Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 68 of 143
Found at i:22209767 original size:149 final size:149
Alignment explanation
Indices: 22209495--22209880 Score: 425
Period size: 149 Copynumber: 2.6 Consensus size: 149
22209485 AAGGAAACAT
* *
22209495 GAAGATATGAAGGGAAAGGTTGAGGTCGCAACAACGAACCCAGTACCTTAAAAGATGTGATGGGA
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATGTGATGGGA
* * * * * * * *
22209560 AAGGTTAAGGCTGCAATGACGAACTCAGCACCTTAGAAGACATGAAGGGAAAGGTTGAGGTCGCA
66 AAGATTGAGGCCGCAACGACAAACCCAGCACCTTAAAAGACATGAAGGGAAAGGTTGAGGCCGCA
* *
22209625 ACAACGAA-CCTGGTACCAC
131 ACAACAAATCC-GATACCAC
* * * * * * *
22209644 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAGAATATGTGATGGGA
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATGTGATGGGA
* * * ** * *
22209709 AAGATTGAGGCCGCAACGATAAACCCAGTACGTTAAAAGATGTGACGGG-AAGGATTGAGGCCGT
66 AAGATTGAGGCCGCAACGACAAACCCAGCACCTTAAAAGACATGAAGGGAAAGG-TTGAGGCCGC
* *
22209773 AACGACAAATCCGATACCAT
130 AACAACAAATCCGATACCAC
* * * * *
22209793 GAAGACATAAAGGGAAAGATTGAGGCCGCAACGACAAACCCAGTACCTTAAAAGATGTGATAGGA
1 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATGTGATGGGA
* *
22209858 AGGATTGAGGCCTCAACGACAAA
66 AAGATTGAGGCCGCAACGACAAA
22209881 TTCGGTACCA
Statistics
Matches: 192, Mismatches: 43, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
148 4 0.02
149 186 0.97
150 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (149 bp):
GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATGTGATGGGA
AAGATTGAGGCCGCAACGACAAACCCAGCACCTTAAAAGACATGAAGGGAAAGGTTGAGGCCGCA
ACAACAAATCCGATACCAC
Found at i:22209876 original size:99 final size:99
Alignment explanation
Indices: 22209492--22209941 Score: 410
Period size: 99 Copynumber: 4.5 Consensus size: 99
22209482 ACCAAGGAAA
* *
22209492 CATGAAGATATGAAGGGAAAGGTTGAGGTCGCAACAACGAACCCAGTACCTTAAAAGATGTGATG
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATGTGATG
* * * * *
22209557 GGAAAGGTTAAGG-CTGCAATGACGAA-CTCAGCAC
66 GGAAAGGTTGAGGCCT-CAACGACAAATC-CGGTAC
* * * * ** *
22209591 CTTAGAAGACATGAAGGGAAAGGTTGAGGTCGCAACAACGAACCTGGTACC--ACGAAGATGTGA
1 CAT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTA-AAAGATGTGA
* * * * *
22209654 TGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTAC
64 TGGGAAAGGTTGAGGCCTCAACGACAAATCCGGTAC
* * * * * ** * *
22209690 CTTAGAATATGTGATGGGAAAGATTGAGGCCGCAACGATAAACCCAGTACGTTAAAAGATGTGAC
1 CAT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATGTGAT
*
22209755 GGG-AAGGATTGAGGCCGT-AACGACAAATCCGATAC
65 GGGAAAGG-TTGAGGCC-TCAACGACAAATCCGGTAC
* * * * *
22209790 CATGAAGACATAAAGGGAAAGATTGAGGCCGCAACGACAAACCCAGTACCTTAAAAGATGTGATA
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATGTGATG
*
22209855 GG-AAGGATTGAGGCCTCAACGACAAATTCGGTAC
66 GGAAAGG-TTGAGGCCTCAACGACAAATCCGGTAC
* * * * * *
22209889 CATGAAGATGTGATGGGAAAGGTGGAGGCCGCAAAGGCGAACCCAATACCTTA
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTA
22209942 GGAACATGAC
Statistics
Matches: 290, Mismatches: 52, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
98 2 0.01
99 207 0.71
100 80 0.28
101 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (99 bp):
CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATGTGATG
GGAAAGGTTGAGGCCTCAACGACAAATCCGGTAC
Found at i:22210185 original size:38 final size:38
Alignment explanation
Indices: 22210060--22210814 Score: 563
Period size: 38 Copynumber: 19.3 Consensus size: 38
22210050 ATCACCATCA
* * *
22210060 AATCTCTTACCCCAATCATGGGGCAGATTGTAGTCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAG-AATCC
** * * *
22210099 AATCTCTTACCCCGATCATAAGGTAAATT-ACAGCCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGA-AG-AATCC
*
22210138 AATCTCTTACCCCGATCATGGAGCAGATTGAAGAATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC
*** * * *
22210176 AATCTCTTACCTTAATCA-GAGGGCAAATTAAAGACAATTC
1 AATCTCTTACCCCGATCATG-GGGCAGATTGAAG--AATCC
* * *
22210216 AATCTCTTACCTCGATCATGAGGAAGATTGAAGACAATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAG--AATCC
* * *
22210256 AATCTTTTACCCTGATCATGGGGCAGATTGAAGAATTC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC
* * * * *
22210294 AATCTCTTA-CCCTAGTTA-GAGGGCATATTAAAGAAACACC
1 AATCTCTTACCCCGA-TCATG-GGGCAGATTGAAG-AA-TCC
* * * *
22210334 AATCTCTTATCCCGATCATGGGGCAAATTGAAGCATCT
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC
* * * *
22210372 AATCTTTTA-CCCTAGTCA-GAAGGCAGATTGAAGACACACC
1 AATCTCTTACCCCGA-TCATG-GGGCAGATTGAAGA-A-TCC
* * **
22210412 AATTTCTTACCCCGATTATGGGGCAGATTGAATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC
* * * *
22210450 AATCTCTTACCCCGATCATAGGGCAGACTAAAGAATAC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC
** ** *
22210488 AATCTCTTACCCTAATCAAAGAGCAGATTGAAGACAATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAG--AATCC
* *
22210528 AATCTTTTACCCCGATCATGGGGCAGATTGAAGCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC
* * *
22210566 AATTTCTTTCCCCAATCATGGGGCAGATTGAAGAATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC
* ** *
22210604 AATATCTTACCCTAATTA-GAGGGCAGATTGAAGATAATCC
1 AATCTCTTACCCCGATCATG-GGGCAGATTGAAG--AATCC
* * * *
22210644 AATCTCTTACCTCAATCATGGGGCAAATTGAAGCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC
* ** * **
22210682 AATCTCGTACCCTAATCATAGGGC-GTATTGACATCATCC
1 AATCTCTTACCCCGATCATGGGGCAG-ATTGA-AGAATCC
22210721 AATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAG--A--ATCC
* * * *
22210763 AATCTCTTACCTCGATCTTGGGGCAGATTAAAGTTATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAG-AATCC
*
22210802 AATCTTTTACCCC
1 AATCTCTTACCCC
22210815 TAAAATCAAG
Statistics
Matches: 566, Mismatches: 119, Indels: 62
0.76 0.16 0.08
Matches are distributed among these distances:
37 11 0.02
38 230 0.41
39 108 0.19
40 171 0.30
41 12 0.02
42 34 0.06
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (38 bp):
AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC
Found at i:22210219 original size:78 final size:78
Alignment explanation
Indices: 22210060--22210814 Score: 592
Period size: 78 Copynumber: 9.7 Consensus size: 78
22210050 ATCACCATCA
* * ** ** * *
22210060 AATCTCTTACCCCAATCATGGGGCAGATTGTAGTCATCCAATCTCTTACCCCGATCATAAGGTAA
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTCTTACCCCGATCATGGGGCAG
*
22210125 ATT-ACAGCCATCC
66 ATTGA-AGCAATCC
* ***
22210138 AATCTCTTACCCCGATCATGGAGCAGATTGAAG-AATCCAATCTCTTACCTTAATCA-GAGGGCA
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTCTTACCCCGATCATG-GGGCA
* * *
22210201 AATTAAAGACAATTC
65 GATTGAAG-CAATCC
* * * * *
22210216 AATCTCTTACCTCGATCATGAGGAAGATTGAAGACAATCCAATCTTTTACCCTGATCATGGGGCA
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGA-AATCCAATCTCTTACCCCGATCATGGGGCA
*
22210281 GATTGAAG-AATTC
65 GATTGAAGCAATCC
* * * * * *
22210294 AATCTCTTA-CCCTAGTTA-GAGGGCATATTAAAGAAACACCAATCTCTTATCCCGATCATGGGG
1 AATCTCTTACCCCGA-TCATG-GGGCAGATTGAAGAAA-TCCAATCTCTTACCCCGATCATGGGG
* *
22210357 CAAATTGAAGC-ATCT
63 CAGATTGAAGCAATCC
* * * * *
22210372 AATCTTTTA-CCCTAGTCA-GAAGGCAGATTGAAGACACA-CCAATTTCTTACCCCGATTATGGG
1 AATCTCTTACCCCGA-TCATG-GGGCAGATTGAAGA-A-ATCCAATCTCTTACCCCGATCATGGG
*
22210434 GCAGATTGAATC-ATCC
62 GCAGATTGAAGCAATCC
* * * * ** ** *
22210450 AATCTCTTACCCCGATCATAGGGCAGACTAAAG-AATACAATCTCTTACCCTAATCAAAGAGCAG
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTCTTACCCCGATCATGGGGCAG
22210514 ATTGAAGACAATCC
66 ATTGAAG-CAATCC
* * * * *
22210528 AATCTTTTACCCCGATCATGGGGCAGATTGAAG-CATCCAATTTCTTTCCCCAATCATGGGGCAG
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTCTTACCCCGATCATGGGGCAG
22210592 ATTGAAG-AATCC
66 ATTGAAGCAATCC
* ** * * *
22210604 AATATCTTACCCTAATTA-GAGGGCAGATTGAAGATAATCCAATCTCTTACCTCAATCATGGGGC
1 AATCTCTTACCCCGATCATG-GGGCAGATTGAAGA-AATCCAATCTCTTACCCCGATCATGGGGC
*
22210668 AAATTGAAGC-ATCC
64 AGATTGAAGCAATCC
* ** * **
22210682 AATCTCGTACCCTAATCATAGGGC-GTATTGACA-TCATCCAATCTCTTACCCCGATCATGGGGC
1 AATCTCTTACCCCGATCATGGGGCAG-ATTGA-AGAAATCCAATCTCTTACCCCGATCATGGGGC
22210745 AGATTGAAGACATCATCC
64 AGATTGAAG-CA--ATCC
* * * ** *
22210763 AATCTCTTACCTCGATCTTGGGGCAGATTAAAGTTATCCAATCTTTTACCCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTCTTACCCC
22210815 TAAAATCAAG
Statistics
Matches: 546, Mismatches: 101, Indels: 57
0.78 0.14 0.08
Matches are distributed among these distances:
75 2 0.00
76 58 0.11
77 70 0.13
78 332 0.61
79 6 0.01
80 33 0.06
81 44 0.08
82 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (78 bp):
AATCTCTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTCTTACCCCGATCATGGGGCAG
ATTGAAGCAATCC
Found at i:22210464 original size:116 final size:118
Alignment explanation
Indices: 22210060--22210814 Score: 604
Period size: 116 Copynumber: 6.4 Consensus size: 118
22210050 ATCACCATCA
* * *
22210060 AATCTCTTACCCCAATCATGGGGCAGATTGTAGTCATCCAATCTCTTACCCCGATCATAAGGTAA
1 AATCTCTTACCCCAATCATGGGGCAGATTG-AATCATCCAATCTCTTACCCCGATCATAGGGCAA
* *
22210125 ATT-ACAGCCATCCAATCTCTTACCC-CGATCATGGA-GCAGATTGAAG--AATCC
65 ATTGA-AG-CATCCAATCTCTTACCCTAGATCATGAAGGCAGATTGAAGACAATCC
** * * * * *
22210176 AATCTCTTACCTTAATCA-GAGGGCAAATTAAAGACAATTCAATCTCTTACCTCGATCAT-GAGG
1 AATCTCTTACCCCAATCATG-GGGCAGATTGAA-TC-ATCCAATCTCTTACCCCGATCATAG-GG
* * *
22210239 -AAGATTGAAGACAATCCAATCTTTTACCCT-GATCATG-GGGCAGATTGAAG--AATTC
62 CAA-ATTGAAG-C-ATCCAATCTCTTACCCTAGATCATGAAGGCAGATTGAAGACAATCC
* * * * * * *
22210294 AATCTCTTACCCTAGTTA-GAGGGCATATTAAAGAAACA-CCAATCTCTTATCCCGATCATGGGG
1 AATCTCTTACCCCAATCATG-GGGCAGATT---GAATCATCCAATCTCTTACCCCGATCATAGGG
* *
22210357 CAAATTGAAGCATCTAATCTTTTACCCTAG-TCA-GAAGGCAGATTGAAGACACA-CC
62 CAAATTGAAGCATCCAATCTCTTACCCTAGATCATGAAGGCAGATTGAAGACA-ATCC
* * * *
22210412 AATTTCTTACCCCGATTATGGGGCAGATTGAATCATCCAATCTCTTACCCCGATCATAGGGCAGA
1 AATCTCTTACCCCAATCATGGGGCAGATTGAATCATCCAATCTCTTACCCCGATCATAGGGCAAA
* * * *
22210477 CTAAAGAATACAATCTCTTACCCTA-ATCA--AAGAGCAGATTGAAGACAATCC
66 TTGAAGCATCCAATCTCTTACCCTAGATCATGAAG-GCAGATTGAAGACAATCC
* * * * * * * *
22210528 AATCTTTTACCCCGATCATGGGGCAGATTGAAGCATCCAATTTCTTTCCCCAATCATGGGGCAGA
1 AATCTCTTACCCCAATCATGGGGCAGATTGAATCATCCAATCTCTTACCCCGATCATAGGGCAAA
* * * * *
22210593 TTGAAGAATCCAATATCTTACCCTA-ATTA-GAGGGCAGATTGAAGATAATCC
66 TTGAAGCATCCAATCTCTTACCCTAGATCATGAAGGCAGATTGAAGACAATCC
* * * * ** **
22210644 AATCTCTTACCTCAATCATGGGGCAAATTGAAGCATCCAATCTCGTACCCTAATCATAGGGCGTA
1 AATCTCTTACCCCAATCATGGGGCAGATTGAATCATCCAATCTCTTACCCCGATCATAGGGCAAA
* * *
22210709 TTGACATCATCCAATCTCTTACCC-CGATCATG-GGGCAGATTGAAGACATCATCC
66 TTGA-AGCATCCAATCTCTTACCCTAGATCATGAAGGCAGATTGAAGACA--ATCC
* * * * * *
22210763 AATCTCTTACCTCGATCTTGGGGCAGATTAAAGTTATCCAATCTTTTACCCC
1 AATCTCTTACCCCAATCATGGGGCAGATTGAA-TCATCCAATCTCTTACCCC
22210815 TAAAATCAAG
Statistics
Matches: 528, Mismatches: 80, Indels: 58
0.79 0.12 0.09
Matches are distributed among these distances:
115 12 0.02
116 278 0.53
117 67 0.13
118 115 0.22
119 38 0.07
120 16 0.03
121 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (118 bp):
AATCTCTTACCCCAATCATGGGGCAGATTGAATCATCCAATCTCTTACCCCGATCATAGGGCAAA
TTGAAGCATCCAATCTCTTACCCTAGATCATGAAGGCAGATTGAAGACAATCC
Found at i:22212499 original size:30 final size:29
Alignment explanation
Indices: 22212465--22212651 Score: 112
Period size: 30 Copynumber: 6.3 Consensus size: 29
22212455 AAAACTCAAA
*
22212465 TTTGACCTTCAAACTTCCTAAAAATTCGAT
1 TTTGACCCTCAAACTTCCTAAAAATT-GAT
* * *
22212495 TTTGACTCTCGAACTATCC-AAAAATTTAGT
1 TTTGACCCTCAAACT-TCCTAAAAATTGA-T
* *
22212525 TTTGACCCTCAAATTTTCTAAAAATTGCAT
1 TTTGACCCTCAAACTTCCTAAAAATTG-AT
* * * *
22212555 TTTAACCCTGAAACTTTCTAAAAATTTCAT
1 TTTGACCCTCAAACTTCCTAAAAA-TTGAT
* * ** * *
22212585 TTTAACCC-CTAAGCTTTTTGAAAATTACAT
1 TTTGACCCTC-AAACTTCCTAAAAATT-GAT
*
22212615 TTTGACCCTCAAACTTTCC-AAAATTTTGA-
1 TTTGACCCTCAAAC-TTCCTAAAA-ATTGAT
22212644 TTTGACCC
1 TTTGACCC
22212652 CTTTTTTTCC
Statistics
Matches: 123, Mismatches: 24, Indels: 21
0.73 0.14 0.12
Matches are distributed among these distances:
29 13 0.11
30 99 0.80
31 11 0.09
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.39
Consensus pattern (29 bp):
TTTGACCCTCAAACTTCCTAAAAATTGAT
Found at i:22212557 original size:60 final size:59
Alignment explanation
Indices: 22212465--22212651 Score: 159
Period size: 60 Copynumber: 3.1 Consensus size: 59
22212455 AAAACTCAAA
* * * * *
22212465 TTTGACCTTCAAACTTCCTAAAAATTCGATTTTGACTCTCGAACTATCCAAAAATTTAGT
1 TTTGACCCTCAAATTTTCTAAAAATTC-ATTTTGACCCTCGAACTTTCCAAAAATTTAGT
* *
22212525 TTTGACCCTCAAATTTTCTAAAAATTGCATTTTAACCCT-GAAACTTTCTAAAAATTTCA-T
1 TTTGACCCTCAAATTTTCTAAAAATT-CATTTTGACCCTCG-AACTTTCCAAAAATTT-AGT
* * * * * *
22212585 TTTAACCC-CTAAGCTTTT-TGAAAATTACATTTTGACCCTCAAACTTTCC-AAAATTTTGA
1 TTTGACCCTC-AA-ATTTTCTAAAAATT-CATTTTGACCCTCGAACTTTCCAAAAATTTAGT
22212644 TTTGACCC
1 TTTGACCC
22212652 CTTTTTTTCC
Statistics
Matches: 103, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
59 16 0.16
60 81 0.79
61 6 0.06
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.39
Consensus pattern (59 bp):
TTTGACCCTCAAATTTTCTAAAAATTCATTTTGACCCTCGAACTTTCCAAAAATTTAGT
Found at i:22212742 original size:29 final size:31
Alignment explanation
Indices: 22212687--22212766 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 31
22212677 ACCCCAAAAC
* * *
22212687 TTTTATTTTTATTTTAATTTAATCCTTTATT
1 TTTTATTTCTATTTAAAATTAATCCTTTATT
**
22212718 TTTTATTTCT-TTTAAAATTAA-CCTTTAAA
1 TTTTATTTCTATTTAAAATTAATCCTTTATT
*
22212747 CTTTATTT-TATTTCAAAATT
1 TTTTATTTCTATTT-AAAATT
22212767 GGCCCTTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 1 0.02
29 16 0.39
30 15 0.37
31 9 0.22
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTATTTCTATTTAAAATTAATCCTTTATT
Found at i:22215048 original size:23 final size:22
Alignment explanation
Indices: 22215017--22215060 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
22215007 AAAGAAATAA
*
22215017 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
22215039 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
22215061 GAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:22218278 original size:19 final size:19
Alignment explanation
Indices: 22218256--22218316 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
22218246 CAACAATAAC
22218256 GTGCGACAGCAACGGTAGT
1 GTGCGACAGCAACGGTAGT
*
22218275 GTGCGGCAGCGATAACGGT-GAT
1 GTGCGACAGC---AACGGTAG-T
*
22218297 GTGCGACAGCAACGTTAGT
1 GTGCGACAGCAACGGTAGT
22218316 G
1 G
22218317 CTTCAGCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
19 16 0.47
20 1 0.03
21 1 0.03
22 16 0.47
ACGTcount: A:0.25, C:0.20, G:0.38, T:0.18
Consensus pattern (19 bp):
GTGCGACAGCAACGGTAGT
Found at i:22220665 original size:22 final size:23
Alignment explanation
Indices: 22220640--22220709 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 23
22220630 TTTTTCACAC
22220640 AAATTT-ATATCAATTTCTCTCT
1 AAATTTCATATCAATTTCTCTCT
* *
22220662 AAATTTCACT-T-AATTTCTTTTT
1 AAATTTCA-TATCAATTTCTCTCT
22220684 AAATTTCATA-CAAATTTCTCTCT
1 AAATTTCATATC-AATTTCTCTCT
22220707 AAA
1 AAA
22220710 GCTCTCAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 1 0.03
22 23 0.59
23 14 0.36
24 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATTTCATATCAATTTCTCTCT
Found at i:22220867 original size:10 final size:10
Alignment explanation
Indices: 22220849--22220914 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
22220839 GAGTTAATTT
*
22220849 TATTTTTTAA
1 TATTATTTAA
22220859 TATTATTTAA
1 TATTATTTAA
*
22220869 TATCATTTAA
1 TATTATTTAA
22220879 T-TT-TTATAA
1 TATTATT-TAA
*
22220888 T-TTAATT-A
1 TATTATTTAA
22220896 -ATT-TTTAA
1 TATTATTTAA
22220904 TATTATTTAA
1 TATTATTTAA
22220914 T
1 T
22220915 TATTTTATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 2 0.04
8 6 0.13
9 11 0.24
10 26 0.58
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTTAA
Found at i:22220884 original size:17 final size:17
Alignment explanation
Indices: 22220864--22220915 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
22220854 TTTAATATTA
*
22220864 TTTAATATCATTTAATT
1 TTTAATATTATTTAATT
*
22220881 TTT-ATAATTTAATTAATT
1 TTTAAT-A-TTATTTAATT
22220899 TTTAATATTATTTAATT
1 TTTAATATTATTTAATT
22220916 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 2 0.07
17 13 0.45
18 12 0.41
19 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATATTATTTAATT
Found at i:22220898 original size:18 final size:20
Alignment explanation
Indices: 22220875--22220920 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
22220865 TTAATATCAT
22220875 TTAATTTTT-ATA-ATTTAA
1 TTAATTTTTAATATATTTAA
22220893 TTAATTTTTAATATTATTTAA
1 TTAATTTTTAATA-TATTTAA
22220914 TT-ATTTT
1 TTAATTTT
22220921 ATTTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.36
19 3 0.12
20 5 0.20
21 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTAATTTTTAATATATTTAA
Found at i:22220904 original size:45 final size:47
Alignment explanation
Indices: 22220842--22220948 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 47
22220832 ATGGTAAGAG
22220842 TTAATTT-TATTTTTTAATATTATTTAA-TATCATTTA-ATTTTTATAAT
1 TTAATTTATA-TTTTTAATATTATTTAATTAT--TTTATATTTTTATAAT
*
22220889 TTAA-TTA-ATTTTTAATATTATTTAATTATTTTATTTTTTTATAAT
1 TTAATTTATATTTTTAATATTATTTAATTATTTTATATTTTTATAAT
22220934 TTAATTTATATTTTT
1 TTAATTTATATTTTT
22220949 TTATGTGAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
44 4 0.07
45 31 0.57
46 9 0.17
47 10 0.19
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (47 bp):
TTAATTTATATTTTTAATATTATTTAATTATTTTATATTTTTATAAT
Found at i:22220925 original size:24 final size:24
Alignment explanation
Indices: 22220853--22220939 Score: 67
Period size: 24 Copynumber: 3.8 Consensus size: 24
22220843 TAATTTTATT
* *
22220853 TTTTAATATTATTTAATATCATTTAA
1 TTTTAATATAATTTAAT-T-ATTTTA
*
22220879 TTTT--TATAATTTAATTA--AT-
1 TTTTAATATAATTTAATTATTTTA
*
22220898 TTTTAATATTATTTAATTATTTTA
1 TTTTAATATAATTTAATTATTTTA
**
22220922 TTTTTTTATAATTTAATT
1 TTTTAATATAATTTAATT
22220940 TATATTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
19 4 0.08
21 12 0.25
22 1 0.02
23 2 0.04
24 25 0.52
26 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTAATATAATTTAATTATTTTA
Found at i:22224717 original size:18 final size:18
Alignment explanation
Indices: 22224676--22224710 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
22224666 ACTAGAAAAC
22224676 GGATACATATAAGGGTTA
1 GGATACATATAAGGGTTA
22224694 GGATACATATAAGGGTT
1 GGATACATATAAGGGTT
22224711 TTGATACGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
GGATACATATAAGGGTTA
Found at i:22231389 original size:16 final size:16
Alignment explanation
Indices: 22231368--22231400 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22231358 TGGAAATAGA
*
22231368 CTTCAGATTGTCGAAG
1 CTTCAGATTGTCAAAG
22231384 CTTCAGATTGTCAAAG
1 CTTCAGATTGTCAAAG
22231400 C
1 C
22231401 ATTTCTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (16 bp):
CTTCAGATTGTCAAAG
Found at i:22237276 original size:18 final size:18
Alignment explanation
Indices: 22237250--22237296 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
22237240 CTCAAGTCAT
22237250 TTCCAATCGCCACCTCAA
1 TTCCAATCGCCACCTCAA
* *
22237268 TTCCTATCGCCACCTTAA
1 TTCCAATCGCCACCTCAA
*
22237286 TTCCCATCGCC
1 TTCCAATCGCC
22237297 TTATAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.21, C:0.45, G:0.06, T:0.28
Consensus pattern (18 bp):
TTCCAATCGCCACCTCAA
Found at i:22237631 original size:62 final size:59
Alignment explanation
Indices: 22237520--22237655 Score: 173
Period size: 62 Copynumber: 2.2 Consensus size: 59
22237510 GCATTGATTT
* * *
22237520 ATTTCGAATATTTTTGTAAACATTATTTTTATATTTTATCATTTAATGAAATCGAAGTTC
1 ATTT-GAATATTTTTGTAAACATTATTTTCATATTGTATCATTTAATGAAATAGAAGTTC
* *
22237580 ATTTGAATATTTTTGTACACATTAGTTTTGGCATATTGTATCATTTAATGAAATAGATGTTC
1 ATTTGAATATTTTTGTAAACATTA-TTTT--CATATTGTATCATTTAATGAAATAGAAGTTC
* *
22237642 TTTTAAATATTTTT
1 ATTTGAATATTTTT
22237656 CAACATTGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 19 0.29
60 8 0.12
62 39 0.59
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (59 bp):
ATTTGAATATTTTTGTAAACATTATTTTCATATTGTATCATTTAATGAAATAGAAGTTC
Found at i:22238247 original size:22 final size:22
Alignment explanation
Indices: 22238222--22238312 Score: 75
Period size: 21 Copynumber: 4.2 Consensus size: 22
22238212 AAAAAAAACA
*
22238222 TAATTTAATATATCCTAAACCC
1 TAATTTAAAATATCCTAAACCC
* *
22238244 TAATTTAAAAAAT-C-AATACCT
1 TAATTTAAAATATCCTAA-ACCC
*
22238265 TTATTTAAAATA-CCATAAACCC
1 TAATTTAAAATATCC-TAAACCC
*
22238287 TAATTTAAAA-A-CCATAAACCT
1 TAATTTAAAATATCC-TAAACCC
22238308 TAATT
1 TAATT
22238313 ACACCAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
20 2 0.04
21 30 0.53
22 23 0.40
23 2 0.04
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (22 bp):
TAATTTAAAATATCCTAAACCC
Found at i:22238302 original size:21 final size:21
Alignment explanation
Indices: 22238237--22238312 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
22238227 TAATATATCC
22238237 TAAACCCTAATTTAAAAA--A
1 TAAACCCTAATTTAAAAACCA
* *
22238256 TCAATACCTTTATTTAAAATACCA
1 T-AA-ACCCTAATTTAAAA-ACCA
22238280 TAAACCCTAATTTAAAAACCA
1 TAAACCCTAATTTAAAAACCA
*
22238301 TAAACCTTAATT
1 TAAACCCTAATT
22238313 ACACCAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 27 0.57
22 13 0.28
23 2 0.04
24 2 0.04
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAACCCTAATTTAAAAACCA
Found at i:22239642 original size:19 final size:20
Alignment explanation
Indices: 22239617--22239658 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
22239607 CATAAAATCA
22239617 AATAATAAATATATAATTCTAT
1 AATAA-AAATATAT-ATTCTAT
22239639 AATAAAAATATATATTCTAT
1 AATAAAAATATATATTCTAT
22239659 GTATACCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 8 0.40
22 5 0.25
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAAAATATATATTCTAT
Found at i:22242641 original size:94 final size:91
Alignment explanation
Indices: 22242462--22242677 Score: 245
Period size: 94 Copynumber: 2.3 Consensus size: 91
22242452 ACTTTATCAC
* * *
22242462 TATTTTTATTAAAAATTAATTTTAATTCCACATTGACTAGAGAACACTTTCATGCTCACACTTAC
1 TATTTTTATTAAAAATTAATTTTAA-TCCACAATGACTAGAGAACACTCTCATGATCACACTTAC
22242527 CTTATAAATAAGTGTCAATTTCTTCAT
65 CTTATAAATAAGTGTCAATTTCTTCAT
* * * * * **
22242554 TTTTTTTATTAAAAAGTTCATTTTAATCCTATAATGACTAGAGCACACTCTCATATATCACGTTT
1 TATTTTTATTAAAAA-TTAATTTTAATCC-ACAATGACTAGAGAACACTCTCAT-GATCACACTT
*
22242619 ACCTTATAAATAAGTGAT-AATTTCTTCCT
63 ACCTTATAAATAAGTG-TCAATTTCTTCAT
**
22242648 TATTTTCATAAAAAAAATTAATTTTAATCC
1 TATTTT--TATTAAAAATTAATTTTAATCC
22242678 CATATTAGCC
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
92 17 0.17
93 29 0.28
94 37 0.36
95 13 0.13
96 7 0.07
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (91 bp):
TATTTTTATTAAAAATTAATTTTAATCCACAATGACTAGAGAACACTCTCATGATCACACTTACC
TTATAAATAAGTGTCAATTTCTTCAT
Found at i:22242811 original size:69 final size:67
Alignment explanation
Indices: 22242689--22242881 Score: 273
Period size: 69 Copynumber: 2.8 Consensus size: 67
22242679 ATATTAGCCA
* * * *
22242689 ACTCCCATAGCTCACTTCTTCACTAGTTTCATTTAAAAAGCTAATTTTAATCTCATATTGACTAG
1 ACTCTCATAGCTCACTTC-T-ACTATTTTCA-TTAAAAAGATAATTTTAATCTCATATTGACCAG
22242754 AGAAT
63 AGAAT
*
22242759 ACTCTCATAGCTCACTTCTAAACTATTTTCATTAAAAAGTTAATTTTAATCTCATATTGACCAGA
1 ACTCTCATAGCTCACTTCT--ACTATTTTCATTAAAAAGATAATTTTAATCTCATATTGACCAGA
22242824 GAAT
64 GAAT
*
22242828 ACTCTCATAGTTCACTTC-ACTATTTTCATTAAAAA-ATAATTTTAATCTCATATT
1 ACTCTCATAGCTCACTTCTACTATTTTCATTAAAAAGATAATTTTAATCTCATATT
22242882 TACCCTATAA
Statistics
Matches: 115, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
65 18 0.16
66 17 0.15
69 54 0.47
70 26 0.23
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (67 bp):
ACTCTCATAGCTCACTTCTACTATTTTCATTAAAAAGATAATTTTAATCTCATATTGACCAGAGA
AT
Found at i:22244013 original size:38 final size:37
Alignment explanation
Indices: 22243971--22244055 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 37
22243961 TTTTTTAGAT
22243971 ATTTTAAAACA-TTTTTATCATTTTTTATTCAAAAATAA
1 ATTTTAAAACATTTTTTATCA-TTTTTATTCAAAAAT-A
* *
22244009 ATTTTAAAATATTTTTTTATCATTTTTATTCAAAAATG
1 ATTTTAAAACA-TTTTTTATCATTTTTATTCAAAAATA
22244047 ATTTTAAAA
1 ATTTTAAAA
22244056 AAAAATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 19 0.44
39 15 0.35
40 9 0.21
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (37 bp):
ATTTTAAAACATTTTTTATCATTTTTATTCAAAAATA
Found at i:22244476 original size:29 final size:30
Alignment explanation
Indices: 22244443--22244501 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
22244433 TATGGTTTAA
*
22244443 TGTGCAAT-TGTATGCAT-AAATTTAGATTT
1 TGTGCAATCT-TATACATGAAATTTAGATTT
*
22244472 TGTGCAATCTTATACATGAAATTTTGATTT
1 TGTGCAATCTTATACATGAAATTTAGATTT
22244502 GATCTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (30 bp):
TGTGCAATCTTATACATGAAATTTAGATTT
Found at i:22244714 original size:29 final size:30
Alignment explanation
Indices: 22244681--22244742 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
22244671 ATTTTACGTG
* *
22244681 TATAATT-ATATTAAATTAAAATTCATATA
1 TATAATTAACATTAAATCAAAATTCATATA
*
22244710 TATAATTACACATTAAATCAAAATTCATGTA
1 TATAATTA-ACATTAAATCAAAATTCATATA
22244741 TA
1 TA
22244743 ATTTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 7 0.25
31 21 0.75
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (30 bp):
TATAATTAACATTAAATCAAAATTCATATA
Found at i:22245251 original size:5 final size:6
Alignment explanation
Indices: 22245235--22245259 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22245225 TTATAAATAC
22245235 CAAAAA CAAAAA CAAAAA CAAAAA C
1 CAAAAA CAAAAA CAAAAA CAAAAA C
22245260 CCTCCTGTAA
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:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:22265292 original size:28 final size:28
Alignment explanation
Indices: 22265256--22265320 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
22265246 TGAGGAGAAA
22265256 ACAAAACATACCAGGTATTCATGAATTC
1 ACAAAACATACCAGGTATTCATGAATTC
22265284 ACAAAACATACCAGGTATTCATGAATTC
1 ACAAAACATACCAGGTATTCATGAATTC
*
22265312 ACTAAACAT
1 ACAAAACAT
22265321 TACACCTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.25
Consensus pattern (28 bp):
ACAAAACATACCAGGTATTCATGAATTC
Found at i:22299903 original size:17 final size:17
Alignment explanation
Indices: 22299877--22299914 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
22299867 ACTAAAATAT
22299877 AATTTTTTTTATTAATTTA
1 AATTTTTTTTA--AATTTA
22299896 AATTTTTTTTAAATTTA
1 AATTTTTTTTAAATTTA
22299913 AA
1 AA
22299915 GAGTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTTTTTTTAAATTTA
Found at i:22301371 original size:2 final size:2
Alignment explanation
Indices: 22301364--22301404 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
22301354 TTCAAATTGC
22301364 TA TA TA TA TA TA TA TA TA TA TA TA 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 TA TA TA T
22301405 TAGATTTGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22307873 original size:10 final size:9
Alignment explanation
Indices: 22307851--22307909 Score: 55
Period size: 9 Copynumber: 6.1 Consensus size: 9
22307841 ATTTTAAAAT
22307851 TAAAAATTA
1 TAAAAATTA
22307860 TAAAAATTA
1 TAAAAATTA
22307869 CTAAAAATTAA
1 -TAAAAATT-A
*
22307880 TTAAAAATCA
1 -TAAAAATTA
*
22307890 TAAAATTCTA
1 TAAAAAT-TA
*
22307900 TAAAATTTA
1 TAAAAATTA
22307909 T
1 T
22307910 TTTATTCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
9 18 0.42
10 17 0.40
11 8 0.19
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:22307884 original size:30 final size:29
Alignment explanation
Indices: 22307848--22307906 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
22307838 TTCATTTTAA
*
22307848 AATTAAAAATTATAAAAATTACTA-AAAATT
1 AATTAAAAATCAT-AAAATT-CTATAAAATT
22307878 AATTAAAAATCATAAAATTCTATAAAATT
1 AATTAAAAATCATAAAATTCTATAAAATT
22307907 TATTTTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 3 0.11
29 12 0.44
30 12 0.44
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (29 bp):
AATTAAAAATCATAAAATTCTATAAAATT
Found at i:22310066 original size:48 final size:48
Alignment explanation
Indices: 22309663--22310035 Score: 602
Period size: 48 Copynumber: 7.8 Consensus size: 48
22309653 ACCAGTCACT
* * * * *
22309663 CCTTCAGTGCCTGCAACACCAACTCAACATTGGGCTCCAGGTCCTGCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
*
22309711 CCTTCAGTGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
*
22309759 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTACAGCTCCTCCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
* * *
22309807 CCTTCAATGCCTGCAACCCCAACTCAACCTTGGACTACAGCTTCTCCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
* *
22309855 CCTTCAATGCCTACGACACCAACTCAACCTTGGACTCCAGCTCCTCCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
* *
22309903 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTACAGCTCCTCCT
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
22309951 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
* *
22309999 CCTTTAGTGCCTGCAACACCAACTCAACCTTGGACTC
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTC
22310036 TAGGTCCTGC
Statistics
Matches: 304, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 304 1.00
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.22
Consensus pattern (48 bp):
CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
Found at i:22310169 original size:66 final size:65
Alignment explanation
Indices: 22310063--22310372 Score: 404
Period size: 66 Copynumber: 4.7 Consensus size: 65
22310053 CCAGCATCAA
* * *
22310063 CACCGGCTACACCTTCTGTGCCAGCAACACCATCTAACCCTTGGGCTCCAACCCCTGCATCCTGG
1 CACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCAACCCCTGCA-CCTGG
22310128 G
65 G
** * * * * *
22310129 CACCAGCTACACCACCTGTGCCAACAGCACCCTCTGACCCTTGGGCTTCAACCCCTGTATCATGG
1 CACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCAACCCCTGCA-CCTGG
22310194 G
65 G
* * * *
22310195 CACCAGCTACACCTTCTGTGCCAACACCACCATCTGACTCTTGGACTCCAAGCCCTGCACCTTGG
1 CACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCAACCCCTGCACC-TGG
22310260 G
65 G
* * * *
22310261 CACCAGCTACACCTTCTGTGCCAGCAACACCTTCTGACCCTTGGGCTCCAAGCCCTTCACCTCGG
1 CACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCAACCCCTGCACCT-GG
22310326 G
65 G
* *
22310327 CACCAACTACACCTTCTCTGCCAACAACACCATCTGACCCTTGGGC
1 CACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGC
22310373 ACCAGCTACA
Statistics
Matches: 212, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
65 2 0.01
66 210 0.99
ACGTcount: A:0.21, C:0.42, G:0.17, T:0.20
Consensus pattern (65 bp):
CACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCAACCCCTGCACCTGGG
Found at i:22310382 original size:45 final size:45
Alignment explanation
Indices: 22310324--22310424 Score: 157
Period size: 45 Copynumber: 2.2 Consensus size: 45
22310314 CCTTCACCTC
* *
22310324 GGGCACCAACTACACCTTCTCTGCCAACAACACCATCTGACCCTT
1 GGGCACCAGCTACACCTTCTCTACCAACAACACCATCTGACCCTT
* *
22310369 GGGCACCAGCTACACCTTCTGTACCAGCAACACCATCTGACCCTT
1 GGGCACCAGCTACACCTTCTCTACCAACAACACCATCTGACCCTT
*
22310414 GGGCTCCAGCT
1 GGGCACCAGCT
22310425 CCAGCTCCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.20
Consensus pattern (45 bp):
GGGCACCAGCTACACCTTCTCTACCAACAACACCATCTGACCCTT
Found at i:22310394 original size:18 final size:18
Alignment explanation
Indices: 22310373--22310407 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22310363 ACCCTTGGGC
* *
22310373 ACCAGCTACACCTTCTGT
1 ACCAGCAACACCATCTGT
22310391 ACCAGCAACACCATCTG
1 ACCAGCAACACCATCTG
22310408 ACCCTTGGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.40, G:0.11, T:0.20
Consensus pattern (18 bp):
ACCAGCAACACCATCTGT
Found at i:22310427 original size:6 final size:6
Alignment explanation
Indices: 22310417--22310462 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
22310407 GACCCTTGGG
* *
22310417 CTCCAG CTCCAG CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCC
1 CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCC
22310463 CTATCTATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.15, C:0.52, G:0.04, T:0.28
Consensus pattern (6 bp):
CTCCAT
Found at i:22314653 original size:30 final size:30
Alignment explanation
Indices: 22314617--22314676 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
22314607 TTACTCAAGA
22314617 ATGAAGTGATTTAAAATGAGGGGGAGAGGC
1 ATGAAGTGATTTAAAATGAGGGGGAGAGGC
*
22314647 ATGAAGTGATTTACAATGAGGGGGAGAGGC
1 ATGAAGTGATTTAAAATGAGGGGGAGAGGC
22314677 CTCTATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.05, G:0.40, T:0.20
Consensus pattern (30 bp):
ATGAAGTGATTTAAAATGAGGGGGAGAGGC
Found at i:22319861 original size:21 final size:20
Alignment explanation
Indices: 22319837--22319880 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
22319827 TGAAAACTAT
22319837 TTACAGATAAAATCTCTAAGA
1 TTACA-ATAAAATCTCTAAGA
*
22319858 TTACAATCAAATCTCTAAGA
1 TTACAATAAAATCTCTAAGA
22319878 TTA
1 TTA
22319881 TACTAATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (20 bp):
TTACAATAAAATCTCTAAGA
Found at i:22319871 original size:20 final size:21
Alignment explanation
Indices: 22319846--22319903 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
22319836 TTTACAGATA
22319846 AAATCTCTAAGATTAC-AATC
1 AAATCTCTAAGATTACTAATC
22319866 AAATCTCTAAGATTATACTAATC
1 AAATCTCTAAGA-T-TACTAATC
*
22319889 ATATCTTCTAAGATT
1 AAATC-TCTAAGATT
22319904 TACATATCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 12 0.36
21 1 0.03
22 4 0.12
23 9 0.27
24 7 0.21
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
AAATCTCTAAGATTACTAATC
Found at i:22319894 original size:23 final size:21
Alignment explanation
Indices: 22319848--22319915 Score: 84
Period size: 23 Copynumber: 3.1 Consensus size: 21
22319838 TACAGATAAA
*
22319848 ATCTCTAAGA-TTACAATCAA
1 ATCTCTAAGATTTACAATCAT
22319868 ATCTCTAAGATTATACTAATCAT
1 ATCTCTAAGATT-TAC-AATCAT
22319891 ATCTTCTAAGATTTACATATCAT
1 ATC-TCTAAGATTTACA-ATCAT
22319914 AT
1 AT
22319916 AAGATTGCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
20 10 0.24
21 1 0.02
22 4 0.10
23 18 0.43
24 9 0.21
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (21 bp):
ATCTCTAAGATTTACAATCAT
Found at i:22319911 original size:18 final size:17
Alignment explanation
Indices: 22319888--22319930 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
22319878 TTATACTAAT
*
22319888 CATATCTTCTAAGATTTA
1 CATATCTTATAAGA-TTA
* *
22319906 CATATCATATAAGATTG
1 CATATCTTATAAGATTA
22319923 CATATCTT
1 CATATCTT
22319931 GATGATTACG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (17 bp):
CATATCTTATAAGATTA
Found at i:22321428 original size:21 final size:23
Alignment explanation
Indices: 22321377--22321428 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
22321367 TTTCTTTATT
* *
22321377 TTCCATTTTCTTCTCCTTCTCCC
1 TTCCTTTTTCTTCTCCTTCTCCA
**
22321400 TTTGTTTTTC-TC-CCTTCTCCA
1 TTCCTTTTTCTTCTCCTTCTCCA
22321421 TTCCTTTT
1 TTCCTTTT
22321429 AACGTACTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 14 0.61
22 2 0.09
23 7 0.30
ACGTcount: A:0.04, C:0.37, G:0.02, T:0.58
Consensus pattern (23 bp):
TTCCTTTTTCTTCTCCTTCTCCA
Found at i:22329198 original size:38 final size:38
Alignment explanation
Indices: 22329142--22329235 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
22329132 AAAAGAGAAA
* *
22329142 TACTGATTATATTGAATGCTTGCTTAAGCGAGCA-AATC
1 TACTGATTATACTGAATGCTTGCTCAAGCGAG-AGAATC
*
22329180 TACTAATTATACTGAATGCTTGCTCAAGCGAGAGAATC
1 TACTGATTATACTGAATGCTTGCTCAAGCGAGAGAATC
* *
22329218 CACTGATTTTACTGAATG
1 TACTGATTATACTGAATG
22329236 TTCACTCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
37 1 0.02
38 48 0.98
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (38 bp):
TACTGATTATACTGAATGCTTGCTCAAGCGAGAGAATC
Found at i:22334791 original size:18 final size:19
Alignment explanation
Indices: 22334757--22334792 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22334747 AAAATTAGGA
*
22334757 GTTTCAATCTTTTCTTGCT
1 GTTTCAATCTATTCTTGCT
22334776 GTTTCAATC-ATTCTTGC
1 GTTTCAATCTATTCTTGC
22334793 ACAAAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.14, C:0.22, G:0.11, T:0.53
Consensus pattern (19 bp):
GTTTCAATCTATTCTTGCT
Found at i:22337783 original size:30 final size:30
Alignment explanation
Indices: 22337748--22337902 Score: 188
Period size: 30 Copynumber: 5.2 Consensus size: 30
22337738 TTAAAAATCT
* *
22337748 CATTTTAACCCTCAAACTTCTCTAAAATTG
1 CATTTTAACCCTCAAACTTTTCTAAAATTA
* * * *
22337778 TATTTTAAACCTCAAACTTTTATAAAATCA
1 CATTTTAACCCTCAAACTTTTCTAAAATTA
*
22337808 CATTTTAACCCTTAAACTTTTCTAAAATTA
1 CATTTTAACCCTCAAACTTTTCTAAAATTA
** *
22337838 CATTTTGGCCCT-AAACTTTTCCAAAATTA
1 CATTTTAACCCTCAAACTTTTCTAAAATTA
*
22337867 CATTTTAACCC-CTAAAATTTTCTAAAATTA
1 CATTTTAACCCTC-AAACTTTTCTAAAATTA
22337897 CATTTT
1 CATTTT
22337903 GGCCCCTAAA
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
29 25 0.24
30 80 0.76
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.41
Consensus pattern (30 bp):
CATTTTAACCCTCAAACTTTTCTAAAATTA
Found at i:22337834 original size:60 final size:58
Alignment explanation
Indices: 22337737--22337902 Score: 197
Period size: 59 Copynumber: 2.8 Consensus size: 58
22337727 CCTTGTTTTC
* * * **
22337737 TTTAAAAATCTCATTTTAACCCTCAAACTTCTCTAAAATTGTATTTTAAACCTCAAACT
1 TTTAAAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTAAACCT-AAACT
***
22337796 TTTATAAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGGCCCTAAACT
1 TTTA-AAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTAAACCTAAACT
* * * *
22337855 TTTCCAAAATTACATTTTAACCCCTAAAATTTTCTAAAATTACATTTT
1 TTT-AAAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTT
22337903 GGCCCCTAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
59 52 0.56
60 41 0.44
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (58 bp):
TTTAAAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTAAACCTAAACT
Found at i:22337863 original size:29 final size:29
Alignment explanation
Indices: 22337748--22337926 Score: 169
Period size: 30 Copynumber: 6.0 Consensus size: 29
22337738 TTAAAAATCT
* * *
22337748 CATTTTAACCCTCAAACTTCTCTAAAATTG
1 CATTTTAGCCCT-AAACTTTTCTAAAATTA
* ** * *
22337778 TATTTTAAACCTCAAACTTTTATAAAATCA
1 CATTTTAGCCCT-AAACTTTTCTAAAATTA
*
22337808 CATTTTAACCCTTAAACTTTTCTAAAATTA
1 CATTTTAGCCC-TAAACTTTTCTAAAATTA
* *
22337838 CATTTTGGCCCTAAACTTTTCCAAAATTA
1 CATTTTAGCCCTAAACTTTTCTAAAATTA
* *
22337867 CATTTTAACCCCTAAAATTTTCTAAAATTA
1 CATTTT-AGCCCTAAACTTTTCTAAAATTA
* * *
22337897 CATTTTGGCCCCTAAACTTCTCCAAAATTA
1 CATTTTAG-CCCTAAACTTTTCTAAAATTA
22337927 TGATTTTGCC
Statistics
Matches: 124, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
29 23 0.19
30 100 0.81
31 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39
Consensus pattern (29 bp):
CATTTTAGCCCTAAACTTTTCTAAAATTA
Found at i:22337888 original size:59 final size:60
Alignment explanation
Indices: 22337791--22337926 Score: 211
Period size: 59 Copynumber: 2.3 Consensus size: 60
22337781 TTTAAACCTC
** * * *
22337791 AAACTTTTATAAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGG-CCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAAATTTTCTAAAATTACATTTTGGCCCCT
22337850 AAACTTTTCCAAAATTACATTTTAACCCCTAAAATTTTCTAAAATTACATTTTGGCCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAAATTTTCTAAAATTACATTTTGGCCCCT
*
22337910 AAACTTCTCCAAAATTA
1 AAACTTTTCCAAAATTA
22337927 TGATTTTGCC
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 50 0.71
60 20 0.29
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (60 bp):
AAACTTTTCCAAAATTACATTTTAACCCCTAAAATTTTCTAAAATTACATTTTGGCCCCT
Found at i:22337961 original size:29 final size:29
Alignment explanation
Indices: 22337920--22337996 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
22337910 AAACTTCTCC
** *
22337920 AAAATTATGATTTTGCCCCTGAATATCCA
1 AAAATTACCATTTTACCCCTGAATATCCA
* *
22337949 AAAATTACCATTTTACCCTTGAACATCCA
1 AAAATTACCATTTTACCCCTGAATATCCA
*
22337978 AAAATTACTATTTTACCCC
1 AAAATTACCATTTTACCCC
22337997 CACATTTCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTGAATATCCA
Found at i:22337961 original size:60 final size:59
Alignment explanation
Indices: 22337801--22337962 Score: 166
Period size: 59 Copynumber: 2.7 Consensus size: 59
22337791 AAACTTTTAT
* * * * * * *
22337801 AAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGGCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAAATATCCAAAAATTACATTTTGGCCCTAAACTTCTCC
* * *
22337860 AAAATTACATTTTAACCCCTAAAATTTTCTAAAATTACATTTTGGCCCCTAAACTTCTCC
1 AAAATTACATTTTAACCCCTAAAATATCCAAAAATTACATTTTGG-CCCTAAACTTCTCC
* * *
22337920 AAAATTATGATTTT-GCCCCT-GAATATCCAAAAATTACCATTTT
1 AAAATTA-CATTTTAACCCCTAAAATATCCAAAAATTA-CATTTT
22337963 ACCCTTGAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
59 54 0.60
60 31 0.34
61 5 0.06
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
AAAATTACATTTTAACCCCTAAAATATCCAAAAATTACATTTTGGCCCTAAACTTCTCC
Found at i:22340623 original size:19 final size:20
Alignment explanation
Indices: 22340577--22340623 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
22340567 TAAATTAAAA
22340577 TATTAAA-ATTTTAATTGAT
1 TATTAAATATTTTAATTGAT
*
22340596 TATAAAAATATTTTAATTG-T
1 TAT-TAAATATTTTAATTGAT
22340616 TATTAAAT
1 TATTAAAT
22340624 TAAGTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 7 0.29
20 7 0.29
21 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TATTAAATATTTTAATTGAT
Found at i:22348214 original size:13 final size:13
Alignment explanation
Indices: 22348196--22348252 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 13
22348186 AGCAAATTAT
22348196 TTCTTTTTTTTTA
1 TTCTTTTTTTTTA
* *
22348209 TTCTTTTCTCTTA
1 TTCTTTTTTTTTA
*
22348222 TTCTTTTCTTTCTTT
1 TTCTTTT-TTT-TTA
22348237 TTCTCTCTTTTTTTA
1 TTCT-T-TTTTTTTA
22348252 T
1 T
22348253 AGGTAACTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 18 0.53
14 1 0.03
15 9 0.26
16 4 0.12
17 2 0.06
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTTTTTTTTA
Found at i:22349238 original size:14 final size:16
Alignment explanation
Indices: 22349208--22349245 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
22349198 CTCTTCCTTC
22349208 TCTTCTTCAAGGTCCT
1 TCTTCTTCAAGGTCCT
22349224 TC-TCTTCAA-GTCCT
1 TCTTCTTCAAGGTCCT
22349238 TCTTCTTC
1 TCTTCTTC
22349246 TCCTTCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 12 0.57
16 2 0.10
ACGTcount: A:0.11, C:0.34, G:0.08, T:0.47
Consensus pattern (16 bp):
TCTTCTTCAAGGTCCT
Found at i:22349858 original size:12 final size:11
Alignment explanation
Indices: 22349825--22349859 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
22349815 ATTCTCCTGC
22349825 TTTTCCTTCTT
1 TTTTCCTTCTT
22349836 TTTTCCTTTCTCT
1 TTTTCC-TTCT-T
22349849 TTTTCCTTCTT
1 TTTTCCTTCTT
22349860 CTTGGGTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.32
12 8 0.36
13 7 0.32
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTCCTTCTT
Found at i:22352351 original size:3 final size:3
Alignment explanation
Indices: 22352343--22352391 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
22352333 ATTTATTTCT
* ** *
22352343 TTA TTA TTA ATA TTA TTA TTA CAA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22352391 T
1 T
22352392 AAATAATGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:22353129 original size:6 final size:6
Alignment explanation
Indices: 22353102--22353184 Score: 75
Period size: 6 Copynumber: 14.2 Consensus size: 6
22353092 GACTTTCATC
* * *
22353102 ATTTAA ATTTACA A--TAA TTTTAA ATTTAA ATATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
**
22353149 A-TTAA ATTTAA ATTTTAA A-ACAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA A
22353185 AATAAAGTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
4 1 0.02
5 10 0.16
6 43 0.69
7 8 0.13
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:22353141 original size:18 final size:17
Alignment explanation
Indices: 22353102--22353213 Score: 127
Period size: 18 Copynumber: 6.4 Consensus size: 17
22353092 GACTTTCATC
*
22353102 ATTTAAATTTACAATAA
1 ATTTAAATTTAAAATAA
*
22353119 TTTTAAATTTAAATATAA
1 ATTTAAATTTAAA-ATAA
* *
22353137 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
*
22353154 ATTTAAATTTTAAAACAA
1 ATTTAAA-TTTAAAATAA
22353172 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
*
22353190 AGTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
22353207 ATTTAAA
1 ATTTAAA
22353214 ATGGGTTTAG
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
17 37 0.47
18 42 0.53
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:22353143 original size:35 final size:33
Alignment explanation
Indices: 22353102--22353213 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 33
22353092 GACTTTCATC
*
22353102 ATTTAAATTTACAATAATTTTAAATTTAAATATAA
1 ATTTAAATTTA-AATAAATTTAAATTTAAA-ATAA
* *
22353137 ATTTAAACTTAAATTAAATTTAAATTTTAAAACAA
1 ATTTAAATTTAAA-TAAATTTAAA-TTTAAAATAA
*
22353172 ATTTAAATTTAAAAATAAAGTT-AATCTTAAAATAA
1 ATTTAAATTT--AAATAAATTTAAAT-TTAAAATAA
22353207 ATTTAAA
1 ATTTAAA
22353214 ATGGGTTTAG
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
34 3 0.05
35 48 0.73
36 12 0.18
37 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (33 bp):
ATTTAAATTTAAATAAATTTAAATTTAAAATAA
Found at i:22370444 original size:44 final size:44
Alignment explanation
Indices: 22370381--22370470 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
22370371 ACGTGGTGGT
22370381 CAGTTTGGAAAGGGGAGTTACGAATTCTGTGGTTAAGCAATTGG
1 CAGTTTGGAAAGGGGAGTTACGAATTCTGTGGTTAAGCAATTGG
22370425 CAGTTTGGAAAGGGGAGTTACGAATTCTGTGGTTAAGCAATTGG
1 CAGTTTGGAAAGGGGAGTTACGAATTCTGTGGTTAAGCAATTGG
22370469 CA
1 CA
22370471 TGACAACATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.28, C:0.10, G:0.33, T:0.29
Consensus pattern (44 bp):
CAGTTTGGAAAGGGGAGTTACGAATTCTGTGGTTAAGCAATTGG
Found at i:22375398 original size:14 final size:14
Alignment explanation
Indices: 22375379--22375409 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22375369 CACAGTTTTA
22375379 AAAATAATAATAAT
1 AAAATAATAATAAT
*
22375393 AAAATATTAATAAT
1 AAAATAATAATAAT
22375407 AAA
1 AAA
22375410 TAGTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:22380702 original size:18 final size:18
Alignment explanation
Indices: 22380681--22380717 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
22380671 AAAAATTAAA
22380681 AGATAAGGAAACATGATT
1 AGATAAGGAAACATGATT
22380699 AGATAAGGAAACATGATT
1 AGATAAGGAAACATGATT
22380717 A
1 A
22380718 AATGGTGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (18 bp):
AGATAAGGAAACATGATT
Found at i:22383285 original size:92 final size:92
Alignment explanation
Indices: 22383103--22383293 Score: 244
Period size: 92 Copynumber: 2.1 Consensus size: 92
22383093 TGAAATTATT
* *
22383103 GATACCTTAGCTTAGGTATCGATATTTTTACATAAATATTTATACAAATCCTTAAAATCGAGACC
1 GATACCTTAGCTAAGGTATCGATATTTTTACATAAATATTGATACAAATCCTTAAAATCGAGACC
* * *
22383168 AAAGACCCATTCTGTCAATTGGGTATC
66 AAAAACCAATTCTGTCAACTGGGTATC
* * *
22383195 GATACCTTATCTAAGGTATCGATATTTTTCCATAAATATTGATAC-AGTCCTTTAAAATCGAGAC
1 GATACCTTAGCTAAGGTATCGATATTTTTACATAAATATTGATACAAATCC-TTAAAATCGAGAC
* *
22383259 CAAAAAGGCAATT-TG-GAACTGTGGTATC
65 CAAAAA-CCAATTCTGTCAACTG-GGTATC
22383287 GATACCT
1 GATACCT
22383294 ACAGTAAAGG
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
91 8 0.09
92 74 0.86
93 4 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (92 bp):
GATACCTTAGCTAAGGTATCGATATTTTTACATAAATATTGATACAAATCCTTAAAATCGAGACC
AAAAACCAATTCTGTCAACTGGGTATC
Found at i:22384029 original size:22 final size:22
Alignment explanation
Indices: 22384001--22384066 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
22383991 CACAAATGAA
22384001 CGGAGAGCACAAACGTGCTAAT
1 CGGAGAGCACAAACGTGCTAAT
22384023 CGGAGAGCACAAACGTGCTAAT
1 CGGAGAGCACAAACGTGCTAAT
22384045 CGGAGAGCACAATACGTGCTAA
1 CGGAGAGCACAA-ACGTGCTAA
22384067 ATAAATGGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 34 0.79
23 9 0.21
ACGTcount: A:0.36, C:0.23, G:0.27, T:0.14
Consensus pattern (22 bp):
CGGAGAGCACAAACGTGCTAAT
Found at i:22388302 original size:24 final size:24
Alignment explanation
Indices: 22388270--22388327 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
22388260 TGAATTATAA
22388270 GTATCGGTAGTTCTTAACATTGAT
1 GTATCGGTAGTTCTTAACATTGAT
22388294 GTATCGGTAGTTCTTAACATTGAT
1 GTATCGGTAGTTCTTAACATTGAT
*
22388318 GTACCGGTAG
1 GTATCGGTAG
22388328 AAGTTGCAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (24 bp):
GTATCGGTAGTTCTTAACATTGAT
Found at i:22392053 original size:14 final size:14
Alignment explanation
Indices: 22392034--22392061 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22392024 TTGGCACCAC
22392034 CCTGCAGAACACAT
1 CCTGCAGAACACAT
22392048 CCTGCAGAACACAT
1 CCTGCAGAACACAT
22392062 TCATTAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (14 bp):
CCTGCAGAACACAT
Found at i:22394460 original size:18 final size:18
Alignment explanation
Indices: 22394437--22394471 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
22394427 TTTTTTCTCA
22394437 AGAAACCTTCAATGCCAG
1 AGAAACCTTCAATGCCAG
22394455 AGAAACCTTCAATGCCA
1 AGAAACCTTCAATGCCA
22394472 CAAATGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (18 bp):
AGAAACCTTCAATGCCAG
Found at i:22395186 original size:3 final size:3
Alignment explanation
Indices: 22395178--22395206 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
22395168 GGAGAGGGGA
22395178 GGC GGC GGC GGC GGC GGC GGC GGC GGC GG
1 GGC GGC GGC GGC GGC GGC GGC GGC GGC GG
22395207 TGGATCTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.69, T:0.00
Consensus pattern (3 bp):
GGC
Found at i:22395602 original size:7 final size:7
Alignment explanation
Indices: 22395590--22395631 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
22395580 GTTTGGTAAG
22395590 TAGCAAC
1 TAGCAAC
22395597 TAGCAAC
1 TAGCAAC
22395604 TAGCAAC
1 TAGCAAC
*
22395611 TAGCAAT
1 TAGCAAC
22395618 TAGCAAC
1 TAGCAAC
22395625 TAGCAAC
1 TAGCAAC
22395632 CTAACCTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (7 bp):
TAGCAAC
Found at i:22396375 original size:12 final size:12
Alignment explanation
Indices: 22396358--22396383 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22396348 GAACATCTTT
22396358 ATTATTTGTATA
1 ATTATTTGTATA
22396370 ATTATTTGTATA
1 ATTATTTGTATA
22396382 AT
1 AT
22396384 AGGGAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
ATTATTTGTATA
Found at i:22397550 original size:42 final size:42
Alignment explanation
Indices: 22397491--22397574 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
22397481 CAAATATTTT
* *
22397491 TAAACCCAAATATAATTTCATTCTTCAAA-AACAGTCATAAAC
1 TAAACCCAAATATAATTTCATTCTT-AAATAACACTCAGAAAC
*
22397533 TAAACCCAAATATAATTTTATTCTTAAATAACACTCAGAAAC
1 TAAACCCAAATATAATTTCATTCTTAAATAACACTCAGAAAC
22397575 AACTCCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCTTAAATAACACTCAGAAAC
Found at i:22399501 original size:24 final size:24
Alignment explanation
Indices: 22399448--22399498 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
22399438 TATAAAAATA
*
22399448 TTTTAATAATATTTTATTAAATTT
1 TTTTAATAAAATTTTATTAAATTT
** *
22399472 ACTTAATAAAATTTT-TTAATTTT
1 TTTTAATAAAATTTTATTAAATTT
22399495 TTTT
1 TTTT
22399499 TAAAATATGC
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTAATAAAATTTTATTAAATTT
Found at i:22399658 original size:23 final size:20
Alignment explanation
Indices: 22399614--22399658 Score: 54
Period size: 23 Copynumber: 2.1 Consensus size: 20
22399604 TGACTAATAC
22399614 AATTTTAAAAATTTATATAG
1 AATTTTAAAAATTTATATAG
*
22399634 AATTTATAATAAATTATTTATAG
1 AATTT-TAA-AAATT-TATATAG
22399657 AA
1 AA
22399659 CTATTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 5 0.24
23 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
AATTTTAAAAATTTATATAG
Found at i:22400913 original size:84 final size:84
Alignment explanation
Indices: 22400756--22401097 Score: 355
Period size: 84 Copynumber: 4.2 Consensus size: 84
22400746 ACGAGCACGA
* * * * * *
22400756 GCATAAGCATGAACGAGTAAGGCATAGTCTTCACAGACAAGTA-GTAGAGGTGCCAAGAACCATA
1 GCATGAGCATGAACGAGCAAGGCATAGTCTTGACAGACAA-AAGGTAGAGATGCCAAGAACCTTA
* *
22400820 AATGATAACTTGTAATACAT
65 AATGGTAACTTGTATTACAT
* * *
22400840 GTATGAGCATGAACGAGCAAGGCATAGTCTTGACAGACAAAAGGTAGAGGTGCCAAGAACCTTAC
1 GCATGAGCATGAACGAGCAAGGCATAGTCTTGACAGACAAAAGGTAGAGATGCCAAGAACCTTAA
22400905 ATGGTAACTTGTATTACAT
66 ATGGTAACTTGTATTACAT
* * *
22400924 GCATGAGCAT----GA--AA---ATAGTCTTGACAGACAAATGATAGAGAAGCCAAGAACCTTAA
1 GCATGAGCATGAACGAGCAAGGCATAGTCTTGACAGACAAAAGGTAGAGATGCCAAGAACCTTAA
*
22400980 ATGGTAACTCGTATTACAT
66 ATGGTAACTTGTATTACAT
* * * * * * *
22400999 GCATGAGC-TGAAGCCAGCATGGGTATAGTGTTGACAGACAAATGGCAGAGATGCCAAGAGCCTT
1 GCATGAGCATGAA-CGAGCA-AGGCATAGTCTTGACAGACAAAAGGTAGAGATGCCAAGAACCTT
* * *
22401063 GAATGGTAACTTGTACTGCAT
64 AAATGGTAACTTGTATTACAT
22401084 GCATGAGCATGAAC
1 GCATGAGCATGAAC
22401098 TTGCCCATAT
Statistics
Matches: 218, Mismatches: 27, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
74 1 0.00
75 63 0.29
78 2 0.01
79 1 0.00
80 2 0.01
81 1 0.00
83 1 0.00
84 82 0.38
85 61 0.28
86 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (84 bp):
GCATGAGCATGAACGAGCAAGGCATAGTCTTGACAGACAAAAGGTAGAGATGCCAAGAACCTTAA
ATGGTAACTTGTATTACAT
Found at i:22400963 original size:75 final size:74
Alignment explanation
Indices: 22400863--22401010 Score: 233
Period size: 75 Copynumber: 2.0 Consensus size: 74
22400853 CGAGCAAGGC
* ** * *
22400863 ATAGTCTTGACAGACAAAAGGTAGAGGTGCCAAGAACCTTACATGGTAACTTGTATTACATGCAT
1 ATAGTCTTGACAGACAAAAGATAGAGAAGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
22400928 GAGCATGAAA
66 GAGC-TGAAA
*
22400938 ATAGTCTTGACAGACAAATGATAGAGAAGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
1 ATAGTCTTGACAGACAAAAGATAGAGAAGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
22401003 GAGCTGAA
66 GAGCTGAA
22401011 GCCAGCATGG
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
74 4 0.06
75 63 0.94
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (74 bp):
ATAGTCTTGACAGACAAAAGATAGAGAAGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
GAGCTGAAA
Found at i:22401072 original size:85 final size:86
Alignment explanation
Indices: 22400938--22401096 Score: 230
Period size: 85 Copynumber: 1.9 Consensus size: 86
22400928 GAGCATGAAA
* *
22400938 ATAGTCTTGACAGACAAATGATAGAGAAGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
1 ATAGTCTTGACAGACAAATGACAGAGAAGCCAAGAACCTTAAATGGTAACTCGTACTACATGCAT
22401003 GAGC-TGAAGCCAGCATGGGT
66 GAGCATGAAGCCAGCATGGGT
* * * * * * *
22401023 ATAGTGTTGACAGACAAATGGCAGAGATGCCAAGAGCCTTGAATGGTAACTTGTACTGCATGCAT
1 ATAGTCTTGACAGACAAATGACAGAGAAGCCAAGAACCTTAAATGGTAACTCGTACTACATGCAT
22401088 GAGCATGAA
66 GAGCATGAA
22401097 CTTGCCCATA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
85 60 0.94
86 4 0.06
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (86 bp):
ATAGTCTTGACAGACAAATGACAGAGAAGCCAAGAACCTTAAATGGTAACTCGTACTACATGCAT
GAGCATGAAGCCAGCATGGGT
Found at i:22401872 original size:78 final size:78
Alignment explanation
Indices: 22401779--22401934 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 78
22401769 TAAACTAATT
* *
22401779 TGCAACTTGTTTAGATGTAATCAATAATCATATGAATTTAGAATTAGTTAGGCACTAAACATCAA
1 TGCAACTTGTTTAGATGTAATCAATAATCATAAGAATTTACAATTAGTTAGGCACTAAACATCAA
22401844 GTAAAGCAAAGCA
66 GTAAAGCAAAGCA
*
22401857 TGCAACTTGTTTAGATGTAGTCAATAATCATAAGAATTTACAATTAGTTAGGCACTAAACATCAA
1 TGCAACTTGTTTAGATGTAATCAATAATCATAAGAATTTACAATTAGTTAGGCACTAAACATCAA
*
22401922 GTGAAGCAAAGCA
66 GTAAAGCAAAGCA
22401935 ACCACCGATA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (78 bp):
TGCAACTTGTTTAGATGTAATCAATAATCATAAGAATTTACAATTAGTTAGGCACTAAACATCAA
GTAAAGCAAAGCA
Found at i:22402369 original size:84 final size:83
Alignment explanation
Indices: 22402228--22402633 Score: 346
Period size: 84 Copynumber: 4.8 Consensus size: 83
22402218 TTCATGCTCA
* * * * * * *
22402228 TGCTCATGCATGCAGTACAAGTTACCATTCAAGGCTCTTGACATCTCTACCATTTGTCTGTCAAC
1 TGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCATTTGTCTGTCAAG
*
22402293 ACTATACCTCGCTGGCTTC
66 ACTATGCCTCGCT-GCTTC
* * *
22402312 TGCTCATGCATGTAATACGAGTTACCATTTAAGGTTCTTGGCATCTCTAGCATTTGTCTGTCAAG
1 TGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCATTTGTCTGTCAAG
* *
22402377 ACTAT---T---TTCATC
66 ACTATGCCTCGCTGCTTC
* *
22402389 --CTCATGCATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCTTTTGTCTGTCAAG
1 TGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCATTTGTCTGTCAAG
22402452 ACTATGCCTCGCT-CGTTC
66 ACTATGCCTCGCTGC-TTC
* * * * * *
22402470 ATGATCA-GTCATGTAATACAAGTTATCATTTATGGTTCTTAGCACCTCTACCACTTGTCTGTGA
1 -TGCTCATG-CATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCATTTGTCTGTCA
*
22402534 AGACTATGCCTCACTCGTTCATCCTTATGCTC
64 AGACTATG---C-CTCG--C-TGC---T--TC
** * * *
22402566 GTGCTCATGCATGTAAGGCAAGTTACCATTCAAGGTTCTCGGCACCTCTACCAATTGTCTGTCAA
1 -TGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCATTTGTCTGTCAA
22402631 GAC
65 GAC
22402634 CAGGCCTCAA
Statistics
Matches: 262, Mismatches: 36, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
75 63 0.24
77 3 0.01
78 2 0.01
80 1 0.00
81 4 0.02
83 1 0.00
84 121 0.46
87 1 0.00
88 4 0.02
90 1 0.00
91 1 0.00
92 1 0.00
94 1 0.00
96 57 0.22
97 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (83 bp):
TGCTCATGCATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCATTTGTCTGTCAAG
ACTATGCCTCGCTGCTTC
Found at i:22402443 original size:75 final size:75
Alignment explanation
Indices: 22402314--22402456 Score: 241
Period size: 75 Copynumber: 1.9 Consensus size: 75
22402304 CTGGCTTCTG
* * * *
22402314 CTCATGCATGTAATACGAGTTACCATTTAAGGTTCTTGGCATCTCTAGCATTTGTCTGTCAAGAC
1 CTCATGCATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCATTTGTCTGTCAAGAC
22402379 TATTTTCATC
66 TATTTTCATC
*
22402389 CTCATGCATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCTTTTGTCTGTCAAGAC
1 CTCATGCATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCATTTGTCTGTCAAGAC
22402454 TAT
66 TAT
22402457 GCCTCGCTCG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (75 bp):
CTCATGCATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCATTTGTCTGTCAAGAC
TATTTTCATC
Found at i:22402519 original size:159 final size:159
Alignment explanation
Indices: 22402225--22402540 Score: 413
Period size: 159 Copynumber: 2.0 Consensus size: 159
22402215 AAGTTCATGC
* * *
22402225 TCATGCTCATGCATGCAGTACAAGTTACCATTCAAGGCTCTTGACATCTCTACCATTTGTCTGTC
1 TCATCCTCATGCATGCAATACAAGTTACCATTCAAGGCTCTTGACACCTCTACCATTTGTCTGTC
* * * *
22402290 AACACTATACCTCGCTGGCTTCTGCTCATGCATGTAATACGAGTTACCATTTAAGGTTCTTGGCA
66 AACACTATACCTCGCTCGCTTCTGATCATGCATGTAATACAAGTTACCATTTAAGGTTCTTAGCA
* * *
22402355 TCTCTAGCATTTGTCTGTCAAGACTATTT
131 CCTCTACCACTTGTCTGTCAAGACTATTT
* * * *
22402384 TCATCCTCATGCATGTAATACAAGTTACCATGT-AAGGTTCTTGGCACCTCTACCTTTTGTCTGT
1 TCATCCTCATGCATGCAATACAAGTTACCAT-TCAAGGCTCTTGACACCTCTACCATTTGTCTGT
* * * *
22402448 CAAGACTATGCCTCGCTCG-TTCATGATCA-GTCATGTAATACAAGTTATCATTTATGGTTCTTA
65 CAACACTATACCTCGCTCGCTTC-TGATCATG-CATGTAATACAAGTTACCATTTAAGGTTCTTA
*
22402511 GCACCTCTACCACTTGTCTGTGAAGACTAT
128 GCACCTCTACCACTTGTCTGTCAAGACTAT
22402541 GCCTCACTCG
Statistics
Matches: 135, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
158 4 0.03
159 130 0.96
160 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (159 bp):
TCATCCTCATGCATGCAATACAAGTTACCATTCAAGGCTCTTGACACCTCTACCATTTGTCTGTC
AACACTATACCTCGCTCGCTTCTGATCATGCATGTAATACAAGTTACCATTTAAGGTTCTTAGCA
CCTCTACCACTTGTCTGTCAAGACTATTT
Found at i:22405712 original size:2 final size:2
Alignment explanation
Indices: 22405705--22405730 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22405695 TAAAAATGAA
22405705 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
22405731 TATTTCTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22409497 original size:71 final size:71
Alignment explanation
Indices: 22409381--22409521 Score: 264
Period size: 71 Copynumber: 2.0 Consensus size: 71
22409371 AATATAAGTA
*
22409381 CCGTTTGCGAAAGGGTTAGAGAAAAATGGGAGAACACTGTGCCGCTTAGCTGTGGCATCATGTAC
1 CCGTTTGCGAAAGGGTTAGAGAAAAATGGGAGAACACTGTGCCGCTTAGCTGTGGCATCAAGTAC
22409446 AAGAAT
66 AAGAAT
*
22409452 CCGTTTGCGAAAGGGTTAGAGTAAAATGGGAGAACACTGTGCCGCTTAGCTGTGGCATCAAGTAC
1 CCGTTTGCGAAAGGGTTAGAGAAAAATGGGAGAACACTGTGCCGCTTAGCTGTGGCATCAAGTAC
22409517 AAGAA
66 AAGAA
22409522 ATCCCGTACA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (71 bp):
CCGTTTGCGAAAGGGTTAGAGAAAAATGGGAGAACACTGTGCCGCTTAGCTGTGGCATCAAGTAC
AAGAAT
Found at i:22409687 original size:16 final size:15
Alignment explanation
Indices: 22409651--22409683 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22409641 AATAGTCGGG
22409651 TGAT-AAAAAATTAA
1 TGATAAAAAAATTAA
*
22409665 TTATAAAAAAATTAA
1 TGATAAAAAAATTAA
22409680 TGAT
1 TGAT
22409684 TAAATTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
14 3 0.19
15 13 0.81
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
TGATAAAAAAATTAA
Found at i:22421934 original size:7 final size:7
Alignment explanation
Indices: 22421922--22421949 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
22421912 TCGGTTGTAA
22421922 AGCTTAT
1 AGCTTAT
22421929 AGCTTAT
1 AGCTTAT
22421936 AGCTTAT
1 AGCTTAT
22421943 AGCTTAT
1 AGCTTAT
22421950 TTACACTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
AGCTTAT
Found at i:22427711 original size:20 final size:20
Alignment explanation
Indices: 22427674--22427730 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
22427664 ACACCAGCAT
* *
22427674 GCATCGAGCAACATCAGGAA
1 GCATCGAGCAATACCAGGAA
* *
22427694 GCATCGAGCAGTACCAGGGA
1 GCATCGAGCAATACCAGGAA
*
22427714 GCATCAAGCAATACCAG
1 GCATCGAGCAATACCAG
22427731 ACATGGTCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.26, G:0.26, T:0.11
Consensus pattern (20 bp):
GCATCGAGCAATACCAGGAA
Found at i:22433831 original size:113 final size:113
Alignment explanation
Indices: 22433599--22433933 Score: 548
Period size: 113 Copynumber: 3.0 Consensus size: 113
22433589 AATGAGATTT
* *
22433599 GGGTGTGATAATTATTTTAAACTATCATACATCATTGTCTCCATGGATGTGATTCGAGTGAT-AA
1 GGGTGTGATAATTATTTTAAACTATCATACATCACTGTCTCCATGGATGTGATTCGAGTGATCGA
*
22433663 CTTGTTATTTTTATTACATCCATGGATGTGATTCGGATGTCTCTGTTC
66 CTTGTTATTTTTATTGCATCCATGGATGTGATTCGGATGTCTCTGTTC
* * * *
22433711 GAGTGTGATAATTATTTTAAACTATCATATATCACTGTCTCCGTGAATGTGATTCGAGTGATCGA
1 GGGTGTGATAATTATTTTAAACTATCATACATCACTGTCTCCATGGATGTGATTCGAGTGATCGA
*
22433776 CTTATTATTTTTATTGCATCCATGGATGTGATTCGGATGTCTCTGTTC
66 CTTGTTATTTTTATTGCATCCATGGATGTGATTCGGATGTCTCTGTTC
*
22433824 GGGTGTGATAATTATTTTAAACTATCATACATCACTGTCTCCATGGATGTGATTCGGGTGATCGA
1 GGGTGTGATAATTATTTTAAACTATCATACATCACTGTCTCCATGGATGTGATTCGAGTGATCGA
*
22433889 CTTGTTATTTTTTATTGCATCCATGGATGTGGTTC-GAGTGTCTCT
66 CTTGTTA-TTTTTATTGCATCCATGGATGTGATTCGGA-TGTCTCT
22433934 ATTTCTTTTT
Statistics
Matches: 205, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
112 57 0.28
113 115 0.56
114 33 0.16
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (113 bp):
GGGTGTGATAATTATTTTAAACTATCATACATCACTGTCTCCATGGATGTGATTCGAGTGATCGA
CTTGTTATTTTTATTGCATCCATGGATGTGATTCGGATGTCTCTGTTC
Found at i:22439842 original size:23 final size:23
Alignment explanation
Indices: 22439785--22439844 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
22439775 CATTAAGGAA
* **
22439785 CACTGTGTGTGCTCTCTGTTTAG
1 CACTCTGTGTGCTCTCTAATTAG
*
22439808 CACGTCT-CGTGCTCTCTAATTAG
1 CAC-TCTGTGTGCTCTCTAATTAG
*
22439831 CACTTTGTGTGCTC
1 CACTCTGTGTGCTC
22439845 AGTACTTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 2 0.07
23 25 0.86
24 2 0.07
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.40
Consensus pattern (23 bp):
CACTCTGTGTGCTCTCTAATTAG
Found at i:22446280 original size:6 final size:6
Alignment explanation
Indices: 22446255--22446293 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
22446245 ACAATTCATA
* * *
22446255 TCACTT TCAATT TTAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
22446294 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (6 bp):
TCACTT
Found at i:22448049 original size:42 final size:42
Alignment explanation
Indices: 22447972--22448055 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
22447962 CAATTGTACT
* **
22447972 CTATTACTGTTTCAAATCCGATTCAAGCACACGGATGTTACA
1 CTATTACTGTTCCAAATCCGATTCAAAAACACGGATGTTACA
* **
22448014 CTATTACTGTTCCAACTCCGATTCAAAAATGCGGATGTTACA
1 CTATTACTGTTCCAAATCCGATTCAAAAACACGGATGTTACA
22448056 GTTGTAGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (42 bp):
CTATTACTGTTCCAAATCCGATTCAAAAACACGGATGTTACA
Found at i:22449984 original size:12 final size:12
Alignment explanation
Indices: 22449967--22449993 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
22449957 CTTTGGCTCG
22449967 GAGCTTGAGCCT
1 GAGCTTGAGCCT
22449979 GAGCTTGAGCCT
1 GAGCTTGAGCCT
22449991 GAG
1 GAG
22449994 TAGTGACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.37, T:0.22
Consensus pattern (12 bp):
GAGCTTGAGCCT
Found at i:22451649 original size:20 final size:20
Alignment explanation
Indices: 22451606--22451669 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
22451596 AAAATATACA
* *
22451606 AAAAAAATAAAAATAATTT-C
1 AAAAAAATCAAAAT-ATTTAT
22451626 AAAAAAATCAAAATATTTAT
1 AAAAAAATCAAAATATTTAT
* *
22451646 AAAATATTACAAAAT-TTTAT
1 AAAAAAAT-CAAAATATTTAT
22451666 AAAA
1 AAAA
22451670 TTATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.11
20 28 0.74
21 6 0.16
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAAATCAAAATATTTAT
Found at i:22451651 original size:11 final size:11
Alignment explanation
Indices: 22451635--22451680 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
22451625 CAAAAAAATC
22451635 AAAATATTTAT
1 AAAATATTTAT
*
22451646 AAAATA-TTAC
1 AAAATATTTAT
22451656 AAAAT-TTTAT
1 AAAATATTTAT
22451666 AAAATTATTT-T
1 AAAA-TATTTAT
22451677 AAAA
1 AAAA
22451681 ACTAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 15 0.50
11 12 0.40
12 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATATTTAT
Found at i:22456792 original size:18 final size:20
Alignment explanation
Indices: 22456761--22456799 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
22456751 AACAAATATG
22456761 AAAAAATACATT-AATTATT
1 AAAAAATACATTAAATTATT
*
22456780 AAAAAATA-TTTAAATTATT
1 AAAAAATACATTAAATTATT
22456799 A
1 A
22456800 TATTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAATACATTAAATTATT
Found at i:22458893 original size:17 final size:19
Alignment explanation
Indices: 22458871--22458905 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
22458861 ATAATAAAAA
22458871 TATAATTT-TAT-TATTTT
1 TATAATTTATATATATTTT
22458888 TATAATTTATATATATTT
1 TATAATTTATATATATTT
22458906 AATTTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TATAATTTATATATATTTT
Found at i:22459655 original size:10 final size:10
Alignment explanation
Indices: 22459640--22459715 Score: 52
Period size: 10 Copynumber: 7.8 Consensus size: 10
22459630 CGTATTAATT
22459640 AATTTTTAAA
1 AATTTTTAAA
22459650 AA-TTTTAAA
1 AATTTTTAAA
*
22459659 AATAATTTTAAT
1 AAT--TTTTAAA
*
22459671 ACTTTTT--A
1 AATTTTTAAA
*
22459679 AATTTTTAAT
1 AATTTTTAAA
*
22459689 AATTTTT-AT
1 AATTTTTAAA
*
22459698 AATTTTTGAA
1 AATTTTTAAA
*
22459708 ATTTTTTA
1 AATTTTTA
22459716 TTTTTTATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
8 6 0.12
9 18 0.35
10 20 0.38
12 8 0.15
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:22459687 original size:18 final size:19
Alignment explanation
Indices: 22459639--22459722 Score: 75
Period size: 18 Copynumber: 4.5 Consensus size: 19
22459629 ACGTATTAAT
* *
22459639 TAATTTTTAAAAATTTTAA
1 TAATTTTTAATAATTTTTA
* *
22459658 AAATAATTTTAATACTTTTTA
1 TAAT--TTTTAATAATTTTTA
22459679 -AATTTTTAATAATTTTTA
1 TAATTTTTAATAATTTTTA
*
22459697 TAATTTTTGA-AATTTTT-
1 TAATTTTTAATAATTTTTA
*
22459714 TATTTTTTA
1 TAATTTTTA
22459723 TATTTAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
17 7 0.13
18 21 0.39
19 11 0.20
20 3 0.06
21 12 0.22
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (19 bp):
TAATTTTTAATAATTTTTA
Found at i:22459692 original size:27 final size:28
Alignment explanation
Indices: 22459659--22459713 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
22459649 AAATTTTAAA
*
22459659 AATAATTTTAATACTTTTT-AAATTTTT
1 AATAATTTTAATAATTTTTGAAATTTTT
*
22459686 AATAATTTTTATAATTTTTGAAATTTTT
1 AATAATTTTAATAATTTTTGAAATTTTT
22459714 TATTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
AATAATTTTAATAATTTTTGAAATTTTT
Found at i:22459704 original size:9 final size:9
Alignment explanation
Indices: 22459660--22459724 Score: 64
Period size: 9 Copynumber: 7.3 Consensus size: 9
22459650 AATTTTAAAA
*
22459660 ATAATTTTA
1 ATAATTTTT
*
22459669 ATACTTTTT
1 ATAATTTTT
22459678 A-AATTTTT
1 ATAATTTTT
22459686 AATAATTTTT
1 -ATAATTTTT
22459696 ATAATTTTT
1 ATAATTTTT
22459705 GA-AATTTTT
1 -ATAATTTTT
*
22459714 -TATTTTTT
1 ATAATTTTT
22459722 ATA
1 ATA
22459725 TTTAAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
8 12 0.26
9 27 0.57
10 8 0.17
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:22460215 original size:11 final size:11
Alignment explanation
Indices: 22460145--22460215 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 11
22460135 TAACTTTGAG
*
22460145 TTTAAATTAAT
1 TTTAAATTTAT
22460156 TTTAAATTTAT
1 TTTAAATTTAT
*
22460167 TTTAAAATTTAAAA
1 TTT-AAATTT--AT
*
22460181 TTTAAAATTACTT
1 TTTAAATTTA--T
*
22460194 ATTTAAGTTTAT
1 -TTTAAATTTAT
22460206 TTTAAATTTA
1 TTTAAATTTA
22460216 AATTTGAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
11 23 0.49
12 7 0.15
13 5 0.11
14 12 0.26
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:22461515 original size:22 final size:22
Alignment explanation
Indices: 22461473--22461515 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
22461463 GACGTCGGAG
**
22461473 CGTCGGTGCGTGGACTGGGGAT
1 CGTCGGTGCGTGGACCAGGGAT
22461495 CGTCGCGTGCGT-GACCAGGGA
1 CGTCG-GTGCGTGGACCAGGGA
22461516 CGGCGTCGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.19
Consensus pattern (22 bp):
CGTCGGTGCGTGGACCAGGGAT
Found at i:22462179 original size:30 final size:29
Alignment explanation
Indices: 22462145--22462329 Score: 244
Period size: 30 Copynumber: 6.2 Consensus size: 29
22462135 AATTATCCAG
22462145 AAATTACATTTTGACCCCAAAACTTTCTA
1 AAATTACATTTTGACCCCAAAACTTTCTA
* *
22462174 GAAATTACATTTTGACCCTAAAACTTTTTCA
1 -AAATTACATTTTGACCCCAAAACTTTCT-A
*
22462205 AAATTATATTTTGACCCCAAAACTTTCTA
1 AAATTACATTTTGACCCCAAAACTTTCTA
* * *
22462234 AAAGTTACATTTTAACCCTAAAACTTTTTCA
1 AAA-TTACATTTTGACCCCAAAACTTTCT-A
*
22462265 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAAC-TTTCTA
*
22462295 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAAC-TTTCTA
22462325 AAATT
1 AAATT
22462330 CCCAAAACTT
Statistics
Matches: 138, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
29 4 0.03
30 126 0.91
31 8 0.06
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (29 bp):
AAATTACATTTTGACCCCAAAACTTTCTA
Found at i:22462223 original size:60 final size:59
Alignment explanation
Indices: 22462145--22462329 Score: 298
Period size: 60 Copynumber: 3.1 Consensus size: 59
22462135 AATTATCCAG
22462145 AAATTACATTTTGACCCCAAAACTTTCTAGAAATTACATTTTGACCCTAAAACTTTTTCA
1 AAATTACATTTTGACCCCAAAACTTTCTA-AAATTACATTTTGACCCTAAAACTTTTTCA
* *
22462205 AAATTATATTTTGACCCCAAAACTTTCTAAAAGTTACATTTTAACCCTAAAACTTTTTCA
1 AAATTACATTTTGACCCCAAAACTTTCTAAAA-TTACATTTTGACCCTAAAACTTTTTCA
* * *
22462265 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAAC-TTTCTAAAATTACATTTTGACCCTAAAACTTTTTCA
22462325 AAATT
1 AAATT
22462330 CCCAAAACTT
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
59 3 0.03
60 105 0.91
61 8 0.07
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (59 bp):
AAATTACATTTTGACCCCAAAACTTTCTAAAATTACATTTTGACCCTAAAACTTTTTCA
Found at i:22462306 original size:90 final size:90
Alignment explanation
Indices: 22462148--22462320 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 90
22462138 TATCCAGAAA
* * * *
22462148 TTACATTTTGACCCCAAAACTTTCTAGAAATTACATTTTGACCCTAAAACTTTTTCAAAATTATA
1 TTACATTTTAACCCCAAAACTTTCTAGAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACA
22462213 TTTTGACCCCAAAACTTTCTAAAAG
66 TTTTGACCCCAAAACTTTCTAAAAG
* *
22462238 TTACATTTTAACCCTAAAACTTTTTCA-AAATTACATTTTGACCCCAAAACTTTTCCAAAATTAC
1 TTACATTTTAACCCCAAAACTTTCT-AGAAATTACATTTTGACCCCAAAACTTTTCCAAAATTAC
22462302 ATTTTGACCCCAAAACTTT
65 ATTTTGACCCCAAAACTTT
22462321 TCCAAAATTC
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
90 75 0.99
91 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (90 bp):
TTACATTTTAACCCCAAAACTTTCTAGAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACA
TTTTGACCCCAAAACTTTCTAAAAG
Found at i:22462316 original size:19 final size:19
Alignment explanation
Indices: 22462263--22462316 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 19
22462253 AAAACTTTTT
22462263 CAAAATTACATTTTGACCC
1 CAAAATTACATTTTGACCC
22462282 C-AAA--AC-TTTT----C
1 CAAAATTACATTTTGACCC
22462293 CAAAATTACATTTTGACCC
1 CAAAATTACATTTTGACCC
22462312 CAAAA
1 CAAAA
22462317 CTTTTCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 16
0.63 0.00 0.37
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
14 2 0.07
15 8 0.30
16 2 0.07
18 3 0.11
19 7 0.26
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.30
Consensus pattern (19 bp):
CAAAATTACATTTTGACCC
Found at i:22462327 original size:11 final size:11
Alignment explanation
Indices: 22462311--22462347 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22462301 CATTTTGACC
22462311 CCAAAACTTTT
1 CCAAAACTTTT
*
22462322 CCAAAA--TTC
1 CCAAAACTTTT
22462331 CCAAAACTTTT
1 CCAAAACTTTT
22462342 CCAAAA
1 CCAAAA
22462348 TCATATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (11 bp):
CCAAAACTTTT
Found at i:22462335 original size:20 final size:20
Alignment explanation
Indices: 22462310--22462348 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
22462300 ACATTTTGAC
22462310 CCCAAAACTTTTCCAAAATT
1 CCCAAAACTTTTCCAAAATT
22462330 CCCAAAACTTTTCCAAAAT
1 CCCAAAACTTTTCCAAAAT
22462349 CATATTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (20 bp):
CCCAAAACTTTTCCAAAATT
Found at i:22465704 original size:39 final size:39
Alignment explanation
Indices: 22465650--22465952 Score: 401
Period size: 39 Copynumber: 7.8 Consensus size: 39
22465640 GTTATCAAAT
22465650 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
1 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
22465689 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
1 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
*
22465728 TACTGAACTGGTAGTGACACTGTAAACACTGCAATACGA
1 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
22465767 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
1 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
* * **
22465806 TACTGAACTGGTAGTGACACTGGAAACACTGCAATATAA
1 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
* * * * *
22465845 TACTAAACTGGCAGTGACATTGTAAATACTGTAATACAA
1 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
* *** * * * * *
22465884 TACTGAATTGATGGTGGCACTGTAAACACCGTAATGCTA
1 TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
* *
22465923 TACTGAA-TAGGTAGTGAGACTGTAAACACT
1 TACTGAACT-GGCAGTGACACTGTAAACACT
22465953 ACTAGACTGA
Statistics
Matches: 234, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
38 1 0.00
39 233 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (39 bp):
TACTGAACTGGCAGTGACACTGTAAACACTGCAATACGA
Found at i:22468166 original size:20 final size:20
Alignment explanation
Indices: 22468141--22468179 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
22468131 GGTTCAGATG
22468141 AAAGGGTAAATTGAGTCCGC
1 AAAGGGTAAATTGAGTCCGC
22468161 AAAGGGTAAATTGAGTCCG
1 AAAGGGTAAATTGAGTCCG
22468180 TGTTTTATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.21
Consensus pattern (20 bp):
AAAGGGTAAATTGAGTCCGC
Found at i:22469909 original size:39 final size:39
Alignment explanation
Indices: 22469791--22469919 Score: 127
Period size: 39 Copynumber: 3.3 Consensus size: 39
22469781 CTGGCAGTGT
* *
22469791 CACTGTAAACACTAG-AATACGATACTGAATTG-GTAGTGA
1 CACTGTAAACACT-GCAATACAATACTGAATTGACT-GTGA
* * * * * **
22469830 AACTGAAAACACTGCAATATAATACTAAACTGACAATGA
1 CACTGTAAACACTGCAATACAATACTGAATTGACTGTGA
*
22469869 CACTGTAAACACTGCAATACAATATTGAATTGACTGTGA
1 CACTGTAAACACTGCAATACAATACTGAATTGACTGTGA
*
22469908 CATTGTAAACAC
1 CACTGTAAACAC
22469920 CGTAATGCTA
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
38 1 0.01
39 69 0.99
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25
Consensus pattern (39 bp):
CACTGTAAACACTGCAATACAATACTGAATTGACTGTGA
Found at i:22473440 original size:20 final size:19
Alignment explanation
Indices: 22473411--22473472 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
22473401 CGGAAAATGA
* *
22473411 TTTTTCAAAAAGGACTT-GT
1 TTTTTTAAAAA-GACTTACT
22473430 TTTTTTGAAAAAGACTTACT
1 TTTTTT-AAAAAGACTTACT
*
22473450 TTTTTTAAAAA-AC-TAAT
1 TTTTTTAAAAAGACTTACT
22473467 TTTTTT
1 TTTTTT
22473473 GGTGTTTGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
17 9 0.24
18 2 0.05
19 15 0.39
20 12 0.32
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (19 bp):
TTTTTTAAAAAGACTTACT
Found at i:22473459 original size:18 final size:17
Alignment explanation
Indices: 22473429--22473472 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
22473419 AAAGGACTTG
*
22473429 TTTTTTTGAAAAAGACTTAC
1 TTTTTTT-AAAAA-AC-TAA
22473449 TTTTTTTAAAAAACTAA
1 TTTTTTTAAAAAACTAA
22473466 TTTTTTT
1 TTTTTTT
22473473 GGTGTTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 5 0.22
20 7 0.30
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTTTTTAAAAAACTAA
Found at i:22480514 original size:26 final size:26
Alignment explanation
Indices: 22480484--22480536 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
22480474 CTCGGTTGCG
22480484 ATCATCATTGAAAATATCTAAAAAGA
1 ATCATCATTGAAAATATCTAAAAAGA
22480510 ATCATCATTGAAAATATCTAAAAAGA
1 ATCATCATTGAAAATATCTAAAAAGA
22480536 A
1 A
22480537 GTAGGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (26 bp):
ATCATCATTGAAAATATCTAAAAAGA
Found at i:22483197 original size:27 final size:28
Alignment explanation
Indices: 22483167--22483225 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
22483157 GAGTACTTGT
* * *
22483167 CAGGCGACA-CCAGTGGAGGGTTCCTGA
1 CAGGCAACACCCAGTGGAGGGTACCTAA
* *
22483194 CAGGTAACACCCTGTGGAGGGTACCTAA
1 CAGGCAACACCCAGTGGAGGGTACCTAA
22483222 CAGG
1 CAGG
22483226 TGTCACCCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.25, C:0.25, G:0.34, T:0.15
Consensus pattern (28 bp):
CAGGCAACACCCAGTGGAGGGTACCTAA
Found at i:22484560 original size:13 final size:13
Alignment explanation
Indices: 22484542--22484567 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22484532 AATGTTATGT
22484542 GTGAAGAGAGAAA
1 GTGAAGAGAGAAA
22484555 GTGAAGAGAGAAA
1 GTGAAGAGAGAAA
22484568 TGAGAAATGA
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:0.54, C:0.00, G:0.38, T:0.08
Consensus pattern (13 bp):
GTGAAGAGAGAAA
Found at i:22489493 original size:15 final size:16
Alignment explanation
Indices: 22489473--22489504 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
22489463 ATCATAATTT
22489473 TTTTTCTT-CTTTTTC
1 TTTTTCTTCCTTTTTC
22489488 TTTTTCTTCCTTTTTC
1 TTTTTCTTCCTTTTTC
22489504 T
1 T
22489505 CAATTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTCCTTTTTC
Found at i:22513036 original size:17 final size:17
Alignment explanation
Indices: 22513011--22513081 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
22513001 AATAAGTTTG
*
22513011 AATTTATTTTAAATTCA
1 AATTTATTTTAAATTTA
* * * *
22513028 AATTCATTTTGAGTTTG
1 AATTTATTTTAAATTTA
*
22513045 AATTTACTTTAAATTTA
1 AATTTATTTTAAATTTA
*
22513062 AATTTATTTTAAATTAA
1 AATTTATTTTAAATTTA
22513079 AAT
1 AAT
22513082 AAAATTAATG
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:22513043 original size:34 final size:34
Alignment explanation
Indices: 22513005--22513071 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
22512995 TTTTTAAATA
*
22513005 AGTTTGAATTTATTTTAAATTCAAATTCATTTTG
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
* *
22513039 AGTTTGAATTTACTTTAAATTTAAATTTATTTT
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTT
22513072 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55
Consensus pattern (34 bp):
AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
Found at i:22514335 original size:10 final size:10
Alignment explanation
Indices: 22514320--22514349 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
22514310 GCCTTGAAGG
22514320 CCAGAGAGAA
1 CCAGAGAGAA
22514330 CCAGAGAGAA
1 CCAGAGAGAA
*
22514340 TCAGAGAGAA
1 CCAGAGAGAA
22514350 GTTTATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.30, T:0.03
Consensus pattern (10 bp):
CCAGAGAGAA
Done.