Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 57 of 226
Found at i:22896074 original size:14 final size:14
Alignment explanation
Indices: 22896037--22896074 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
22896027 CAATGGAGGC
22896037 AAAAAAAAAGCAAA
1 AAAAAAAAAGCAAA
22896051 AACAAAAAAA-CAAA
1 AA-AAAAAAAGCAAA
22896065 ACAAAAAAAA
1 A-AAAAAAAA
22896075 ACCTCTACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGCAAA
Found at i:22897522 original size:44 final size:44
Alignment explanation
Indices: 22897455--22897684 Score: 241
Period size: 44 Copynumber: 5.2 Consensus size: 44
22897445 AAGTCATTAA
* * *
22897455 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
22897499 AGCAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * * *
22897543 -GCAAATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
22897587 AGCAGATCTTGTCTTCATGTATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * *
22897631 -GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
*
22897675 AACAGATCTT
1 AGCAGATCTT
22897685 ATCTCTCTAA
Statistics
Matches: 151, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
43 43 0.28
44 78 0.52
45 30 0.20
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (44 bp):
AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
Found at i:22897683 original size:88 final size:88
Alignment explanation
Indices: 22897483--22897684 Score: 341
Period size: 88 Copynumber: 2.3 Consensus size: 88
22897473 GTATTGGCGT
* * * *
22897483 GAAGTAGATCGAAGATAGCAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAAA
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTAGGAAGTGGATCGAAGATGCAAA
22897548 TCTTGTCTTCCCATACTGGTGGC
66 TCTTGTCTTCCCATACTGGTGGC
* *
22897571 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGTAGGAAGTGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTAGGAAGTGGATCGAAGATGCAAA
22897636 TCTTGTCTTCCCATACTGGTGGC
66 TCTTGTCTTCCCATACTGGTGGC
*
22897659 GAAGTAGATCGAAGAAAACAGATCTT
1 GAAGTAGATCGAAGAAAGCAGATCTT
22897685 ATCTCTCTAA
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 107 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (88 bp):
GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTAGGAAGTGGATCGAAGATGCAAA
TCTTGTCTTCCCATACTGGTGGC
Found at i:22897831 original size:50 final size:50
Alignment explanation
Indices: 22897750--22898231 Score: 268
Period size: 50 Copynumber: 9.6 Consensus size: 50
22897740 ACAGTAGAGC
* * * * * * *
22897750 AGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * * *
22897800 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCAGTACAGTGGAAC
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * ** * *
22897850 TGATTAAAGCTACAACGACGAATCTTGCTTCCCCAACATTGTAATTTAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * ** * **** *** * *
22897900 AGATTGAAGCCGCAGCAACGAATCTTACTTCCTTGGTGGTGCAGCGGGAC
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * *
22897950 TGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * * * **
22898000 AGATTGAATAC-GCAATGGCGAATCTTACTTCCATGGCAATGCAGTGGAGT
1 AGATTGAA-GCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * *
22898050 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
* * * * * * * **
22898100 AGATTGAAGCCGCAATGGCGAATCTTACTTCCTTGGCGA-TACAGTGGAGC
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGAC-ATTGCAATTGAAA
* * * * * *
22898150 AGATTAAAGCTACGACGGTGAATCTTACTTCCCCGACATTGCAATTTAAA
1 AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
22898200 AGATTGAAGCTGCAACAGG-GAATCTTACTTCC
1 AGATTGAAGCTGCAAC-GGCGAATCTTACTTCC
22898232 TTAGTGGTGC
Statistics
Matches: 295, Mismatches: 132, Indels: 10
0.68 0.30 0.02
Matches are distributed among these distances:
49 2 0.01
50 289 0.98
51 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTGCAACGGCGAATCTTACTTCCCTGACATTGCAATTGAAA
Found at i:22897905 original size:100 final size:100
Alignment explanation
Indices: 22897733--22898292 Score: 683
Period size: 100 Copynumber: 5.6 Consensus size: 100
22897723 CTTATCTCTC
* * * * * * *
22897733 TGGCGGTACAGTAGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
*
22897798 AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCC
66 AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
* * * *
22897833 TGGCAGTACAGTGGAACTGATTAAAGCTACAACGACGAATCTTGCTTCCCCAACATTGTAATTTA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
* **
22897898 AAAGATTGAAGCCGCAGCAACGAATCTTACTTCCT
66 AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
* * * *
22897933 TGGTGGTGCAGCGGGACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
** * *
22897998 AAAGATTGAATACGCAATGGCGAATCTTACTTCCA
66 AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
** * * * * *
22898033 TGGCAATGCAGTGG-AGTAGATTAAAGCTACAACGGTGAATCTTGCTTCCCTGACATTGCAATTA
1 TGGCGGTACAGTGGAACT-GATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTT
*
22898097 AAAAGATTGAAGCCGCAATGGCGAATCTTACTTCCT
65 AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
* * * * * *
22898133 TGGCGATACAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTACTTCCCCGACATTGCAATTTA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
*
22898198 AAAGATTGAAGCTGCAACAGG-GAATCTTACTTCCT
66 AAAGATTGAAGCCGCAAC-GGCGAATCTTACTTCCT
* * * ** * *
22898233 TAGTGGTGCAGCAGAACTGATTAAAGCTAGAACAGCGAATCTTGCTTCCCCGACATTGCA
1 TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
22898293 GTTAATCGGA
Statistics
Matches: 392, Mismatches: 65, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
99 2 0.01
100 388 0.99
101 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (100 bp):
TGGCGGTACAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTA
AAAGATTGAAGCCGCAACGGCGAATCTTACTTCCT
Found at i:22898495 original size:40 final size:41
Alignment explanation
Indices: 22898445--22898641 Score: 143
Period size: 40 Copynumber: 4.7 Consensus size: 41
22898435 ACCACAAAAC
22898445 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAGA-TA
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAGACTA
* * ** * *
22898485 TTATCTCCCTAAGCAGTAGTGGAGCAGACCGAAAAAAACCAA
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAGA-CTA
** * * *
22898527 TCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAAC-CA-CAGA-TC
1 T--TATCTCCCT-AAGCAGTAGTGGAGCAGA-T----CGCATCAGACTA
* * * *
22898573 TTACCTCCCTAAGCAGTAGTGGAGCAGATCACATCA-AGTT
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAGACTA
22898613 TTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 TTATCTCCCTAAGCAGTAGTGGAGCAGAT
22898642 AAAAGAAACC
Statistics
Matches: 121, Mismatches: 23, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
38 1 0.01
39 3 0.02
40 64 0.53
42 3 0.02
43 14 0.12
44 17 0.14
45 14 0.12
46 1 0.01
48 2 0.02
49 1 0.01
50 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (41 bp):
TTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAGACTA
Found at i:22898582 original size:128 final size:127
Alignment explanation
Indices: 22898299--22898692 Score: 594
Period size: 127 Copynumber: 3.1 Consensus size: 127
22898289 TGCAGTTAAT
* * * * *
22898299 CGGATTAAAACTACAAATCTTATCTCCCTATGCAGTAGTGGAACAGATTGCATCAAGTCTTATCT
1 CGGATTAAAACCACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTATTATCT
* * *
22898364 CCCTAAGCAGTAGTGGAGCAGACGAAATAAACCAATCCTATCTCCCTAAAGTTACAATGGAG
66 CCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAG
* *
22898426 CAGATTAAAACCACAAAACTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATC-AGATATTATC
1 CGGATTAAAACCACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG-TATTATC
22898490 TCCCTAAGCAGTAGTGGAGCAGACCGAAAAAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAG
65 TCCCTAAGCAGTAGTGGAGCAGA-CGAAAAAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAG
* * * *
22898554 CGGATTAAAACCACAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTTTTATCT
1 CGGATTAAAACCACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTATTATCT
* * *
22898619 CCCTAAGCAGTAGTGGAGCAGA-TAAAAGAAACCAATCCTATCTTCCTGAAGTTGCAGTGGAG
66 CCCTAAGCAGTAGTGGAGCAGACGAAAA-AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAG
22898681 CGGATTAAAACC
1 CGGATTAAAACC
22898693 CAATCTCATC
Statistics
Matches: 244, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
126 6 0.02
127 121 0.50
128 115 0.47
129 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (127 bp):
CGGATTAAAACCACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTATTATCT
CCCTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAG
Found at i:22900289 original size:18 final size:20
Alignment explanation
Indices: 22900266--22900308 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
22900256 CATATACATG
22900266 CATACATTTT-A-TAATACA
1 CATACATTTTAATTAATACA
22900284 CATACATTTTAATTAATACA
1 CATACATTTTAATTAATACA
22900304 CATAC
1 CATAC
22900309 TTATACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 12 0.52
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (20 bp):
CATACATTTTAATTAATACA
Found at i:22908469 original size:15 final size:16
Alignment explanation
Indices: 22908423--22908475 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
22908413 GAGATATTAA
22908423 ATCTAATTTAATATTT
1 ATCTAATTTAATATTT
22908439 ATCTAGA--TAATA-TT
1 ATCTA-ATTTAATATTT
22908453 AT-TAATTTAATATTT
1 ATCTAATTTAATATTT
*
22908468 ATGTAATT
1 ATCTAATT
22908476 AATTCTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 9 0.28
15 9 0.28
16 10 0.31
17 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (16 bp):
ATCTAATTTAATATTT
Found at i:22910129 original size:23 final size:23
Alignment explanation
Indices: 22910103--22910153 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
22910093 TCCTTCCGCT
* *
22910103 TGTAATATCTCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
22910126 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
22910149 AGTAA
1 TGTAA
22910154 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:22932755 original size:167 final size:171
Alignment explanation
Indices: 22932448--22932757 Score: 430
Period size: 167 Copynumber: 1.8 Consensus size: 171
22932438 ATAGATAATC
* * * *
22932448 AAGAAAAGTTGTTCAGTATTCATCACTGTTTCATTTCAGCTATCTAATGAAGTTCCAGTTCCAAC
1 AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAA----CAGTTCCAAC
* * * *
22932513 TTCCAACACAGATGAATTAATGATTGTCTAATTAACAGGTGCTAGTTCAAGAACAATGACTTCCA
62 TTCCAACACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCA
22932578 ATTATTACCCAATATTTAACGTTTCATTTCAGCAATTTGTAAATA
127 ATTATTACCCAATATTTAACGTTTCATTTCAGCAATTTGTAAATA
*
22932623 AAGAAAA-CTGTTCAATATTCATCAATGTTTCATTTCAGCAATTTAATG-A-AGTTCCAA-TTCC
1 AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAACAGTTCCAACTTCC
* * * * *
22932684 AATACAGATCAATGAATGATTGTGTAATTAACAGCTGCTAGTTCAAGAACAATAACTTTCATTTT
66 AACACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTA
22932749 TTACCCAAT
131 TTACCCAAT
22932758 CTTTCAAGCA
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
167 69 0.57
168 8 0.07
173 1 0.01
174 36 0.30
175 7 0.06
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (171 bp):
AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAACAGTTCCAACTTCC
AACACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTA
TTACCCAATATTTAACGTTTCATTTCAGCAATTTGTAAATA
Found at i:22933622 original size:21 final size:19
Alignment explanation
Indices: 22933566--22933633 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 19
22933556 TATTTATTTA
22933566 TTAAATT-TAATTAGAATAT
1 TTAAATTATAATTA-AATAT
* *
22933585 ATAAATTATATTTAAATAT
1 TTAAATTATAATTAAATAT
22933604 TTAAATATAATAATTAAATAT
1 TTAAAT-T-ATAATTAAATAT
22933625 TTATAATTA
1 TTA-AATTA
22933634 GATATTGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 16 0.39
20 7 0.17
21 15 0.37
22 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (19 bp):
TTAAATTATAATTAAATAT
Found at i:22935561 original size:25 final size:26
Alignment explanation
Indices: 22935525--22935649 Score: 92
Period size: 25 Copynumber: 4.5 Consensus size: 26
22935515 ATGGTGGAGA
*
22935525 AGAGGAACAAAGAACCGGCACAGGGC
1 AGAGGAACAAAGAACCAGCACAGGGC
*
22935551 AGAGG-ACAAAGAACCAGCAGAGGGC
1 AGAGGAACAAAGAACCAGCACAGGGC
*
22935576 AGAGATGAGGGCAAAGAACCAGCGTAGCAGAGGGC
1 AGAG--GA--ACAAAGAACCAGC--A-C--AGGGC
* * *
22935611 AGAGAAACAAAGAACCAGCAGAGAGC
1 AGAGGAACAAAGAACCAGCACAGGGC
*
22935637 AGA-GAGCAAAGAA
1 AGAGGAACAAAGAA
22935650 GAGTACTGGG
Statistics
Matches: 79, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
25 30 0.38
26 12 0.15
27 1 0.01
29 1 0.01
30 12 0.15
31 12 0.15
32 1 0.01
33 1 0.01
35 9 0.11
ACGTcount: A:0.46, C:0.18, G:0.34, T:0.02
Consensus pattern (26 bp):
AGAGGAACAAAGAACCAGCACAGGGC
Found at i:22936114 original size:14 final size:15
Alignment explanation
Indices: 22936088--22936116 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22936078 TATTAAGATC
22936088 ATTTTTAATAATATA
1 ATTTTTAATAATATA
22936103 ATTTTTAA-AATATA
1 ATTTTTAATAATATA
22936117 TATATTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTTTAATAATATA
Found at i:22937654 original size:21 final size:21
Alignment explanation
Indices: 22937630--22937676 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
22937620 GTGATTGTCT
22937630 AGATTGACAATACATCA-AACA
1 AGATTGACAATACAT-ATAACA
* *
22937651 AGATCGACAATGCATATAACA
1 AGATTGACAATACATATAACA
22937672 AGATT
1 AGATT
22937677 CGAGTTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (21 bp):
AGATTGACAATACATATAACA
Found at i:22938615 original size:22 final size:22
Alignment explanation
Indices: 22938587--22938699 Score: 154
Period size: 22 Copynumber: 5.1 Consensus size: 22
22938577 TTAACCTAAA
22938587 TTTAACGTACTAAGCTCTCATG
1 TTTAACGTACTAAGCTCTCATG
* * *
22938609 TTTAACGAACTAAACCCTCATG
1 TTTAACGTACTAAGCTCTCATG
**
22938631 GCTAACGTACTAAGCTCTCATG
1 TTTAACGTACTAAGCTCTCATG
**
22938653 GCTAACGTACTAAGCTCTCATG
1 TTTAACGTACTAAGCTCTCATG
*
22938675 TTTCACGTACTAAGCTCTCATG
1 TTTAACGTACTAAGCTCTCATG
22938697 TTT
1 TTT
22938700 GAACAATAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 80 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
TTTAACGTACTAAGCTCTCATG
Found at i:22938912 original size:21 final size:20
Alignment explanation
Indices: 22938888--22938926 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22938878 GACTAAACCG
22938888 AAAACTCAAAGAATTTTTCAC
1 AAAACTCAAA-AATTTTTCAC
* *
22938909 AAAATTCCAAAATTTTTC
1 AAAACTCAAAAATTTTTC
22938927 CTATATGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAACTCAAAAATTTTTCAC
Found at i:22939745 original size:42 final size:42
Alignment explanation
Indices: 22939685--22939821 Score: 150
Period size: 42 Copynumber: 3.3 Consensus size: 42
22939675 CCAAAGGCTG
* * * * * *
22939685 AACAAAAGCTCATGAGAGCTAAAAAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAAGGTTA
* *
22939727 AACGGAAGCTCGTAAGAGCTGAACAGAAACCCATAAAGGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAAGGTTA
* * *
22939769 AACAGAAGCTCAAAAGAGCTGAACAGAAACTCAT-ATGAGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAAG-GTTA
*
22939811 AATAGAAGCTC
1 AACAGAAGCTC
22939822 GTGAAAGCTA
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 2 0.03
42 78 0.98
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAAGGTTA
Found at i:22939793 original size:21 final size:21
Alignment explanation
Indices: 22939740--22939801 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
22939730 GGAAGCTCGT
*
22939740 AAGAGCTGAACAGAAACCCATA
1 AAGAGCTGAACAGAAACTCA-A
* * *
22939762 AAG-GTTAAACAGAAGCTCAA
1 AAGAGCTGAACAGAAACTCAA
22939782 AAGAGCTGAACAGAAACTCA
1 AAGAGCTGAACAGAAACTCA
22939802 TATGAGTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 4 0.12
21 25 0.78
22 3 0.09
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.11
Consensus pattern (21 bp):
AAGAGCTGAACAGAAACTCAA
Found at i:22945982 original size:21 final size:21
Alignment explanation
Indices: 22945923--22946082 Score: 74
Period size: 21 Copynumber: 7.6 Consensus size: 21
22945913 AAGCCCGAAG
* *
22945923 GCTGAACAAAAGCTCATGAGA
1 GCTGAACGAAAGCTCATAAGA
* * *
22945944 GCTAAACAGAAA-CCCATAAGG
1 GCTGAAC-GAAAGCTCATAAGA
*
22945965 GTTGAACGAAAGCTCATAAGA
1 GCTGAACGAAAGCTCATAAGA
* * *
22945986 GCTGAATAGAAA-CCCATAAGG
1 GCTGAA-CGAAAGCTCATAAGA
* * *
22946007 GTTAAAC-ATAAGCTCAAAAGA
1 GCTGAACGA-AAGCTCATAAGA
* * *
22946028 GCTCAACGAAAGCTTATATGA
1 GCTGAACGAAAGCTCATAAGA
* * * * *
22946049 GTTAAACAAAAGCTCGTGAGA
1 GCTGAACGAAAGCTCATAAGA
*
22946070 GCTAAACGGAAAG
1 GCTGAAC-GAAAG
22946083 TAAACATGAA
Statistics
Matches: 99, Mismatches: 33, Indels: 13
0.68 0.23 0.09
Matches are distributed among these distances:
19 1 0.01
20 6 0.06
21 80 0.81
22 12 0.12
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (21 bp):
GCTGAACGAAAGCTCATAAGA
Found at i:22945987 original size:42 final size:41
Alignment explanation
Indices: 22945925--22946038 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 41
22945915 GCCCGAAGGC
*
22945925 TGAACAAAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGT
1 TGAAC-AAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* *
22945967 TGAACGAAAGCTCATAAGAGCTGAATAGAAACCCATAAGGGT
1 TGAAC-AAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * *
22946009 TAAACATAAGCTCAAAAGAGCTCAAC-GAAA
1 TGAACA-AAGCTCATAAGAGCTAAACAGAAA
22946039 GCTTATATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 5 0.08
42 58 0.92
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (41 bp):
TGAACAAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:22948663 original size:13 final size:13
Alignment explanation
Indices: 22948645--22948693 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
22948635 TAAAAATAAT
22948645 TTAATTAAGAGAA
1 TTAATTAAGAGAA
* *
22948658 TTAATTAAAAATAA
1 TTAATT-AAGAGAA
22948672 TTTAATTAAGAGAA
1 -TTAATTAAGAGAA
22948686 TTAATTAA
1 TTAATTAA
22948694 ATTTATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 14 0.47
14 10 0.33
15 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (13 bp):
TTAATTAAGAGAA
Found at i:22948673 original size:28 final size:28
Alignment explanation
Indices: 22948625--22948708 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
22948615 TAATAAAATT
22948625 AGAATTAAGTTAAAAATAATTTAATTAAG
1 AGAATTAA-TTAAAAATAATTTAATTAAG
22948654 AGAATTAATTAAAAATAATTTAATTAAG
1 AGAATTAATTAAAAATAATTTAATTAAG
** *
22948682 AGAATTAATTAAATTTATTTTAATTAA
1 AGAATTAATTAAAAATAATTTAATTAA
22948709 TTAAAAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 44 0.85
29 8 0.15
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (28 bp):
AGAATTAATTAAAAATAATTTAATTAAG
Found at i:22948678 original size:15 final size:15
Alignment explanation
Indices: 22948629--22948680 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 15
22948619 AAAATTAGAA
22948629 TTAAGTTAAAAATAAT
1 TTAA-TTAAAAATAAT
* *
22948645 TTAATT-AAGAGAA-
1 TTAATTAAAAATAAT
22948658 TTAATTAAAAATAAT
1 TTAATTAAAAATAAT
22948673 TTAATTAA
1 TTAATTAA
22948681 GAGAATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.20
14 10 0.33
15 10 0.33
16 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (15 bp):
TTAATTAAAAATAAT
Found at i:22952339 original size:11 final size:11
Alignment explanation
Indices: 22952323--22952347 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22952313 AGTTTCACCG
22952323 TTGATAATTTT
1 TTGATAATTTT
22952334 TTGATAATTTT
1 TTGATAATTTT
22952345 TTG
1 TTG
22952348 TGTTTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (11 bp):
TTGATAATTTT
Found at i:22952677 original size:21 final size:21
Alignment explanation
Indices: 22952636--22952678 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
22952626 AATAAAGTAG
*
22952636 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
22952657 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
22952678 A
1 A
22952679 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:22952720 original size:17 final size:18
Alignment explanation
Indices: 22952695--22952740 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
22952685 TATAAGAATA
*
22952695 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
22952712 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
22952730 ATTAAATTATA
1 ATTAAATTATA
22952741 TTTTATAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:22953103 original size:16 final size:16
Alignment explanation
Indices: 22953050--22953103 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
22953040 TTAAATTACT
*
22953050 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
* *
22953066 ATTACAGCTCTATTCT
1 ATTACACCTCTATTCC
22953082 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
22953098 ATTACA
1 ATTACA
22953104 GCGAAACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.26, C:0.31, G:0.04, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:22953416 original size:21 final size:20
Alignment explanation
Indices: 22953388--22953426 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22953378 GATCTAATTT
22953388 TTTATTTAATAATAAAAACA
1 TTTATTTAATAATAAAAACA
* *
22953408 TTTAGTTTAGTTATAAAAA
1 TTTA-TTTAATAATAAAAA
22953427 TATAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTATTTAATAATAAAAACA
Found at i:22954270 original size:11 final size:11
Alignment explanation
Indices: 22954256--22954300 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
22954246 AATTTTTTAA
22954256 TTTTAAAATAC
1 TTTTAAAATAC
*
22954267 TTTTAAAAT-T
1 TTTTAAAATAC
22954277 TTTTAAAA-A-
1 TTTTAAAATAC
22954286 TTTTAAAATAC
1 TTTTAAAATAC
22954297 TTTT
1 TTTT
22954301 TTTAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 8 0.27
10 9 0.30
11 13 0.43
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:22955078 original size:20 final size:20
Alignment explanation
Indices: 22955055--22955095 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
22955045 TAAATTTTTA
22955055 TAAAAAC-ATATAAAAATTAT
1 TAAAAACTA-ATAAAAATTAT
*
22955075 TAAAAACTAATAAATATTAT
1 TAAAAACTAATAAAAATTAT
22955095 T
1 T
22955096 CAATTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAACTAATAAAAATTAT
Found at i:22955605 original size:18 final size:17
Alignment explanation
Indices: 22955575--22955608 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22955565 TACCTAATAA
*
22955575 TTATAGTATATTCGAAT
1 TTATAGTAAATTCGAAT
22955592 TTATGAGTAAATTCGAA
1 TTAT-AGTAAATTCGAA
22955609 GAATTTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (17 bp):
TTATAGTAAATTCGAAT
Found at i:22960202 original size:2 final size:2
Alignment explanation
Indices: 22960195--22960221 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22960185 CTGTTAGGTC
22960195 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
22960222 CATATCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:22969221 original size:37 final size:37
Alignment explanation
Indices: 22969179--22969445 Score: 358
Period size: 37 Copynumber: 7.0 Consensus size: 37
22969169 GGTAATTTTA
22969179 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
**
22969216 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
* **
22969253 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
22969290 GTTACACTTATCTGATCAAGTGACAAAGTGATAAGT-
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
* *
22969326 GCTAAACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAA---GT-G
22969367 CTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT-
1 -----GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
22969408 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
22969445 G
1 G
22969446 TAGCCTAGCT
Statistics
Matches: 208, Mismatches: 11, Indels: 22
0.86 0.05 0.09
Matches are distributed among these distances:
36 66 0.32
37 106 0.51
39 2 0.01
43 2 0.01
46 32 0.15
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
Found at i:22969435 original size:82 final size:81
Alignment explanation
Indices: 22969292--22969487 Score: 324
Period size: 82 Copynumber: 2.4 Consensus size: 81
22969282 GATAAGTGGT
22969292 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
*
22969357 TAAGTGGTAGCTTTAGC
66 TAAGTGGTAGC-CTAGC
* * *
22969374 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTACACTTATCTGATCAAGTGGCAAAGTGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
22969439 TAAGTGGTAGCCTAGC
66 TAAGTGGTAGCCTAGC
*
22969455 TACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTG
22969488 ATCATACGTA
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
79 12 0.11
80 5 0.05
81 19 0.17
82 73 0.67
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (81 bp):
TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
TAAGTGGTAGCCTAGC
Found at i:22973591 original size:33 final size:33
Alignment explanation
Indices: 22973551--22973617 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
22973541 TTTCTCATAA
22973551 AAATATTAAAAAATTAGAA-AAAATAAAAAATAT
1 AAATATT-AAAAATTAGAATAAAATAAAAAATAT
* * * *
22973584 AAATATTATAAATTATAATAAATTATAAAATAT
1 AAATATTAAAAATTAGAATAAAATAAAAAATAT
22973617 A
1 A
22973618 TTTTTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (33 bp):
AAATATTAAAAATTAGAATAAAATAAAAAATAT
Found at i:22973627 original size:16 final size:18
Alignment explanation
Indices: 22973606--22973640 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
22973596 TTATAATAAA
22973606 TTATAAAA-T-ATATTTT
1 TTATAAAATTAATATTTT
22973622 TTATAAAATTAATATTTT
1 TTATAAAATTAATATTTT
22973640 T
1 T
22973641 AAAAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATAAAATTAATATTTT
Found at i:22974649 original size:4 final size:4
Alignment explanation
Indices: 22974640--22974681 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
22974630 AGCCCAAAGT
22974640 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
22974682 AAAGAGGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:22976758 original size:31 final size:30
Alignment explanation
Indices: 22976723--22976791 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
22976713 TTTTTCTTAT
22976723 TTTTATAGA-AATTT-AATATGTTGTTATAAAA
1 TTTTATA-ATAATTTAAATATGTT-TTAT-AAA
*
22976754 TTTTA-AATAATTTAAATATGTTTTATTAA
1 TTTTATAATAATTTAAATATGTTTTATAAA
22976783 TTTTATAAT
1 TTTTATAAT
22976792 TTATTAGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
29 8 0.24
30 13 0.38
31 13 0.38
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTTATAATAATTTAAATATGTTTTATAAA
Found at i:22976793 original size:27 final size:26
Alignment explanation
Indices: 22976732--22976821 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 26
22976722 TTTTTATAGA
*
22976732 AATTTAATATGTTGTTATAAAATTTTAAAT
1 AATTTAATATGTT-TTAT-TAATTTT--AT
22976762 AATTTAAATATGTTTTATTAATTTTAT
1 AATTT-AATATGTTTTATTAATTTTAT
* *
22976789 AATTTATTA-GAATTGTATTAATTTTAT
1 AATTTAATATG--TTTTATTAATTTTAT
22976816 AATTTA
1 AATTTA
22976822 TTAGAATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
25 1 0.02
26 3 0.06
27 27 0.50
29 6 0.11
30 9 0.17
31 8 0.15
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (26 bp):
AATTTAATATGTTTTATTAATTTTAT
Found at i:22976822 original size:27 final size:27
Alignment explanation
Indices: 22976777--22976848 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
22976767 AAATATGTTT
22976777 TATTAATTTTATAATTTATTAGAATTG
1 TATTAATTTTATAATTTATTAGAATTG
*
22976804 TATTAATTTTATAATTTATTAGAATTT
1 TATTAATTTTATAATTTATTAGAATTG
* *
22976831 TTTTATTTTTTATAATTT
1 TATTA-ATTTTATAATTT
22976849 TATAACTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 30 0.73
28 11 0.27
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TATTAATTTTATAATTTATTAGAATTG
Found at i:22976831 original size:18 final size:18
Alignment explanation
Indices: 22976808--22976853 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
22976798 GAATTGTATT
22976808 AATTTTATAATTTATTAG
1 AATTTTATAATTTATTAG
* * * *
22976826 AATTTTTTTATTTTTTAT
1 AATTTTATAATTTATTAG
22976844 AATTTTATAA
1 AATTTTATAA
22976854 CTTGATATCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
AATTTTATAATTTATTAG
Found at i:22976848 original size:10 final size:10
Alignment explanation
Indices: 22976810--22976934 Score: 56
Period size: 10 Copynumber: 13.3 Consensus size: 10
22976800 ATTGTATTAA
22976810 TTTTATAATT
1 TTTTATAATT
* *
22976820 TATTAGAATT
1 TTTTATAATT
22976830 TTTT-T-ATT
1 TTTTATAATT
22976838 TTTTATAA--
1 TTTTATAATT
*
22976846 TTTTATAACT
1 TTTTATAATT
**
22976856 TGATATCAA-T
1 TTTTAT-AATT
22976866 TTTTATATATT
1 TTTTATA-ATT
*
22976877 TTTTA-AATA
1 TTTTATAATT
*
22976886 TTTAATAA-T
1 TTTTATAATT
*
22976895 TTGTAT-A-T
1 TTTTATAATT
22976903 TTTTA-AATAT
1 TTTTATAAT-T
*
22976913 TTTTATGATT
1 TTTTATAATT
*
22976923 TTTAAT-ATT
1 TTTTATAATT
22976932 TTT
1 TTT
22976935 ATAGGAAAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 25
0.68 0.12 0.20
Matches are distributed among these distances:
8 22 0.25
9 18 0.21
10 37 0.43
11 10 0.11
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:22976905 original size:37 final size:38
Alignment explanation
Indices: 22976807--22976924 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 38
22976797 AGAATTGTAT
* *
22976807 TAATTTTATAA-TTTATTAGAATTTTT-T-TATTTTTTA
1 TAATTTTATAACTTGA-TATAATTTTTATATATTTTTTA
22976843 TAATTTTATAACTTGATATCAATTTTTATATATTTTTTA
1 TAATTTTATAACTTGATAT-AATTTTTATATATTTTTTA
* *
22976882 -AATATTTAATAATTTG-TAT-ATTTTTAAATA-TTTTTA
1 TAAT-TTT-ATAACTTGATATAATTTTTATATATTTTTTA
*
22976918 TGATTTT
1 TAATTTT
22976925 TAATATTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
36 22 0.31
37 22 0.31
38 4 0.06
39 15 0.21
40 7 0.10
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (38 bp):
TAATTTTATAACTTGATATAATTTTTATATATTTTTTA
Found at i:22976914 original size:18 final size:17
Alignment explanation
Indices: 22976864--22976937 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 17
22976854 CTTGATATCA
*
22976864 ATTTTTATATATTTTTTAA
1 ATTTTTA-ATA-TTTTTAT
* *
22976883 ATATTTAATAATTTGTAT
1 ATTTTTAAT-ATTTTTAT
22976901 ATTTTTAAATATTTTTAT
1 ATTTTT-AATATTTTTAT
22976919 GATTTTTAATATTTTTAT
1 -ATTTTTAATATTTTTAT
22976937 A
1 A
22976938 GGAAAAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
17 1 0.02
18 30 0.64
19 16 0.34
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTTAATATTTTTAT
Found at i:22979025 original size:114 final size:111
Alignment explanation
Indices: 22978802--22979035 Score: 357
Period size: 114 Copynumber: 2.1 Consensus size: 111
22978792 CGAAAAATTT
22978802 TTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAGATAAATTTTTTTTTCTTTGTACT
1 TTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAGATAAATTTTTTTTTCTTTGTACT
22978867 GCGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTAA
66 GCGTA----GTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTAA
22978917 TTTTTTTCGTATTTTTTTATCTGATTCTGACACG-AAAAAAA-ATAAATTTTTTTTTCTTTGTAC
1 TTTTTTTCGTA-TTTTTTATCTGATTCTGACACGAAAAAAAAGATAAATTTTTTTTTCTTTGTAC
* **
22978980 TGTGTA-TGCCGGCCATTGACAGGCCAGCACCCCAAAAATTTTTTTTTG
65 TGCGTAGTGCCGGCCATTGACAGGCCAGCA-CCC-AAAATTTTTTTTAA
22979028 TTTTTTTC
1 TTTTTTTC
22979036 TTTTTCGTAT
Statistics
Matches: 113, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
109 23 0.20
110 3 0.03
111 20 0.18
114 27 0.24
115 18 0.16
116 22 0.19
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (111 bp):
TTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAGATAAATTTTTTTTTCTTTGTACT
GCGTAGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTAA
Found at i:22987758 original size:37 final size:39
Alignment explanation
Indices: 22987685--22987760 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 39
22987675 TAGTCCCATT
* *
22987685 TTAAAAACAAATTAATATTTATATATTAAATCAATTAAA
1 TTAAAAACAAATTAATATTTATATACTAAAGCAATTAAA
*
22987724 TTAAAAA-AAATTAAT-TTTAT-TACTAACGCTAATTAAA
1 TTAAAAACAAATTAATATTTATATACTAAAGC-AATTAAA
22987761 ATATTGAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 6 0.18
37 12 0.36
38 8 0.24
39 7 0.21
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (39 bp):
TTAAAAACAAATTAATATTTATATACTAAAGCAATTAAA
Found at i:23004481 original size:35 final size:35
Alignment explanation
Indices: 23004435--23004505 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
23004425 TTAGTGCAAG
23004435 ATATGGGTATATATGCCTGACATGAGAATGCTCAA
1 ATATGGGTATATATGCCTGACATGAGAATGCTCAA
23004470 ATATGGGTATATATGCCTGACATGAGAATGCTCAA
1 ATATGGGTATATATGCCTGACATGAGAATGCTCAA
23004505 A
1 A
23004506 ATTTTCAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (35 bp):
ATATGGGTATATATGCCTGACATGAGAATGCTCAA
Found at i:23007423 original size:21 final size:21
Alignment explanation
Indices: 23007382--23007424 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
23007372 ACCCCAAACT
* *
23007382 CTCAAATCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
23007403 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
23007424 C
1 C
23007425 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:23011702 original size:16 final size:16
Alignment explanation
Indices: 23011681--23011714 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
23011671 TTCATTCTTG
23011681 ATATTTATTAATTTAT
1 ATATTTATTAATTTAT
*
23011697 ATATTTTTTAATTTAT
1 ATATTTATTAATTTAT
23011713 AT
1 AT
23011715 CTATCATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTTATTAATTTAT
Found at i:23015724 original size:23 final size:24
Alignment explanation
Indices: 23015693--23015738 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
23015683 AAAATACTAT
*
23015693 AAAATTTTTTTATTTATCAAAAAA
1 AAAATTTTTTTATTTACCAAAAAA
23015717 AAAATTTTTTTATTTACCAAAA
1 AAAATTTTTTTATTTACCAAAA
23015739 TATATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAATTTTTTTATTTACCAAAAAA
Found at i:23015845 original size:27 final size:27
Alignment explanation
Indices: 23015815--23015881 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
23015805 CGCCAATGGG
*
23015815 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACA
* *
23015842 ATTGGCGGCACCAATGGTGCCAATACA
1 ATTGGCGGCACCAAAGGTGCCAAAACA
*
23015869 ATTGGTGGCACCA
1 ATTGGCGGCACCA
23015882 GTGTATATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACA
Found at i:23015936 original size:4 final size:4
Alignment explanation
Indices: 23015927--23016051 Score: 109
Period size: 4 Copynumber: 31.0 Consensus size: 4
23015917 GAAGGAGAGG
*
23015927 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AA -AAA GAAG GAAA GAAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
* *
23015974 GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA G-AA GAAAA GGAAA
1 -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA
*
23016019 GGAGAA G-AA GAAA GAAA GAAA GAAG GAAA GAAA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
23016052 AGGAAAGGAA
Statistics
Matches: 102, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
3 15 0.15
4 64 0.63
5 19 0.19
6 4 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:23016054 original size:34 final size:31
Alignment explanation
Indices: 23015928--23016057 Score: 122
Period size: 34 Copynumber: 4.0 Consensus size: 31
23015918 AAGGAGAGGG
*
23015928 AAAGAAAGAAAGAAAGAAAGAAAG-AAA-GAA
1 AAAGAAAGAAAG-AAGAAGGAAAGAAAAGGAA
* *
23015958 AAAGAAGGAAAGAA-AAGGAAAGGAGAAGAGAAAA
1 AAAGAAAGAAAGAAGAAGGAAA-GA-AA-AG-GAA
* *
23015992 AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGA
1 AAAGAAAGAAAGAAGAAGGAAAGAAAAGGA-A
23016024 AGAAGAAAGAAAGAAAGAAGGAAAGAAAAGGAA
1 A-AAGAAAGAAAG-AAGAAGGAAAGAAAAGGAA
23016057 A
1 A
23016058 GGAAAGGAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
28 6 0.07
29 3 0.04
30 11 0.14
31 3 0.04
32 5 0.06
33 15 0.19
34 32 0.40
35 6 0.07
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (31 bp):
AAAGAAAGAAAGAAGAAGGAAAGAAAAGGAA
Found at i:23016116 original size:89 final size:89
Alignment explanation
Indices: 23015932--23016092 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 89
23015922 AGAGGGAAAG
23015932 AAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGA
1 AAAG-AAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGA
**
23015997 AAGAAAGAAGAAGAAAAGGAAAGGA
65 AAGAAAGAAGAAGAAAAGGAAAAAA
* * *
23016022 GAAGAAGAAAGAAAGAAAG-AAG-GAAAG-A--AAAGGAAAGGAAAGGAGAAGAGAAAAAAA-AA
1 AAAGAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
23016081 AG-AAGAAGAAGA
66 AGAAAGAAGAAGA
23016093 GGGAAGGAAG
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
82 10 0.15
83 4 0.06
84 28 0.41
86 1 0.01
87 4 0.06
88 3 0.04
89 15 0.22
90 3 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (89 bp):
AAAGAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
AGAAAGAAGAAGAAAAGGAAAAAA
Found at i:23016121 original size:79 final size:82
Alignment explanation
Indices: 23015937--23016117 Score: 217
Period size: 84 Copynumber: 2.2 Consensus size: 82
23015927 GAAAGAAAGA
* ** *
23015937 AAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAA
1 AAGAAA-AAAAAAAGAAAGAAGGA-AAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAA
23016002 AGAAGAAGAAAAGGAAAGGAG
64 AGAAGAAG--AAGGAAAGGAG
* * *
23016023 AAGAAGAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAAAGGAGAAGAGAAAAAAA-AAAG-AAG
1 AAGAAAAAAAAAAGAAAGAAGGAAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAG
*
23016086 AAGAAG-AGGGAAGGA-
66 AAGAAGAAGGAAAGGAG
*
23016101 AGGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
23016118 AGAAAAGGTA
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
78 14 0.16
79 8 0.09
82 9 0.10
83 4 0.05
84 31 0.36
85 15 0.17
86 5 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (82 bp):
AAGAAAAAAAAAAGAAAGAAGGAAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAG
AAGAAGAAGGAAAGGAG
Found at i:23016879 original size:74 final size:75
Alignment explanation
Indices: 23016756--23016895 Score: 187
Period size: 74 Copynumber: 1.9 Consensus size: 75
23016746 GGTTTATTTC
23016756 GGGTTTTTACCAAAATATTACAAAAAAATAAAAAATACGAAAATATTATAAAAATTTTTTATTTA
1 GGGTTTTTACCAAAATATTACAAAAAAATAAAAAATACGAAAATATTATAAAAATTTTTTATTTA
23016821 CTAGAATAAT
66 CTAGAATAAT
* * * ***
23016831 GGGTTTTTA-CAAATATATT--AAAAAAATTAAAAATAACTAAAATGTTATAAGTTTTTTTTATT
1 GGGTTTTTACCAAA-ATATTACAAAAAAATAAAAAAT-ACGAAAATATTATAAAAATTTTTTATT
23016893 TAC
64 TAC
23016896 CAAAAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
73 14 0.25
74 29 0.51
75 14 0.25
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.39
Consensus pattern (75 bp):
GGGTTTTTACCAAAATATTACAAAAAAATAAAAAATACGAAAATATTATAAAAATTTTTTATTTA
CTAGAATAAT
Found at i:23016912 original size:24 final size:24
Alignment explanation
Indices: 23016885--23016930 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
23016875 TTATAAGTTT
23016885 TTTTTATTTACCAAAAAATATATA
1 TTTTTATTTACCAAAAAATATATA
*
23016909 TTTTTATTTACCAAAATATATA
1 TTTTTATTTACCAAAAAATATA
23016931 AAAAAAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTTTATTTACCAAAAAATATATA
Found at i:23016991 original size:46 final size:46
Alignment explanation
Indices: 23016941--23017028 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
23016931 AAAAAAAGCT
* *
23016941 GCAAA-AGAAAGGGTGATGGTTATTTTTTTACAGAAAATTAATACGA
1 GCAAAGAGAAAGGGTAAGGGTTA-TTTTTTACAGAAAATTAATACGA
* * *
23016987 GCAAAGGGCAGGGGTAAGGGTTATTTTTTACAGAAAATTAAT
1 GCAAAGAGAAAGGGTAAGGGTTATTTTTTACAGAAAATTAAT
23017029 TTAAATAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
46 24 0.67
47 12 0.33
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (46 bp):
GCAAAGAGAAAGGGTAAGGGTTATTTTTTACAGAAAATTAATACGA
Found at i:23017586 original size:23 final size:25
Alignment explanation
Indices: 23017560--23017625 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 25
23017550 AGTTTTTTTG
23017560 ATATATTTTGGTAAAT-AAAAAA-T
1 ATATATTTTGGTAAATAAAAAAATT
*
23017583 ATATATTTTGATAAATAAAAAAATTT
1 ATATATTTTGGTAAATAAAAAAA-TT
23017609 ATAGTATTTTGGTAAAT
1 ATA-TATTTTGGTAAAT
23017626 TTTATTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.41
24 6 0.16
26 4 0.11
27 12 0.32
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (25 bp):
ATATATTTTGGTAAATAAAAAAATT
Found at i:23021443 original size:29 final size:29
Alignment explanation
Indices: 23021411--23021505 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
23021401 TTGGTCATAT
23021411 AACTATGAAAAGTTACAAAATGGTCACTC
1 AACTATGAAAAGTTACAAAATGGTCACTC
* * * * **** *
23021440 AACTATTAGTAATTTTCTTTTTTGGTCA-TAT
1 AACTATGA-AAAGTTAC-AAAATGGTCACT-C
23021471 AACTATGAAAAGTTACAAAATGGTCACTC
1 AACTATGAAAAGTTACAAAATGGTCACTC
23021500 AACTAT
1 AACTAT
23021506 TAGTAAATTT
Statistics
Matches: 44, Mismatches: 18, Indels: 8
0.63 0.26 0.11
Matches are distributed among these distances:
29 19 0.43
30 12 0.27
31 13 0.30
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.35
Consensus pattern (29 bp):
AACTATGAAAAGTTACAAAATGGTCACTC
Found at i:23021467 original size:31 final size:31
Alignment explanation
Indices: 23021431--23021545 Score: 96
Period size: 31 Copynumber: 3.8 Consensus size: 31
23021421 AGTTACAAAA
*
23021431 TGGTCACTCAACTATTAGTAATTTTCTTTTT
1 TGGTCACTCAACTATTAGTAAATTTCTTTTT
* * * ****
23021462 TGGTCA-TATAACTA-T-GAAAAGTTAC-AAAA
1 TGGTCACT-CAACTATTAGTAAA-TTTCTTTTT
23021491 TGGTCACTCAACTATTAGTAAATTTCTTTTT
1 TGGTCACTCAACTATTAGTAAATTTCTTTTT
*
23021522 TGGTCACTCAACTA-TATTAAATTT
1 TGGTCACTCAACTATTAGTAAATTT
23021546 TTGAATGTTT
Statistics
Matches: 62, Mismatches: 16, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
29 14 0.23
30 19 0.31
31 29 0.47
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (31 bp):
TGGTCACTCAACTATTAGTAAATTTCTTTTT
Found at i:23021473 original size:60 final size:60
Alignment explanation
Indices: 23021392--23021527 Score: 256
Period size: 60 Copynumber: 2.3 Consensus size: 60
23021382 TCTAACTATG
23021392 ATTTT-TTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
1 ATTTTCTTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
23021451 ATTTTCTTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
1 ATTTTCTTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
*
23021511 AATTTCTTTTTTGGTCA
1 ATTTTCTTTTTTGGTCA
23021528 CTCAACTATA
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 5 0.07
60 70 0.93
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (60 bp):
ATTTTCTTTTTTGGTCATATAACTATGAAAAGTTACAAAATGGTCACTCAACTATTAGTA
Found at i:23025902 original size:99 final size:99
Alignment explanation
Indices: 23025731--23025929 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
23025721 ATGTGCAACG
23025731 TTGTCTTCTTTTATATTTTAATATTATGTATATTATATTAATTAAAAAAGCATATATAATATATA
1 TTGTCTTCTTTTATATTTTAATATTATGTATATTATATTAATTAAAAAAGCATATATAATATATA
23025796 AATAATGTAAAATTTTAAAAAATATATTTTAAAA
66 AATAATGTAAAATTTTAAAAAATATATTTTAAAA
23025830 TTGTCTTCTTTTATATTTTAATATTATGTATATTATATTAATTAAAAAAGCATATATAATATATA
1 TTGTCTTCTTTTATATTTTAATATTATGTATATTATATTAATTAAAAAAGCATATATAATATATA
23025895 AATAATGTAAAATTTTAAAAAATATATTTTAAAA
66 AATAATGTAAAATTTTAAAAAATATATTTTAAAA
23025929 T
1 T
23025930 AAAATATTTT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (99 bp):
TTGTCTTCTTTTATATTTTAATATTATGTATATTATATTAATTAAAAAAGCATATATAATATATA
AATAATGTAAAATTTTAAAAAATATATTTTAAAA
Found at i:23025938 original size:15 final size:15
Alignment explanation
Indices: 23025906--23025961 Score: 69
Period size: 15 Copynumber: 3.6 Consensus size: 15
23025896 ATAATGTAAA
*
23025906 ATTTTAAAA-AATAT
1 ATTTTAAAATAAAAT
23025920 ATTTTAAAATAAAAT
1 ATTTTAAAATAAAAT
23025935 ATTTTAAAATATATATAT
1 ATTTTAAAATA-A-A-AT
23025953 ATTTTAAAA
1 ATTTTAAAA
23025962 ATTCAGAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 9 0.24
15 15 0.41
16 1 0.03
17 1 0.03
18 11 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTAAAATAAAAT
Found at i:23031340 original size:23 final size:24
Alignment explanation
Indices: 23031304--23031354 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
23031294 AAATTATTTC
*
23031304 TATTTTTCATGTTATTATTATAAT
1 TATTTTTCATGTTACTATTATAAT
* *
23031328 TATTTTTTA-GTTACTATTATTAT
1 TATTTTTCATGTTACTATTATAAT
23031351 TATT
1 TATT
23031355 CCTATTGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TATTTTTCATGTTACTATTATAAT
Found at i:23032860 original size:21 final size:21
Alignment explanation
Indices: 23032835--23032887 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
23032825 CATTGTTTCA
* *
23032835 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAATAACC
*
23032856 AATCTCACCGCTACAATAACT
1 AATCTCACCGCTACAATAACC
23032877 AATCTCACCGC
1 AATCTCACCGC
23032888 CACCACTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.38, G:0.08, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:23042321 original size:3 final size:3
Alignment explanation
Indices: 23042313--23042339 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
23042303 TTTGATGTGA
23042313 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
23042340 TTCTAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23045652 original size:46 final size:46
Alignment explanation
Indices: 23045589--23045690 Score: 186
Period size: 46 Copynumber: 2.2 Consensus size: 46
23045579 GAAAATGCAG
23045589 TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCCTACCCAGT
1 TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCCTACCCAGT
*
23045635 TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCTTACCCAGT
1 TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCCTACCCAGT
*
23045681 TGTTCTTAAT
1 TTTTCTTAAT
23045691 GTTACCCAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.42
Consensus pattern (46 bp):
TTTTCTTAATCTTAAAGTCCAGTGTAGTTTAGCATCCCTACCCAGT
Found at i:23053483 original size:23 final size:23
Alignment explanation
Indices: 23053425--23053483 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
23053415 ATGATTTTTA
23053425 ATTAAATAAAATATTTAAAATTAAG
1 ATTAAA-AAAA-ATTTAAAATTAAG
* * *
23053450 ATTCAATAAAATTTAAATTTAA-
1 ATTAAAAAAAATTTAAAATTAAG
23053472 ATTTAAAAAAAA
1 A-TTAAAAAAAA
23053484 AATCGTCTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 1 0.04
23 19 0.68
24 3 0.11
25 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATTAAAAAAAATTTAAAATTAAG
Found at i:23059532 original size:6 final size:6
Alignment explanation
Indices: 23059521--23059546 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23059511 ACTTCACCAT
23059521 CCCCAG CCCCAG CCCCAG CCCCAG CC
1 CCCCAG CCCCAG CCCCAG CCCCAG CC
23059547 TCTGCACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.69, G:0.15, T:0.00
Consensus pattern (6 bp):
CCCCAG
Found at i:23066350 original size:15 final size:16
Alignment explanation
Indices: 23066327--23066406 Score: 78
Period size: 15 Copynumber: 5.2 Consensus size: 16
23066317 TCTCGATACT
23066327 CATATATTTGACTTTC
1 CATATATTTGACTTTC
**
23066343 CA-ATATTTGA-TACC
1 CATATATTTGACTTTC
23066357 CATATATTTGACTTTC
1 CATATATTTGACTTTC
* **
23066373 TAT-TATTTGA-TACC
1 CATATATTTGACTTTC
*
23066387 CATATCTTTGACTTTC
1 CATATATTTGACTTTC
23066403 CATA
1 CATA
23066407 AATATGGATG
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 8 0.16
15 29 0.59
16 12 0.24
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (16 bp):
CATATATTTGACTTTC
Found at i:23066361 original size:30 final size:30
Alignment explanation
Indices: 23066311--23066404 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
23066301 ATTTCTTATG
* *
23066311 CCAATATCTCGATACTCATATATTTGACTTT
1 CCAATAT-TTGATACCCATATATTTGACTTT
23066342 CCAATATTTGATACCCATATATTTGACTTT
1 CCAATATTTGATACCCATATATTTGACTTT
* * *
23066372 CTATTATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATATTTGACTTT
23066402 CCA
1 CCA
23066405 TAAATATGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 50 0.88
31 7 0.12
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATATTTGACTTT
Found at i:23071958 original size:7 final size:8
Alignment explanation
Indices: 23071936--23071961 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
23071926 ATAAATTTAA
23071936 ATATTTTT
1 ATATTTTT
23071944 ATATTTTT
1 ATATTTTT
23071952 ATATTTTT
1 ATATTTTT
23071960 AT
1 AT
23071962 CCTTTTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATATTTTT
Found at i:23075480 original size:16 final size:15
Alignment explanation
Indices: 23075450--23075485 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
23075440 GAGGAAGAAA
*
23075450 AAAGGAAAAAGATAT
1 AAAGTAAAAAGATAT
23075465 AAAGTAAAAAGAATAT
1 AAAGTAAAAAG-ATAT
23075481 AAAGT
1 AAAGT
23075486 TTTAAAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
AAAGTAAAAAGATAT
Found at i:23081711 original size:13 final size:13
Alignment explanation
Indices: 23081693--23081723 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23081683 TTCCAGCAAC
23081693 TATGAATTTATTT
1 TATGAATTTATTT
23081706 TATGAATTTATTT
1 TATGAATTTATTT
*
23081719 GATGA
1 TATGA
23081724 TGATCCAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:23081893 original size:50 final size:50
Alignment explanation
Indices: 23081818--23082060 Score: 333
Period size: 50 Copynumber: 4.8 Consensus size: 50
23081808 ATTTGGGTAA
23081818 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
*
23081868 AGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *** *
23081918 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATTTAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* ** * * * *
23081968 AGAAGTCCCCCGTAAGACCATGTCTGGGACATGACATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** *
23082018 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
23082061 TGTTATTATC
Statistics
Matches: 168, Mismatches: 24, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 135 0.80
51 33 0.20
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:23085836 original size:58 final size:59
Alignment explanation
Indices: 23085744--23085904 Score: 193
Period size: 58 Copynumber: 2.7 Consensus size: 59
23085734 TTGCATTTTG
* * *
23085744 ACCCCT-AAACTTCTCTAAAATTTCATTTTGACCCCTAAACTTTCTCAAAATTACAGTTAA
1 ACCCCTAAAATTTCT-TAAAATTACATTTTGACCCCTAAACTTT-TAAAAATTACAGTTAA
* *
23085804 ACCCCTAAAATTT-TT-AAATTACATTTTGACCCCTAAACTTTTAAAAATTACATTTTA
1 ACCCCTAAAATTTCTTAAAATTACATTTTGACCCCTAAACTTTTAAAAATTACAGTTAA
* * * * *
23085861 ACTCCTAAACTTTCTTAAAATTACGTTTTGACCCCAAAAGTTTT
1 ACCCCTAAAATTTCTTAAAATTACATTTTGACCCCTAAACTTTT
23085905 GCTGCCATTA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
57 24 0.27
58 27 0.31
59 25 0.28
60 7 0.08
61 5 0.06
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
ACCCCTAAAATTTCTTAAAATTACATTTTGACCCCTAAACTTTTAAAAATTACAGTTAA
Found at i:23085867 original size:29 final size:29
Alignment explanation
Indices: 23085737--23085895 Score: 187
Period size: 30 Copynumber: 5.4 Consensus size: 29
23085727 TAATTTTTTG
*
23085737 CATTTTGACCCCTAAACTTCTCTAAAATTT
1 CATTTTGACCCCTAAACTT-TCTAAAATTA
23085767 CATTTTGACCCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCT-AAAATTA
* ** * *
23085797 CAGTTAAACCCCTAAAATTT-TTAAATTA
1 CATTTTGACCCCTAAACTTTCTAAAATTA
23085825 CATTTTGACCCCTAAACTTT-TAAAAATTA
1 CATTTTGACCCCTAAACTTTCT-AAAATTA
* *
23085854 CATTTTAACTCCTAAACTTTCTTAAAATTA
1 CATTTTGACCCCTAAACTTTC-TAAAATTA
*
23085884 CGTTTTGACCCC
1 CATTTTGACCCC
23085896 AAAAGTTTTG
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 23 0.21
29 28 0.26
30 57 0.52
31 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTCTAAAATTA
Found at i:23085895 original size:87 final size:87
Alignment explanation
Indices: 23085737--23085904 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 87
23085727 TAATTTTTTG
* *
23085737 CATTTTGACCCCTAAACTTCTCTAAAATTTCATTTTGACCCCTAAACTTTCTCAAAATTACAGTT
1 CATTTTGACCCCTAAACTTCTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACAGTT
*
23085802 AAACCCCTAAAATTTTTAAATTA
66 AAACCCC-AAAAGTTTTAAATTA
* *
23085825 CATTTTGACCCCTAAACTT-T-TAAAAATTACATTTTAACTCCTAAACTTTCTTAAAATTAC-GT
1 CATTTTGACCCCTAAACTTCTCT-AAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACAG-
**
23085887 TTTGACCCCAAAAGTTTT
64 TTAAACCCCAAAAGTTTT
23085905 GCTGCCATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
86 10 0.14
87 42 0.59
88 19 0.27
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (87 bp):
CATTTTGACCCCTAAACTTCTCTAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACAGTT
AAACCCCAAAAGTTTTAAATTA
Found at i:23086370 original size:4 final size:4
Alignment explanation
Indices: 23086361--23086415 Score: 73
Period size: 4 Copynumber: 14.5 Consensus size: 4
23086351 GCTGATCGGA
23086361 AAAG AAAG AAAG AAAG -AA- AAAG AGAAG AAAG AAAG AAAG -AAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG
23086407 -AAG AAAG AA
1 AAAG AAAG AA
23086416 GAGAGAAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
3 10 0.22
4 32 0.70
5 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:23086390 original size:15 final size:15
Alignment explanation
Indices: 23086365--23086414 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
23086355 ATCGGAAAAG
23086365 AAAGA-AAGAAAGAA
1 AAAGAGAAGAAAGAA
23086379 AAAGAGAAGAAAGAA
1 AAAGAGAAGAAAGAA
23086394 AGAA-AGAAGAAAGAA
1 A-AAGAGAAGAAAGAA
23086409 GAAAGA
1 -AAAGA
23086415 AGAGAGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.16
15 23 0.72
16 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGAGAAGAAAGAA
Found at i:23086425 original size:7 final size:7
Alignment explanation
Indices: 23086362--23086424 Score: 81
Period size: 7 Copynumber: 8.6 Consensus size: 7
23086352 CTGATCGGAA
23086362 AAGAAAG
1 AAGAAAG
23086369 AAAGAAAG
1 -AAGAAAG
*
23086377 AAAAAGAG
1 AAGAA-AG
23086385 AAGAAAG
1 AAGAAAG
23086392 AAAGAAAG
1 -AAGAAAG
23086400 AAGAAAG
1 AAGAAAG
23086407 AAGAAAG
1 AAGAAAG
*
23086414 AAGAGAG
1 AAGAAAG
23086421 AAGA
1 AAGA
23086425 GGGGAAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
7 30 0.60
8 20 0.40
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:23086565 original size:23 final size:20
Alignment explanation
Indices: 23086536--23086585 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
23086526 AAGCAGCGAA
23086536 AAAAAAACAAAAAACAAAGCAG
1 AAAAAAA-AAAAAA-AAAGCAG
*
23086558 AAAAAAAAAAGAAAAAGCAG
1 AAAAAAAAAAAAAAAAGCAG
*
23086578 CAAAAAAA
1 AAAAAAAA
23086586 TAGCAGGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 14 0.54
21 5 0.19
22 7 0.27
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAGCAG
Found at i:23086567 original size:20 final size:21
Alignment explanation
Indices: 23086536--23086585 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
23086526 AAGCAGCGAA
*
23086536 AAAAAAACAAAAAACAAAGCAG-
1 AAAAAAA-AAAGAA-AAAGCAGC
23086558 AAAAAAAAAAGAAAAAGCAGC
1 AAAAAAAAAAGAAAAAGCAGC
23086579 AAAAAAA
1 AAAAAAA
23086586 TAGCAGGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.27
21 12 0.46
22 7 0.27
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAGAAAAAGCAGC
Found at i:23086572 original size:25 final size:26
Alignment explanation
Indices: 23086524--23086573 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
23086514 TAGTCAAGCC
*
23086524 CAAAGCAGCGAAAAAAAAACAAAAAA
1 CAAAGCAGCAAAAAAAAAACAAAAAA
*
23086550 CAAAGCAG-AAAAAAAAAAGAAAAA
1 CAAAGCAGCAAAAAAAAAACAAAAA
23086574 GCAGCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (26 bp):
CAAAGCAGCAAAAAAAAAACAAAAAA
Found at i:23087199 original size:18 final size:18
Alignment explanation
Indices: 23087176--23087481 Score: 144
Period size: 18 Copynumber: 16.4 Consensus size: 18
23087166 CAATTTTAAA
23087176 AAAAATTTGTCGTG-TTTC
1 AAAAATTT-TCGTGTTTTC
*
23087194 AAAAA-TTTCGAGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
23087211 AAAAAAATTTCTCAT-ATTTC
1 --AAAAATTT-TCGTGTTTTC
23087231 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
**
23087249 AAAAAATTCCCGTGTTTTC
1 -AAAAATTTTCGTGTTTTC
23087268 AAAATTTTCATGTTTTCGTGTTTTC
1 AAAA-----A--TTTTCGTGTTTTC
* *
23087293 AAAAAATTCTCGTGTTTTTTTAA
1 -AAAAATTTTCGTG---TTTT-C
** * *
23087316 AAAAAAATTCATGTTTTA
1 AAAAATTTTCGTGTTTTC
** *
23087334 AAAAAAATTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
*
23087352 -GAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
23087369 AAAATTTTTCGTG---TC
1 AAAAATTTTCGTGTTTTC
* * *
23087384 AAAAAATTCTCATG-TATC
1 -AAAAATTTTCGTGTTTTC
* * *
23087402 GAAAATTTCCTTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
23087420 AAAAAAATTCCGTGTTTTC
1 -AAAAATTTTCGTGTTTTC
23087439 AAAAAATTTTCGTG-TTTC
1 -AAAAATTTTCGTGTTTTC
*
23087457 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
23087475 AAAAATT
1 AAAAATT
23087482 ATTATTGTGT
Statistics
Matches: 224, Mismatches: 38, Indels: 52
0.71 0.12 0.17
Matches are distributed among these distances:
15 2 0.01
16 14 0.06
17 43 0.19
18 68 0.30
19 59 0.26
20 6 0.03
21 3 0.01
22 13 0.06
23 1 0.00
25 11 0.05
26 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:23087231 original size:37 final size:38
Alignment explanation
Indices: 23087169--23087254 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
23087159 TATGGCACAA
* * * *
23087169 TTTTAAAAAAAATTTGTCGTGTTTCAAAAA-TTTCGAG
1 TTTTCAAAAAAATTTCTCATATTTCAAAAATTTTCGAG
*
23087206 TTTTCAAAAAAATTTCTCATATTTCAAAAATTTTCGTG
1 TTTTCAAAAAAATTTCTCATATTTCAAAAATTTTCGAG
23087244 TTTTCAAAAAA
1 TTTTCAAAAAA
23087255 TTCCCGTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 26 0.60
38 17 0.40
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (38 bp):
TTTTCAAAAAAATTTCTCATATTTCAAAAATTTTCGAG
Found at i:23087255 original size:19 final size:19
Alignment explanation
Indices: 23087175--23087479 Score: 165
Period size: 19 Copynumber: 16.3 Consensus size: 19
23087165 ACAATTTTAA
23087175 AAAAAATTTGTCGTG-TTTC
1 AAAAAATTT-TCGTGTTTTC
*
23087194 -AAAAA-TTTCGAGTTTTC
1 AAAAAATTTTCGTGTTTTC
* *
23087211 AAAAAAATTTCTCAT-ATTTC
1 -AAAAAATTT-TCGTGTTTTC
23087231 -AAAAATTTTCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
**
23087249 AAAAAATTCCCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
*
23087268 AAAATTTTCATGTTTTCGTGTTTTC
1 AAAA-----A-ATTTTCGTGTTTTC
* *
23087293 AAAAAATTCTCGTGTTTTTTTA
1 AAAAAATTTTCGTG---TTTTC
** *
23087315 AAAAAAAATTCATGTTTT-
1 AAAAAATTTTCGTGTTTTC
** *
23087333 AAAAAAAATTCATGTTTTC
1 AAAAAATTTTCGTGTTTTC
*
23087352 --GAAATTTTCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
*
23087369 -AAAATTTTTCGTG---TC
1 AAAAAATTTTCGTGTTTTC
* * *
23087384 AAAAAATTCTCATG-TATC
1 AAAAAATTTTCGTGTTTTC
* * *
23087402 -GAAAATTTCCTTGTTTTC
1 AAAAAATTTTCGTGTTTTC
* *
23087420 AAAAAAATTCCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
23087439 AAAAAATTTTCGTG-TTTC
1 AAAAAATTTTCGTGTTTTC
*
23087457 -AAAAATCTTCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
23087475 AAAAA
1 AAAAA
23087480 TTATTATTGT
Statistics
Matches: 223, Mismatches: 38, Indels: 50
0.72 0.12 0.16
Matches are distributed among these distances:
15 2 0.01
16 14 0.06
17 43 0.19
18 58 0.26
19 67 0.30
20 7 0.03
21 2 0.01
22 14 0.06
24 1 0.00
25 15 0.07
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (19 bp):
AAAAAATTTTCGTGTTTTC
Found at i:23087281 original size:17 final size:18
Alignment explanation
Indices: 23087176--23087284 Score: 75
Period size: 17 Copynumber: 6.0 Consensus size: 18
23087166 CAATTTTAAA
*
23087176 AAAAATTTGTCGTG-TTTC
1 AAAAATTT-TCATGTTTTC
23087194 AAAAA-TTTCGA-GTTTTC
1 AAAAATTTTC-ATGTTTTC
*
23087211 AAAAAAATTTCTCAT-ATTTC
1 --AAAAATTT-TCATGTTTTC
*
23087231 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCATGTTTTC
** *
23087249 AAAAAATTCCCGTGTTTTC
1 -AAAAATTTTCATGTTTTC
23087268 -AAAATTTTCATGTTTTC
1 AAAAATTTTCATGTTTTC
23087285 GTGTTTTCAA
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.04
17 23 0.32
18 17 0.23
19 21 0.29
20 7 0.10
21 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (18 bp):
AAAAATTTTCATGTTTTC
Found at i:23087308 original size:27 final size:25
Alignment explanation
Indices: 23087259--23087310 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
23087249 AAAAAATTCC
*
23087259 CGTGTTTTCAAAATTTTCATGTTTT
1 CGTGTTTTCAAAATTCTCATGTTTT
*
23087284 CGTGTTTTCAAAAAATTCTCGTGTTTT
1 CGTGTTTTC--AAAATTCTCATGTTTT
23087311 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
27 14 0.61
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.52
Consensus pattern (25 bp):
CGTGTTTTCAAAATTCTCATGTTTT
Found at i:23087470 original size:36 final size:38
Alignment explanation
Indices: 23087412--23087497 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
23087402 GAAAATTTCC
23087412 TTGT-TTTCAAAAAAATTCCGTGTTTTCAAAAA-ATT-
1 TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
**
23087447 TTCGTGTTTCAAAAATCTT-CGTGTTTTCAAAAATTATTA
1 TT-GTGTTTCAAAAAAATTCCGTGTTTTCAAAAA-TATTA
23087486 TTGTGTTTCAAA
1 TTGTGTTTCAAA
23087498 GTTCTCGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 16 0.36
37 11 0.25
38 13 0.30
39 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (38 bp):
TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
Found at i:23090371 original size:29 final size:29
Alignment explanation
Indices: 23090304--23090398 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 29
23090294 ACAAAAAATA
**
23090304 TAAATTACATTTTGGCCCCTAAACTTTT-
1 TAAATTACATTTTAACCCCTAAACTTTTC
*
23090332 TAAAAATTACATTTTAACCTCTAAACTTTTC
1 T--AAATTACATTTTAACCCCTAAACTTTTC
*
23090363 TAAATTACATTTCAACCCCTAAACTTTCTC
1 TAAATTACATTTTAACCCCTAAACTTT-TC
*
23090393 AAAATT
1 TAAATT
23090399 GTGTGTGTGC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.02
29 24 0.42
30 31 0.54
31 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAATTACATTTTAACCCCTAAACTTTTC
Found at i:23092723 original size:87 final size:86
Alignment explanation
Indices: 23092577--23092746 Score: 304
Period size: 87 Copynumber: 2.0 Consensus size: 86
23092567 TAGAAACAGA
23092577 GAGTTCTGTATTCTGAATACTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
1 GAGTTCTGTATTCTGAATACTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
*
23092642 TTAGGCCCTTAATCATTTCAGG
66 TTA-ACCCTTAATCATTTCAGG
*
23092664 GAGTTCTGTATTCTGAATATTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
1 GAGTTCTGTATTCTGAATACTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
*
23092729 TTAATCCTTAATCATTTC
66 TTAACCCTTAATCATTTC
23092747 TTAACTACTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 13 0.16
87 67 0.84
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (86 bp):
GAGTTCTGTATTCTGAATACTGAAGCTTGAAAATCTTTTTTACACCATGTTTATGTATTTATAGT
TTAACCCTTAATCATTTCAGG
Found at i:23092789 original size:43 final size:43
Alignment explanation
Indices: 23092741--23092827 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
23092731 AATCCTTAAT
23092741 CATTTCTTAA-CTACTTAACTATTATAACTAACAACCCAATAAC
1 CATTTCTTAATC-ACTTAACTATTATAACTAACAACCCAATAAC
* * * * *
23092784 CATTTCTTAATCATTTGATTATTATAATTAACAACTCAATAAC
1 CATTTCTTAATCACTTAACTATTATAACTAACAACCCAATAAC
23092827 C
1 C
23092828 CACTATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.40, C:0.22, G:0.01, T:0.37
Consensus pattern (43 bp):
CATTTCTTAATCACTTAACTATTATAACTAACAACCCAATAAC
Found at i:23096257 original size:25 final size:25
Alignment explanation
Indices: 23096223--23096276 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
23096213 CTTAACTAAC
*
23096223 TAAAACAGTCATGTCCATATATAAT
1 TAAAACAGTCATGACCATATATAAT
23096248 TAAAACAGTCATGACCATATATAAT
1 TAAAACAGTCATGACCATATATAAT
23096273 TAAA
1 TAAA
23096277 TTTTCACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (25 bp):
TAAAACAGTCATGACCATATATAAT
Found at i:23096390 original size:112 final size:113
Alignment explanation
Indices: 23096271--23096481 Score: 318
Period size: 113 Copynumber: 1.9 Consensus size: 113
23096261 ACCATATATA
23096271 ATTAAATTT-TCACACAATTTTAAAAAATTAAAATATAAAATTACCACCATACTA-TTAACAACA
1 ATTAAATTTGTCACACAATTTTAAAAAA-TAAAATATAAAATTACCACCATACTATTTAACAACA
* * * *
23096334 TTAAAAATCGTAATTATATTTTATTTTGATTAATATTTATCTTTATAGG
65 TTAAAAATCGCAACTAAATTTTATTTCGATTAATATTTATCTTTATAGG
* * *
23096383 ATTAAATTTGTCACACAATTTTAAAAAATAAAATGTAAAATTACCACCATACTATTTAATAATAT
1 ATTAAATTTGTCACACAATTTTAAAAAATAAAATATAAAATTACCACCATACTATTTAACAACAT
* *
23096448 TAAAAATTGCCACTAAATTTTATTTCGATTAATA
66 TAAAAATCGCAACTAAATTTTATTTCGATTAATA
23096482 ATTGTCACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
112 34 0.39
113 54 0.61
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.39
Consensus pattern (113 bp):
ATTAAATTTGTCACACAATTTTAAAAAATAAAATATAAAATTACCACCATACTATTTAACAACAT
TAAAAATCGCAACTAAATTTTATTTCGATTAATATTTATCTTTATAGG
Found at i:23103755 original size:2 final size:2
Alignment explanation
Indices: 23103748--23103781 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23103738 AAACATTGTC
23103748 AT AT AT AT 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 AT AT AT AT
23103782 TCTTTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23104914 original size:2 final size:2
Alignment explanation
Indices: 23104898--23104935 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
23104888 CTATCCATAG
*
23104898 TA TA -A TA TT TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23104936 AAGTAAGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:23106528 original size:5 final size:5
Alignment explanation
Indices: 23106518--23106588 Score: 135
Period size: 5 Copynumber: 14.4 Consensus size: 5
23106508 TTTAAAATAC
23106518 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
23106568 TATAT TATAT TATAT TA-AT TA
1 TATAT TATAT TATAT TATAT TA
23106589 AAAAATATTA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.06
5 62 0.94
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:23108390 original size:19 final size:19
Alignment explanation
Indices: 23108366--23108403 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
23108356 AAATACAAAA
*
23108366 TTTTTATATG-AAATATTAT
1 TTTTTAAATGTAAAT-TTAT
23108385 TTTTTAAATGTAAATTTAT
1 TTTTTAAATGTAAATTTAT
23108404 ATATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTTAAATGTAAATTTAT
Found at i:23108671 original size:18 final size:20
Alignment explanation
Indices: 23108628--23108665 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23108618 AGACTTTTAG
* *
23108628 GTTTCTTTATAAATTTTCTA
1 GTTTTTTTAAAAATTTTCTA
23108648 GTTTTTTTAAAAATTTTC
1 GTTTTTTTAAAAATTTTC
23108666 ATTTTTCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (20 bp):
GTTTTTTTAAAAATTTTCTA
Found at i:23129705 original size:29 final size:30
Alignment explanation
Indices: 23129639--23129707 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
23129629 AAATATCGAT
* *
23129639 TTTATACATTAACTTTGTTTTCATGTGTAA
1 TTTATACATGAACTTTGATTTCATGTGTAA
23129669 TTTGATACATGAACTTTGATTT-A-GTGTAA
1 TTT-ATACATGAACTTTGATTTCATGTGTAA
23129698 TTATATACAT
1 TT-TATACAT
23129708 AAAACTTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 14 0.40
30 5 0.14
31 16 0.46
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (30 bp):
TTTATACATGAACTTTGATTTCATGTGTAA
Found at i:23130754 original size:29 final size:30
Alignment explanation
Indices: 23130708--23130787 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
23130698 AAATTTAATC
*
23130708 AAATCAAAATTTAATATATAAAATCGCACA-
1 AAATCAAAA-TTCATATATAAAATCGCACAT
* *
23130738 AAATCAAAATTCATATATAACATTGCACATT
1 AAATCAAAATTCATATATAAAATCGCACA-T
* *
23130769 AAATTAAAATTCATGTATA
1 AAATCAAAATTCATATATA
23130788 GTTTAATATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.40
30 9 0.21
31 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTCATATATAAAATCGCACAT
Found at i:23139210 original size:6 final size:6
Alignment explanation
Indices: 23139199--23139223 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
23139189 TACTTTACAA
23139199 CGATGG CGATGG CGATGG CGATGG C
1 CGATGG CGATGG CGATGG CGATGG C
23139224 CAGCAAGCGA
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:0.20, G:0.48, T:0.16
Consensus pattern (6 bp):
CGATGG
Found at i:23143174 original size:20 final size:20
Alignment explanation
Indices: 23143151--23143188 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23143141 GCTTATTGTT
*
23143151 AATTAAGTAAAGGTTAATTA
1 AATTAAGTAAAGATTAATTA
*
23143171 AATTAATTAAAGATTAAT
1 AATTAAGTAAAGATTAAT
23143189 CTAAGTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
AATTAAGTAAAGATTAATTA
Found at i:23145720 original size:13 final size:13
Alignment explanation
Indices: 23145702--23145731 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
23145692 AGCCCAAACT
23145702 CAATTACCCAACC
1 CAATTACCCAACC
23145715 CAATTACCCAACC
1 CAATTACCCAACC
23145728 CAAT
1 CAAT
23145732 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:23164900 original size:16 final size:16
Alignment explanation
Indices: 23164879--23164911 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
23164869 TAAATATATA
23164879 TTAAGTTTTTTATGTT
1 TTAAGTTTTTTATGTT
23164895 TTAAGTTTTTTATGTT
1 TTAAGTTTTTTATGTT
23164911 T
1 T
23164912 AAAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (16 bp):
TTAAGTTTTTTATGTT
Found at i:23165003 original size:20 final size:20
Alignment explanation
Indices: 23164980--23165020 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
23164970 CCCCTGACAG
*
23164980 TTTAAGTTTTCAATTTTATT
1 TTTAAGTTTTCAATTTCATT
*
23165000 TTTATGTTTTCAATTTCATT
1 TTTAAGTTTTCAATTTCATT
23165020 T
1 T
23165021 CCCCGACAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTAAGTTTTCAATTTCATT
Found at i:23165124 original size:15 final size:16
Alignment explanation
Indices: 23165104--23165136 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
23165094 CTGCACATAG
*
23165104 CAATTGACAG-GATAA
1 CAATTGAAAGTGATAA
23165119 CAATTGAAAGTGATAA
1 CAATTGAAAGTGATAA
23165135 CA
1 CA
23165137 TTGGTGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (16 bp):
CAATTGAAAGTGATAA
Found at i:23165278 original size:16 final size:16
Alignment explanation
Indices: 23165257--23165299 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
23165247 ATTTTGTTAC
* *
23165257 AACAATTAATATACTT
1 AACAATTAATACAATT
23165273 AACAATTAATACAATT
1 AACAATTAATACAATT
23165289 AACAATTAATA
1 AACAATTAATA
23165300 AGTTGATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:23165327 original size:16 final size:16
Alignment explanation
Indices: 23165306--23165347 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
23165296 AATAAGTTGA
*
23165306 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
23165322 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
23165338 TAATTTTAAT
1 TAATTTTAAT
23165348 TTTATCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:23174353 original size:17 final size:15
Alignment explanation
Indices: 23174326--23174364 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
23174316 ATATAAGAAC
*
23174326 ATTTTATTATTAAATT
1 ATTTTAATATT-AATT
23174342 ATATTTAATATTAATT
1 AT-TTTAATATTAATT
23174358 ATTTTAA
1 ATTTTAA
23174365 ATTGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTAATATTAATT
Found at i:23174740 original size:16 final size:15
Alignment explanation
Indices: 23174719--23174748 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
23174709 TAAATTCATA
23174719 TAAGAATTTTGATTAT
1 TAAGAATTTT-ATTAT
23174735 TAAGAATTTTATTA
1 TAAGAATTTTATTA
23174749 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (15 bp):
TAAGAATTTTATTAT
Found at i:23174768 original size:18 final size:17
Alignment explanation
Indices: 23174740--23174774 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23174730 ATTATTAAGA
*
23174740 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
23174757 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
23174775 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:23174915 original size:120 final size:120
Alignment explanation
Indices: 23174502--23174899 Score: 644
Period size: 117 Copynumber: 3.4 Consensus size: 120
23174492 AATTATTTTA
*
23174502 AATTTTATTAAATCATATATTTTAATTAAAATATTTTTAATATTAATTACTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTACTTCAAATTATATTTT
* *
23174567 ATAGTATCATATATTATGATTTTAGCAAATTCATATAAGAATGTTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
23174622 AATTTTATT--A-CATATATTTTAATTAAAATATTTTTAATATTAATTACTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTACTTCAAATTATATTTT
* *
23174684 ATGGTATCATATATTATGATTTTAGTAAATTCATATAAGAATTTTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
* * *
23174739 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTA-TGTTAAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTACT-TCAAATTATATTT
*
23174803 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAG-ATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
* *
23174858 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATA
23174900 ATTATTATGT
Statistics
Matches: 263, Mismatches: 11, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
117 113 0.43
118 1 0.00
119 57 0.22
120 92 0.35
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTACTTCAAATTATATTTT
ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:23175137 original size:45 final size:44
Alignment explanation
Indices: 23175039--23175149 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 44
23175029 TTTTCCATTA
23175039 TGCTATTACACCTCTATTCCA-T----TCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACACTCAACCAAACACAAGAT
* * ***
23175078 TACTATTACGCCTCTATTCCATTACACTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACACTCAACCAAACACAAGA-T
23175123 TGCTATTACACCTCTATTCCATTACAC
1 TGCTATTACACCTCTATTCCATTACAC
23175150 CTCTATTCCA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 19 0.32
40 1 0.02
44 13 0.22
45 26 0.44
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACACTCAACCAAACACAAGAT
Found at i:23175148 original size:16 final size:16
Alignment explanation
Indices: 23175127--23175196 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
23175117 TTGATTTGCT
*
23175127 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
23175143 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
23175159 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
23175175 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
23175191 AATACA
1 ATTACA
23175197 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:23176551 original size:23 final size:23
Alignment explanation
Indices: 23176525--23176576 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
23176515 TAATTTTTTA
*
23176525 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
23176548 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
23176571 GTTTAG
1 ATTTAG
23176577 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:23186252 original size:23 final size:23
Alignment explanation
Indices: 23186204--23186253 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
23186194 ATTTGTAAAT
*
23186204 TTTA-AATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTAATAATA
23186226 TTTAGAATTATTTAGTAATAATA
1 TTTAGAATTATTTAGTAATAATA
23186249 TTTAG
1 TTTAG
23186254 GAAAAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (23 bp):
TTTAGAATTATTTAGTAATAATA
Done.