTTACTAT
1 ATTATT-TTTTTTATTTA--TACTAT
**
2602220 ATTCCTTTTTTTATTTATACTAT
1 ATTATTTTTTTTATTTATACTAT
* *
2602243 ATTATTTTTATTATATATATCTTAT
1 ATTATTTTTTTTATTTATA-C-TAT
*
2602268 ATCATTTT
1 ATTATTTT
2602276 ATATATATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
23 21 0.46
24 1 0.02
25 20 0.43
26 4 0.09
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTATTTTTTTTATTTATACTAT
Found at i:2602267 original size:20 final size:20
Alignment explanation
Indices: 2602227--2602262 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2602217 TATATTCCTT
2602227 TTTTTATTTATACTATATTA
1 TTTTTATTTATACTATATTA
2602247 TTTTTA-TTATA-TATAT
1 TTTTTATTTATACTATAT
2602263 CTTATATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.31
19 5 0.31
20 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTATTTATACTATATTA
Found at i:2602274 original size:25 final size:23
Alignment explanation
Indices: 2602204--2602283 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 23
2602194 ATTATTATTA
* *
2602204 TTTATT-TATTTACTATATTCCTT
1 TTTATTATATATACTATA-TCATT
* *
2602227 TTT-TTATTTATACTATATTATT
1 TTTATTATATATACTATATCATT
2602249 TTTATTATATATATCTTATATCA-T
1 TTTATTATATATA-C-TATATCATT
2602273 TTTA-TATATAT
1 TTTATTATATAT
2602284 GTGTGTGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 8 0.17
23 27 0.57
24 6 0.13
25 6 0.13
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTATTATATATACTATATCATT
Found at i:2602371 original size:21 final size:20
Alignment explanation
Indices: 2602347--2602412 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
2602337 TTCTTAATAT
2602347 TATATTTTATACGGTTTTATA
1 TATATTTTATAC-GTTTTATA
*
2602368 TATA-TTT-T-C--TTAATA
1 TATATTTTATACGTTTTATA
2602383 TTATATTTTATACGTTTTTATA
1 -TATATTTTATACG-TTTTATA
2602405 TATATTTT
1 TATATTTT
2602413 GTTTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
15 5 0.14
16 4 0.11
17 3 0.08
18 2 0.06
19 2 0.06
20 3 0.08
21 12 0.33
22 5 0.14
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (20 bp):
TATATTTTATACGTTTTATA
Found at i:2602376 original size:37 final size:37
Alignment explanation
Indices: 2602335--2602412 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
2602325 GTATATTTTT
2602335 TTTTCTTAATATTATATTTTATACGGTTTTATATATA
1 TTTTCTTAATATTATATTTTATACGGTTTTATATATA
*
2602372 TTTTCTTAATATTATATTTTATACGTTTTTATATATA
1 TTTTCTTAATATTATATTTTATACGGTTTTATATATA
2602409 TTTT
1 TTTT
2602413 GTTTTTTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (37 bp):
TTTTCTTAATATTATATTTTATACGGTTTTATATATA
Found at i:2602456 original size:19 final size:19
Alignment explanation
Indices: 2602425--2602512 Score: 65
Period size: 19 Copynumber: 4.5 Consensus size: 19
2602415 TTTTTTAACA
2602425 TTTTATTCA-TTTTGTTTAT
1 TTTTATT-ATTTTTGTTTAT
* *
2602444 TTTTATTATTTTTATTAAT
1 TTTTATTATTTTTGTTTAT
*
2602463 TTTTA-CATGTTTTG-TTAT
1 TTTTATTAT-TTTTGTTTAT
*
2602481 TTTCTATTTTTTCTTGTTTTAT
1 TTT-TATTATTT-TTG-TTTAT
2602503 TTATTATTAT
1 TT-TTATTAT
2602513 CACGTTTGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
18 9 0.17
19 28 0.53
20 4 0.08
22 11 0.21
23 1 0.02
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTTATTATTTTTGTTTAT
Found at i:2602467 original size:10 final size:9
Alignment explanation
Indices: 2602425--2602467 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
2602415 TTTTTTAACA
2602425 TTTTATTCAT
1 TTTTATT-AT
2602435 TTTGT-TTAT
1 TTT-TATTAT
2602444 TTTTATTAT
1 TTTTATTAT
2602453 TTTTATTAAT
1 TTTTATT-AT
2602463 TTTTA
1 TTTTA
2602468 CATGTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 16 0.53
10 12 0.40
11 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTATTAT
Found at i:2603277 original size:40 final size:39
Alignment explanation
Indices: 2603207--2603292 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 39
2603197 ATTTCGTCCC
*
2603207 ATATATATT-ATTTTTTTAATTATTATTATTTATTTATT
1 ATATATATTCCTTTTTTTAATTATTATTATTTATTTATT
* *
2603245 -TACTATATTCCTTTTTTTATTTA-TACTATATTTTTTTATT
1 ATA-TATATTCCTTTTTTTAATTATTA-T-TATTTATTTATT
2603285 ATATATAT
1 ATATATAT
2603293 CTTATATCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
37 2 0.05
38 8 0.20
39 12 0.30
40 16 0.40
41 2 0.05
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (39 bp):
ATATATATTCCTTTTTTTAATTATTATTATTTATTTATT
Found at i:2603280 original size:19 final size:17
Alignment explanation
Indices: 2603208--2603292 Score: 64
Period size: 18 Copynumber: 4.5 Consensus size: 17
2603198 TTTCGTCCCA
2603208 TATATATTATTTTTTTAAT
1 TATATA-TATTTTTTT-AT
*
2603227 TAT-TATTATTTATTTATT
1 TATATA-TATTTTTTTA-T
*
2603245 TACTATATTCCTTTTTTTATT
1 TA-TATA-T-ATTTTTTTA-T
2603266 TATACTATATTTTTTTAT
1 TATA-TATATTTTTTTAT
2603284 TATATATAT
1 TATATATAT
2603293 CTTATATCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
17 6 0.11
18 19 0.33
19 12 0.21
20 7 0.12
21 13 0.23
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATATATTTTTTTAT
Found at i:2603280 original size:21 final size:22
Alignment explanation
Indices: 2603235--2603291 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
2603225 ATTATTATTA
2603235 TTTATTTATTTACTATATTCCTTTT
1 TTTATTTA--TACTATATT-CTTTT
2603260 TTTATTTATACTATATT-TTTT
1 TTTATTTATACTATATTCTTTT
*
2603281 TATTATATATA
1 T-TTATTTATA
2603292 TCTTATATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.17
22 8 0.27
23 9 0.30
25 8 0.27
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATTTATACTATATTCTTTT
Found at i:2603414 original size:37 final size:37
Alignment explanation
Indices: 2603373--2603450 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
2603363 ATATATTTTT
2603373 TTTTCTTAATATTATATTTTATACGGTTTTATACATA
1 TTTTCTTAATATTATATTTTATACGGTTTTATACATA
* *
2603410 TTTTCTTAATATTATATTTTATACGTTTTTATATATA
1 TTTTCTTAATATTATATTTTATACGGTTTTATACATA
2603447 TTTT
1 TTTT
2603451 GTTTTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (37 bp):
TTTTCTTAATATTATATTTTATACGGTTTTATACATA
Found at i:2603501 original size:26 final size:24
Alignment explanation
Indices: 2603443--2603502 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 24
2603433 CGTTTTTATA
2603443 TATATTTTGTTTTTTTTAACATTT
1 TATATTTTGTTTTTTTTAACATTT
**
2603467 TATTCATTTTGTTTATTTTTATTATTTT
1 TA-T-ATTTTGTTT-TTTTTAACA-TTT
2603495 TATATTTT
1 TATATTTT
2603503 ACATGTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 2 0.07
25 1 0.03
26 14 0.47
27 8 0.27
28 5 0.17
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (24 bp):
TATATTTTGTTTTTTTTAACATTT
Found at i:2603517 original size:25 final size:25
Alignment explanation
Indices: 2603483--2603539 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
2603473 TTTTGTTTAT
*
2603483 TTTTATTATTTTTATATTTTACATG
1 TTTTATTATTTCTATATTTTACATG
* * * *
2603508 TTTTGTTATTTCTATTTTTTTCTTG
1 TTTTATTATTTCTATATTTTACATG
2603533 TTTTATT
1 TTTTATT
2603540 TATTATTCTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (25 bp):
TTTTATTATTTCTATATTTTACATG
Found at i:2606950 original size:32 final size:32
Alignment explanation
Indices: 2606878--2606962 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 32
2606868 TGAGGGCATC
*
2606878 TTTGAAGATTCAACATCAAATACTGGGGTATTT
1 TTTG-AGATTCAACATCAAATACTGAGGTATTT
* **
2606911 TTT-AGATTTAACATCAAATGTTGAGGTATTT
1 TTTGAGATTCAACATCAAATACTGAGGTATTT
*
2606942 TTTGAGATTCAACATCGAATA
1 TTTGAGATTCAACATCAAATA
2606963 TTTGGGCATA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 27 0.61
32 14 0.32
33 3 0.07
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATACTGAGGTATTT
Found at i:2608289 original size:36 final size:36
Alignment explanation
Indices: 2608247--2608405 Score: 181
Period size: 36 Copynumber: 4.6 Consensus size: 36
2608237 GATTTACTCA
2608247 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * **
2608283 AAACAAA------ATC-ATTGA-ATCAGTTTCAGTTG
1 AAACAAATTTTGTCTCTCTTGAGA-CAGTTTCCCTTG
* *
2608312 AAACAAATTTTGTCTCTCTTGGGATAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
2608348 AAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
2608384 AAACAAATTTTGTCTCTCTTGA
1 AAACAAATTTTGTCTCTCTTGA
2608406 AACAAATTTC
Statistics
Matches: 102, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.01
29 21 0.21
30 2 0.02
35 2 0.02
36 75 0.74
37 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:2608402 original size:21 final size:21
Alignment explanation
Indices: 2608377--2608435 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
2608367 TGAGATAGTT
*
2608377 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTCGTC
2608398 TCTCTTGAAACAAATTTCGTC
1 TCTCTTGAAACAAATTTCGTC
* *
2608419 TCCCTTGAGA-AAATTTC
1 TCTCTTGAAACAAATTTC
2608436 TTTTAGAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 7 0.20
21 28 0.80
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTCGTC
Found at i:2608436 original size:57 final size:58
Alignment explanation
Indices: 2608344--2608458 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 58
2608334 GATAGTTTCC
* * * *
2608344 CTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGA-AAC-AAATTTTGTCTCT
1 CTTGAAACAAATTTCGTCTCCCTTGAGAAAATTTCT-TTGAGAACTAAATTTTGTCTCT
* *
2608401 CTTGAAACAAATTTCGTCTCCCTTGAGAAAATTTCTTTTAGAACTAAGTTTTGTCTCT
1 CTTGAAACAAATTTCGTCTCCCTTGAGAAAATTTCTTTGAGAACTAAATTTTGTCTCT
2608459 TGAGACAGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 3 0.06
57 35 0.70
58 12 0.24
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (58 bp):
CTTGAAACAAATTTCGTCTCCCTTGAGAAAATTTCTTTGAGAACTAAATTTTGTCTCT
Found at i:2608589 original size:65 final size:64
Alignment explanation
Indices: 2608455--2608675 Score: 234
Period size: 65 Copynumber: 3.4 Consensus size: 64
2608445 TAAGTTTTGT
* *** *
2608455 CTCTTGAGACAGTTTCTCTTGAAACATAAATATT-AAAA-ATTTCCCTTGAAGTGAATTTTGTCT
1 CTCTTGAGATAGTTTCTCTTGAAACA-AAATATTGAAAACATTTCCCTTGAAACAAATTTTGTCA
* ** * *
2608518 CTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCCGTTTCCCTTGAAACAAATTTCATTT
1 CTCTTGAGATAGTTTCTCTTGAAACAAAAT-ATTGAAAACATTTCCCTTGAAACAAATTT--TGT
2608583 C-
63 CA
* * **
2608584 C-CTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAATATTTCCCTTGAAATGAATTTTGTCA
1 CTCTTGAGATAGTTTCTCTTGAAACA-AAATATTGAAAACATTTCCCTTGAAACAAATTTTGTCA
*
2608648 CTCTTGAGATAGTTTCCCTTGAAACAAA
1 CTCTTGAGATAGTTTCTCTTGAAACAAA
2608676 TTTTGTCTCC
Statistics
Matches: 130, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
62 4 0.03
63 30 0.23
64 5 0.04
65 83 0.64
66 5 0.04
67 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (64 bp):
CTCTTGAGATAGTTTCTCTTGAAACAAAATATTGAAAACATTTCCCTTGAAACAAATTTTGTCA
Found at i:2608671 original size:36 final size:36
Alignment explanation
Indices: 2608624--2608706 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
2608614 ATTGAAAATA
** * *
2608624 TTTCCCTTGAAATGAATTTTGTCACTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCACCCTTGAGACAG
*
2608660 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCACCCTTGAGACAG
*
2608696 TTTCTCTTGAA
1 TTTCCCTTGAA
2608707 GCATAAACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCACCCTTGAGACAG
Found at i:2608726 original size:30 final size:30
Alignment explanation
Indices: 2608692--2608750 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2608682 CTCCCTTGAG
*
2608692 ACAGTTT-CTCTTGAAGCATAAA-CTTTGAAA
1 ACAGTTTCCT-TTGAAACA-AAATCTTTGAAA
2608722 ACAGTTTCCTTTGAAACAAAATCTTTGAA
1 ACAGTTTCCTTTGAAACAAAATCTTTGAA
2608751 TATGTTCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 21 0.81
31 2 0.08
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (30 bp):
ACAGTTTCCTTTGAAACAAAATCTTTGAAA
Found at i:2608826 original size:21 final size:20
Alignment explanation
Indices: 2608805--2608863 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
2608795 TTTTGGAAGT
2608805 TTTTGTCTCTCTTGAGACAG
1 TTTTGTCTCTCTTGAGACAG
*
2608825 --TT-TCTCT-TT-AAACAAG
1 TTTTGTCTCTCTTGAGAC-AG
2608841 TTTTGTCTCTCTTGAGACAG
1 TTTTGTCTCTCTTGAGACAG
2608861 TTT
1 TTT
2608864 CCCTTGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
15 3 0.10
16 4 0.13
17 5 0.16
18 4 0.13
19 5 0.16
20 7 0.23
21 3 0.10
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTTGTCTCTCTTGAGACAG
Found at i:2608845 original size:36 final size:36
Alignment explanation
Indices: 2608762--2608873 Score: 122
Period size: 36 Copynumber: 3.2 Consensus size: 36
2608752 ATGTTCTACG
* * * *
2608762 TTAAACAAATTTCGTTTCCCTTGAGACAGTTTCT-T
1 TTAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
**
2608797 TT--GGAAGTTTTTGTCTCTCTTGAGACAGTTTCTCT
1 TTAAACAAG-TTTTGTCTCTCTTGAGACAGTTTCTCT
*
2608832 TTAAACAAGTTTTGTCTCTCTTGAGACAGTTTCCCT
1 TTAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
*
2608868 TGAAAC
1 TTAAAC
2608874 TTCAACCTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
33 2 0.03
34 22 0.35
35 5 0.08
36 31 0.49
37 3 0.05
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (36 bp):
TTAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
Found at i:2608917 original size:33 final size:33
Alignment explanation
Indices: 2608877--2608971 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
2608867 TTGAAACTTC
*
2608877 AACCTTTGAAATTGTTTATCTTGAAACACAAAA
1 AACCTTTGAAATTGTTTCTCTTGAAACACAAAA
*
2608910 AACCTTTGAAATTGTTTCTCTTGAAACATAAAA
1 AACCTTTGAAATTGTTTCTCTTGAAACACAAAA
* *
2608943 AACCTTTGAAAATATTTCTCTTGAAACAC
1 AACCTTTGAAATTGTTTCTCTTGAAACAC
2608972 CAAACCCTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (33 bp):
AACCTTTGAAATTGTTTCTCTTGAAACACAAAA
Found at i:2609208 original size:84 final size:84
Alignment explanation
Indices: 2609011--2609217 Score: 245
Period size: 84 Copynumber: 2.5 Consensus size: 84
2609001 TCAAGGGAAT
* ** * * *
2609011 ATCATTTACAGCATAACTCAAGGTTATAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACT
1 ATCATTTACAGCATAGCTCAAGGCAAGAAGGGATATCTGCCACCAAAAGACCTTCGAGTTTGACT
* * *
2609076 ATGCTCATCTCTAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
* * * * * *
2609095 ATCATTTGCAGCATAGCTTATGTCGAGAAGGGATATCTGCCAACC-AAATACCTTCGAGTTTGAC
1 ATCATTTACAGCATAGCTCAAGGCAAGAAGGGATATCTGCC-ACCAAAAGACCTTCGAGTTTGAC
2609159 TACGCTCAGCTCCAAGGCAC
65 TACGCTCAGCTCCAAGGCAC
* *
2609179 ATCATTTACAGCATAGCTCAAGGCAAGAAGAGCTATCTG
1 ATCATTTACAGCATAGCTCAAGGCAAGAAGGGATATCTG
2609218 TCAATAAAAT
Statistics
Matches: 101, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
84 98 0.97
85 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (84 bp):
ATCATTTACAGCATAGCTCAAGGCAAGAAGGGATATCTGCCACCAAAAGACCTTCGAGTTTGACT
ACGCTCAGCTCCAAGGCAC
Found at i:2610323 original size:14 final size:14
Alignment explanation
Indices: 2610304--2610343 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 14
2610294 TATTCCTTTT
2610304 TTATTTATATTATA
1 TTATTTATATTATA
2610318 TTATTTATATTATA
1 TTATTTATATTATA
2610332 TATATCTTATAT
1 T-TAT-TTATAT
2610344 CATTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.62
15 3 0.12
16 6 0.25
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:2610445 original size:39 final size:38
Alignment explanation
Indices: 2610400--2610501 Score: 152
Period size: 37 Copynumber: 2.7 Consensus size: 38
2610390 ATTTACTATG
2610400 TATATATTTTTTCTTAATATTATATTTTATACGTTTTTA
1 TATATATTTTTT-TTAATATTATATTTTATACGTTTTTA
*
2610439 TATATA-TTTTATTAATATTATATTTTATACGTTTTTA
1 TATATATTTTTTTTAATATTATATTTTATACGTTTTTA
* *
2610476 TATATATTATTTTTTAACATTTTATT
1 TATATATT-TTTTTTAATATTATATT
2610502 CATTTTGTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
37 32 0.56
38 5 0.09
39 20 0.35
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (38 bp):
TATATATTTTTTTTAATATTATATTTTATACGTTTTTA
Found at i:2610446 original size:21 final size:21
Alignment explanation
Indices: 2610420--2610483 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
2610410 TTCTTAATAT
2610420 TATATTTTATACGTTTTTATA
1 TATATTTTATACGTTTTTATA
**
2610441 TATA-TTT-TA--TTAATAT-
1 TATATTTTATACGTTTTTATA
2610457 TATATTTTATACGTTTTTATA
1 TATATTTTATACGTTTTTATA
2610478 TATATT
1 TATATT
2610484 ATTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
16 4 0.12
17 8 0.24
18 2 0.06
19 2 0.06
20 8 0.24
21 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATATTTTATACGTTTTTATA
Found at i:2610498 original size:24 final size:26
Alignment explanation
Indices: 2610444--2610501 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
2610434 TTTTATATAT
2610444 ATTTTATTAATATTATATTTTATACG
1 ATTTTATTAATATTATATTTTATACG
* *
2610470 TTTTTA-TATATATTATTTTTTA-AC-
1 ATTTTATTA-ATATTATATTTTATACG
2610494 ATTTTATT
1 ATTTTATT
2610502 CATTTTGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 5 0.19
25 5 0.19
26 17 0.63
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (26 bp):
ATTTTATTAATATTATATTTTATACG
Found at i:2610517 original size:19 final size:17
Alignment explanation
Indices: 2610470--2610531 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 17
2610460 ATTTTATACG
* *
2610470 TTTTTATATATATTATT
1 TTTTTATTTTTATTATT
* *
2610487 TTTTAACATTTTATTCATT
1 TTTTTA-TTTTTATT-ATT
2610506 TTGTTTATTTTTATTATT
1 TT-TTTATTTTTATTATT
2610524 TTTTTATT
1 TTTTTATT
2610532 ATTTTTTACG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 11 0.31
18 10 0.28
19 12 0.33
20 3 0.08
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTTATTTTTATTATT
Found at i:2610529 original size:11 final size:11
Alignment explanation
Indices: 2610513--2610538 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2610503 ATTTTGTTTA
2610513 TTTTTATTATT
1 TTTTTATTATT
2610524 TTTTTATTATT
1 TTTTTATTATT
2610535 TTTT
1 TTTT
2610539 ACGTCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:2611065 original size:26 final size:26
Alignment explanation
Indices: 2611036--2611085 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2611026 TTATTAGATT
2611036 ATATTAATTTATTAAAGAAAATAACC
1 ATATTAATTTATTAAAGAAAATAACC
2611062 ATATTAATTTATTAAAGAAAATAA
1 ATATTAATTTATTAAAGAAAATAA
2611086 TATGGGAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (26 bp):
ATATTAATTTATTAAAGAAAATAACC
Found at i:2611473 original size:27 final size:26
Alignment explanation
Indices: 2611417--2611474 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
2611407 TATTATTATT
* *
2611417 TAATTTAATTTTAATAAGAATATAAT
1 TAATTTAATTTTAATAAAAATATAAA
*
2611443 TAATTTATATTTTATTAAAAAT-TACAA
1 TAATTTA-ATTTTAATAAAAATATA-AA
2611470 TAATT
1 TAATT
2611475 ATAGGATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
TAATTTAATTTTAATAAAAATATAAA
Found at i:2612234 original size:21 final size:22
Alignment explanation
Indices: 2612196--2612239 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2612186 AATGTCAGAG
*
2612196 GGGAACCGATTCCCCTGCTATA
1 GGGAACCGATTACCCTGCTATA
2612218 GGGAACCGA-TACCCTGCTATA
1 GGGAACCGATTACCCTGCTATA
2612239 G
1 G
2612240 TACTGCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTACCCTGCTATA
Found at i:2613068 original size:31 final size:31
Alignment explanation
Indices: 2613008--2613070 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2612998 GAACCTCGGT
*
2613008 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
2613039 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
2613070 A
1 A
2613071 CCCTCGACTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:2613995 original size:21 final size:21
Alignment explanation
Indices: 2613969--2614008 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2613959 TTTTCCATTA
2613969 GGGGGAATC-GATACCCCCTAG
1 GGGGGAATCTG-TACCCCCTAG
2613990 GGGGGAATCTGTACCCCCT
1 GGGGGAATCTGTACCCCCT
2614009 GCATAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTAG
Found at i:2614068 original size:21 final size:21
Alignment explanation
Indices: 2614039--2614078 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2614029 TTCAATCCCA
*
2614039 GAAAATCACTGT-TCAACTAC
1 GAAAATCACTATATCAACTAC
2614059 GAAAATTCACTATATCAACT
1 GAAAA-TCACTATATCAACT
2614079 TAAATTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (21 bp):
GAAAATCACTATATCAACTAC
Found at i:2617015 original size:20 final size:21
Alignment explanation
Indices: 2616990--2617041 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2616980 TTTTCCCAAT
*
2616990 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
**
2617010 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATAAGAAAAA
2617031 TCGCAATGCGA
1 TCGCAATGCGA
2617042 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:2617076 original size:41 final size:41
Alignment explanation
Indices: 2616987--2617123 Score: 102
Period size: 41 Copynumber: 3.3 Consensus size: 41
2616977 TGATTTTCCC
* * * * *
2616987 AATTCGCAATGCGAAT-AAGTAAATCGCAATGCGAA-TTTGAA
1 AATTCGCAATGCGATTGACGT-ATTCGCAATGC-AATTTTCAT
* *
2617028 AAATCGCAATGCGATACTGAC-TA-TCGCAATGCAATTTTCCT
1 AATTCGCAATGCGAT--TGACGTATTCGCAATGCAATTTTCAT
* * ** *
2617069 AATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCAT
1 AATTCGCAATGCGATTGACGTATTCGCAATGCAATTTTCAT
2617110 AATTCGCAATGCGA
1 AATTCGCAATGCGA
2617124 ATTAGGAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
39 3 0.04
40 4 0.05
41 65 0.86
42 1 0.01
43 2 0.03
44 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (41 bp):
AATTCGCAATGCGATTGACGTATTCGCAATGCAATTTTCAT
Found at i:2617085 original size:21 final size:21
Alignment explanation
Indices: 2616948--2617123 Score: 76
Period size: 21 Copynumber: 8.5 Consensus size: 21
2616938 ATTATGACTA
*
2616948 TCGCAATGCGATTTTCCA-ATT
1 TCGCAATGCGATTTT-CATAAT
** * **
2616969 TCGCGTTGTGATTTTCCCAAT
1 TCGCAATGCGATTTTCATAAT
* * *
2616990 TCGCAATGCGA--ATAAGTAAA
1 TCGCAATGCGATTTTCA-TAAT
* * * *
2617010 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGATTTTCATAAT
** *
2617031 TCGCAATGCGATACTGACT-A-
1 TCGCAATGCGATTTTCA-TAAT
* *
2617051 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
2617072 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
2617092 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
2617113 TCGCAATGCGA
1 TCGCAATGCGA
2617124 ATTAGGAAAA
Statistics
Matches: 113, Mismatches: 34, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
19 2 0.02
20 44 0.39
21 65 0.58
22 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:2617137 original size:21 final size:21
Alignment explanation
Indices: 2617113--2617166 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
2617103 TTTTCATAAT
*
2617113 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
2617134 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
2617154 TCGCAATGCGAAT
1 TCGCAATGCGAAT
2617167 CTTACTATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:2617742 original size:19 final size:19
Alignment explanation
Indices: 2617704--2617770 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2617694 TTCGAGAATG
2617704 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
2617724 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
2617743 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
2617762 AAAATCGCA
1 AAAATCGCA
2617771 TTGCGATAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:2617788 original size:19 final size:19
Alignment explanation
Indices: 2617766--2617850 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
2617756 GAAACCAAAA
*
2617766 TCGCATTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
2617785 TCGCGTTGCGAT--TC---
1 TCGCGTTGCGATAGTCATT
*
2617799 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
2617818 TCCGCGTTGCGATTA-TCATT
1 T-CGCGTTGCGA-TAGTCATT
*
2617838 ATCTCGTTGCGAT
1 -TCGCGTTGCGAT
2617851 TTTCATTTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
14 11 0.20
16 2 0.04
17 2 0.04
19 13 0.24
20 23 0.43
21 3 0.06
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:2617836 original size:20 final size:20
Alignment explanation
Indices: 2617802--2617859 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
2617792 GCGATTCTCT
2617802 CGTTGCGA-TAGTCATTTCCG
1 CGTTGCGATTA-TCATTTCCG
*
2617822 CGTTGCGATTATCATTAT-CT
1 CGTTGCGATTATCATT-TCCG
*
2617842 CGTTGCGATTTTCATTTC
1 CGTTGCGATTATCATTTC
2617860 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 1 0.03
20 29 0.88
21 3 0.09
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTATCATTTCCG
Found at i:2620029 original size:42 final size:42
Alignment explanation
Indices: 2619950--2620038 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
2619940 GACTCGCCTG
* * * *
2619950 TCATCCCTCAAGAGTCCACTCCTATCGTTGAATAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
2619992 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
2620034 TCATC
1 TCATC
2620039 GTTGAAAAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.38, G:0.16, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:2621443 original size:14 final size:14
Alignment explanation
Indices: 2621424--2621459 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2621414 ATTGTTTAAT
2621424 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2621438 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2621452 TGATTTGT
1 TGATTTGT
2621460 TTAATTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2621590 original size:19 final size:19
Alignment explanation
Indices: 2621566--2621612 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2621556 AAAAAGTACT
*
2621566 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2621585 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2621604 ATCGCAACG
1 ATCGCAACG
2621613 AGATAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2621659 original size:19 final size:19
Alignment explanation
Indices: 2621637--2621787 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
2621627 CGAAATTAAA
2621637 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2621656 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2621671 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
2621689 TTTGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
2621703 TCCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2621722 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2621737 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
2621755 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
2621774 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2621788 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2621683 original size:33 final size:33
Alignment explanation
Indices: 2621641--2621767 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
2621631 ATTAAATTCG
2621641 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* * *
2621674 CGTTGCGATTTTCATTTTGCATTGCGAAAT-CCG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCCCT
*
2621707 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
2621740 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2621768 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 2 0.02
33 81 0.95
34 2 0.02
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:2621719 original size:66 final size:66
Alignment explanation
Indices: 2621634--2621766 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
2621624 ACGCGAAATT
* *
2621634 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTTGCATTGC
1 AAATCCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2621699 G
66 G
*
2621700 AAATCCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATCCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2621765 G
66 G
2621766 A
1 A
2621767 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATCCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:2622003 original size:12 final size:12
Alignment explanation
Indices: 2621988--2622012 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2621978 ATTTTAAAGA
2621988 TGATTGCCTTTT
1 TGATTGCCTTTT
2622000 TGATTGCCTTTT
1 TGATTGCCTTTT
2622012 T
1 T
2622013 CTTGACACCA
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:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (12 bp):
TGATTGCCTTTT
Found at i:2624285 original size:24 final size:24
Alignment explanation
Indices: 2624251--2624304 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2624241 CTGAAAAATC
2624251 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2624275 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2624299 ATCAAA
1 ATCAAA
2624305 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2626965 original size:143 final size:143
Alignment explanation
Indices: 2626739--2627026 Score: 567
Period size: 143 Copynumber: 2.0 Consensus size: 143
2626729 TTATTTAACA
2626739 TCTTATTTTACAATTAATTCTCTCAAATCGCTGGATTTTATAGCATATTCGTTTTCAACTTATTT
1 TCTTATTTTACAATTAATTCTCTCAAATCGCTGGATTTTATAGCATATTCGTTTTCAACTTATTT
2626804 TGTACAATCAACTCTTTTAAAAATGTGTTTATCAAACACTAAAAATAAAGGGTTTGACTACTAAT
66 TGTACAATCAACTCTTTTAAAAATGTGTTTATCAAACACTAAAAATAAAGGGTTTGACTACTAAT
2626869 CAACTATTTATGC
131 CAACTATTTATGC
2626882 TCTTATTTTACAATTAATTCTCTCAAATCGCTGGATTTTATAGCATATTCGTTTTCAACTTATTT
1 TCTTATTTTACAATTAATTCTCTCAAATCGCTGGATTTTATAGCATATTCGTTTTCAACTTATTT
*
2626947 TGTACAATCAACTTTTTTAAAAATGTGTTTATCAAACACTAAAAATAAAGGGTTTGACTACTAAT
66 TGTACAATCAACTCTTTTAAAAATGTGTTTATCAAACACTAAAAATAAAGGGTTTGACTACTAAT
2627012 CAACTATTTATGC
131 CAACTATTTATGC
2627025 TC
1 TC
2627027 AAATAAGTTA
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 144 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (143 bp):
TCTTATTTTACAATTAATTCTCTCAAATCGCTGGATTTTATAGCATATTCGTTTTCAACTTATTT
TGTACAATCAACTCTTTTAAAAATGTGTTTATCAAACACTAAAAATAAAGGGTTTGACTACTAAT
CAACTATTTATGC
Found at i:2628033 original size:17 final size:17
Alignment explanation
Indices: 2628013--2628051 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2628003 CGTATAAATT
2628013 TAAT-TTATAATAATAAA
1 TAATATTATAA-AATAAA
*
2628030 TAATATTATAACATAAA
1 TAATATTATAAAATAAA
2628047 TAATA
1 TAATA
2628052 AACAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATATTATAAAATAAA
Found at i:2630869 original size:3 final size:3
Alignment explanation
Indices: 2630861--2630932 Score: 117
Period size: 3 Copynumber: 24.0 Consensus size: 3
2630851 ATTGATTTAT
* * *
2630861 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2630909 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
2630933 AATATATTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2632974 original size:24 final size:23
Alignment explanation
Indices: 2632934--2632978 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2632924 TAATTTTATA
2632934 TATATATATATACATATTATTTT
1 TATATATATATACATATTATTTT
* *
2632957 TATAGTATTTATATATATTATT
1 TATA-TATATATACATATTATT
2632979 AATATTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TATATATATATACATATTATTTT
Found at i:2632992 original size:34 final size:35
Alignment explanation
Indices: 2632912--2632993 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 35
2632902 AAAATTTCAT
*
2632912 ATATTTAATTTATAATTTTATATATATATATATAC
1 ATATTTATTTTATAATTTTATATATATATATATAC
*
2632947 ATA-TTATTTTTATAGTATTTATATATAT-TAT-TA-
1 ATATTTA-TTTTATAAT-TTTATATATATATATATAC
2632980 ATATTTCATTTTAT
1 ATATTT-ATTTTAT
2632994 TTACAAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
33 3 0.07
34 13 0.32
35 14 0.34
36 11 0.27
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (35 bp):
ATATTTATTTTATAATTTTATATATATATATATAC
Found at i:2643664 original size:21 final size:22
Alignment explanation
Indices: 2643629--2643691 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 22
2643619 ATTATGCTTG
*
2643629 AAGAGAAAAAGAAAGAAAGAAA
1 AAGAGAAAAAGAAAGAAAAAAA
* *
2643651 TAGA-AAAAAAAAAGAAAAAAA
1 AAGAGAAAAAGAAAGAAAAAAA
2643672 AAGAGAAAAAGAAAGAAAAA
1 AAGAGAAAAAGAAAGAAAAA
2643692 GGAAAAAAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (22 bp):
AAGAGAAAAAGAAAGAAAAAAA
Found at i:2643668 original size:10 final size:10
Alignment explanation
Indices: 2643632--2643691 Score: 66
Period size: 10 Copynumber: 5.7 Consensus size: 10
2643622 ATGCTTGAAG
*
2643632 AGAAAAAGAA
1 AGAAAAAAAA
* *
2643642 AGAAAGAAAT
1 AGAAAAAAAA
2643652 AGAAAAAAAAA
1 AG-AAAAAAAA
2643663 AGAAAAAAAA
1 AGAAAAAAAA
2643673 AGAGAAAAAGAA
1 AGA-AAAAA-AA
2643685 AGAAAAA
1 AGAAAAA
2643692 GGAAAAAAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
10 20 0.48
11 17 0.40
12 5 0.12
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:2643686 original size:12 final size:12
Alignment explanation
Indices: 2643629--2643696 Score: 58
Period size: 11 Copynumber: 6.2 Consensus size: 12
2643619 ATTATGCTTG
2643629 AAGAGAAAAAG-
1 AAGAGAAAAAGA
2643640 AA-AG--AAAGA
1 AAGAGAAAAAGA
*
2643649 AATAGAAAAA-A
1 AAGAGAAAAAGA
* *
2643660 AAAAGAAAAAAA
1 AAGAGAAAAAGA
2643672 AAGAGAAAAAGA
1 AAGAGAAAAAGA
*
2643684 AAGA-AAAAGGA
1 AAGAGAAAAAGA
2643695 AA
1 AA
2643697 AAAGGGGGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
8 4 0.08
9 2 0.04
10 4 0.08
11 20 0.42
12 18 0.38
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (12 bp):
AAGAGAAAAAGA
Found at i:2643690 original size:29 final size:30
Alignment explanation
Indices: 2643632--2643699 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
2643622 ATGCTTGAAG
*
2643632 AGAAAAAGAAAGAAAGAAATAGAAAAAAAAA
1 AGAAAAA-AAAGAAAGAAAAAGAAAAAAAAA
* *
2643663 AGAAAAAAAA-AGAGAAAAAGAAAGAAAAA
1 AGAAAAAAAAGAAAGAAAAAGAAAAAAAAA
*
2643692 GGAAAAAA
1 AGAAAAAA
2643700 GGGGGTCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 23 0.70
30 3 0.09
31 7 0.21
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (30 bp):
AGAAAAAAAAGAAAGAAAAAGAAAAAAAAA
Found at i:2645201 original size:83 final size:83
Alignment explanation
Indices: 2645060--2645365 Score: 490
Period size: 83 Copynumber: 3.7 Consensus size: 83
2645050 AACAAATGCC
* *
2645060 ATGTGCTCATAGCATCTTCTAGAAGTGTTATTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
2645125 ATTGAATTTGGAAGAATA
66 ATTGAATTTGGAAGAATA
*
2645143 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
**
2645208 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAATA
*
2645226 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
*
2645291 ATTGAATTTGAAAG-ATAA
66 ATTGAATTTGGAAGAAT-A
* *
2645309 ATAG-ACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 AT-GTGC-TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
2645366 TGAAACCACA
Statistics
Matches: 208, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
83 158 0.76
84 50 0.24
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.39
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
ATTGAATTTGGAAGAATA
Found at i:2646580 original size:113 final size:112
Alignment explanation
Indices: 2646311--2646816 Score: 758
Period size: 113 Copynumber: 4.6 Consensus size: 112
2646301 TAAACAGTGT
2646311 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAA
* *
2646376 TTTGTTCAAACTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
65 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTC
2646424 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAG--GAAGAAGTTCATAATGAGAAGAAT
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAT
*
2646487 TTGTTCAACCTTTTGCTCAAACCCATCACTTGATGGATCAACTTTTC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTC
2646534 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAA
*
2646599 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
65 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTC
*
2646647 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAA-AAG-A-AAGTTCATAATGAGAAGAAC
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAT
* * ** * * * * **
2646709 TTGTTTAACCCTTTGCTTGAATTCATCATTTGATGGATCAGCATCGC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTC
**** *
2646756 CAAAGAGAGTTCGTAATGAGAAGAACTCATCTGAAGAA-AAG-A-AAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
2646817 CTCATTTGAA
Statistics
Matches: 368, Mismatches: 22, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
109 111 0.30
110 107 0.29
111 4 0.01
112 1 0.00
113 145 0.39
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (112 bp):
CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTC
Done.