Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold874
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: 104557
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1464 original size:33 final size:33
Alignment explanation
Indices: 1399--1474 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
1389 TTCGAAATAG
* * * * *
1399 CCTAAACTCGAAAGAACTTGAACTCAAAAGAAC
1 CCTAAACCCGAAAAAACCTAAACCCAAAAGAAC
*
1432 CCTAAACCCGAAAAAACCTAAACCCAAGAGAAC
1 CCTAAACCCGAAAAAACCTAAACCCAAAAGAAC
*
1465 TC-AAACCCGA
1 CCTAAACCCGA
1475 GACTGATCCG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.49, C:0.30, G:0.11, T:0.11
Consensus pattern (33 bp):
CCTAAACCCGAAAAAACCTAAACCCAAAAGAAC
Found at i:1667 original size:22 final size:22
Alignment explanation
Indices: 1652--1695 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1642 AAATAGTAAT
1652 TTATCAAAAAGTAAATTATATC
1 TTATCAAAAAGTAAATTATATC
1674 TTATCAAAAAGTAAATTATATC
1 TTATCAAAAAGTAAATTATATC
1696 ATGAGCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (22 bp):
TTATCAAAAAGTAAATTATATC
Found at i:2631 original size:18 final size:18
Alignment explanation
Indices: 2608--2660 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
2598 AATTATTGAA
2608 AAATTAATTTTATATAAC
1 AAATTAATTTTATATAAC
*
2626 AAATTAATTTTATA-AAT
1 AAATTAATTTTATATAAC
2643 AAATATAGATTTTA-ATAA
1 AAAT-TA-ATTTTATATAA
2661 ATAAATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 6 0.19
18 17 0.55
19 8 0.26
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATTAATTTTATATAAC
Found at i:2660 original size:20 final size:19
Alignment explanation
Indices: 2614--2669 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
2604 TGAAAAATTA
*
2614 ATTTTATATAACAAAT-TA-
1 ATTTTATA-AATAAATATAG
2632 ATTTTATAAATAAATATAG
1 ATTTTATAAATAAATATAG
2651 ATTTTAATAAATAAATATA
1 ATTTT-ATAAATAAATATA
2670 TTGAAAATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.18
18 10 0.29
19 5 0.15
20 13 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTTATAAATAAATATAG
Found at i:4475 original size:2 final size:2
Alignment explanation
Indices: 4468--4509 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4458 ACACGGTGGA
4468 AT AT AT AT 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 AT AT AT AT
4510 GTCATAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4673 original size:2 final size:2
Alignment explanation
Indices: 4666--4695 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4656 AATATCTTCC
4666 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
4696 TAATATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5144 original size:3 final size:3
Alignment explanation
Indices: 5126--5161 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
5116 TCAAGCTCTG
5126 TAA TAA -AA TGAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
5162 GCTTACATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6486 original size:21 final size:21
Alignment explanation
Indices: 6462--6501 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6452 TAATGATGTA
6462 ATAAT-TAATTTATATTAAATT
1 ATAATGTAATTTA-ATTAAATT
*
6483 ATAATGTGATTTAATTAAA
1 ATAATGTAATTTAATTAAA
6502 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
ATAATGTAATTTAATTAAATT
Found at i:7054 original size:19 final size:19
Alignment explanation
Indices: 7030--7072 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
7020 AAATACTGCT
* *
7030 TTAAAATATATTTTAAAAA
1 TTAAAAAATAATTTAAAAA
7049 TTAAAAAATAATTTAAAAA
1 TTAAAAAATAATTTAAAAA
*
7068 ATAAA
1 TTAAA
7073 TATGGGCCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAAAATAATTTAAAAA
Found at i:7319 original size:2 final size:2
Alignment explanation
Indices: 7312--7338 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7302 CAAAGTCATG
7312 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
7339 CACTATTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7540 original size:21 final size:23
Alignment explanation
Indices: 7515--7557 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
7505 CATTTGGTTA
*
7515 TTTAAAATAA-TATT-ATAATTT
1 TTTAAAAAAATTATTAATAATTT
7536 TTTAAAAAAATTATTAATAATT
1 TTTAAAAAAATTATTAATAATT
7558 ATAATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAAAAAAATTATTAATAATTT
Found at i:7961 original size:20 final size:20
Alignment explanation
Indices: 7938--8016 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
7928 TATTTTAAAA
*
7938 AATTAATTTTTGTAAAAATT
1 AATTAATTTTTTTAAAAATT
* *
7958 AATTAATTTTTATTTAAAATG
1 AATTAATTTTT-TTAAAAATT
*
7979 AATAAATTTTTTTAAAAA-T
1 AATTAATTTTTTTAAAAATT
* *
7998 GATTGA-TTTTTTAAAAATT
1 AATTAATTTTTTTAAAAATT
8017 TATATTATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
18 11 0.23
19 4 0.08
20 17 0.35
21 16 0.33
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
AATTAATTTTTTTAAAAATT
Found at i:8126 original size:19 final size:21
Alignment explanation
Indices: 8098--8145 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 21
8088 TTTTAAAATA
8098 ATTTT-ATTTTTT-ATTTAA-
1 ATTTTAATTTTTTAATTTAAT
8116 A-TTTAATTTTTTAATTTAAT
1 ATTTTAATTTTTTAATTTAAT
8136 ATTTTAATTT
1 ATTTTAATTT
8146 AAATCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.12
18 8 0.31
19 6 0.23
20 1 0.04
21 8 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTAATTTTTTAATTTAAT
Found at i:8131 original size:13 final size:13
Alignment explanation
Indices: 8115--8157 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
8105 TTTTTATTTA
8115 AATTTAATTTTTT
1 AATTTAATTTTTT
*
8128 AATTTAATATTTT
1 AATTTAATTTTTT
8141 AATTTAAATCTTTTT
1 AATTT-AAT-TTTTT
8156 AA
1 AA
8158 ATATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 17 0.65
14 3 0.12
15 6 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
AATTTAATTTTTT
Found at i:9197 original size:3 final size:3
Alignment explanation
Indices: 9189--9229 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
9179 TTTTCTGTAT
* *
9189 TCA TCA TCA TC- TCA TCA TCA TCG TCA TCA TCA TCA TTA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
9230 GCCTGCTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.29, C:0.32, G:0.02, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:10120 original size:22 final size:21
Alignment explanation
Indices: 10095--10142 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
10085 TAATTTCAAT
10095 TAAACTTTAAATTAAGTTAATC
1 TAAA-TTTAAATTAAGTTAATC
* * *
10117 TAAATTTGAATTTATTTAATC
1 TAAATTTAAATTAAGTTAATC
10138 TAAAT
1 TAAAT
10143 CAACAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
TAAATTTAAATTAAGTTAATC
Found at i:10752 original size:28 final size:28
Alignment explanation
Indices: 10712--10765 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
10702 TTTTGGAAGA
*
10712 GAAAACCCAGTTAAGTTGGAGGCTAAGT
1 GAAAACCCAGTTAAGTTGGAAGCTAAGT
*
10740 GAAAACCTAGTTAAGTTGGAAGCTAA
1 GAAAACCCAGTTAAGTTGGAAGCTAA
10766 ATACACTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (28 bp):
GAAAACCCAGTTAAGTTGGAAGCTAAGT
Found at i:21258 original size:33 final size:33
Alignment explanation
Indices: 21210--21273 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
21200 TGGCAGAAGA
* * *
21210 ACAGGAACCATTTTCAGTAGTAGTGGAAAACTG
1 ACAGAAACCACTTTCAGTAGTAGGGGAAAACTG
*
21243 ACAGAAACCACTTTCATTAGTAGGGGAAAAC
1 ACAGAAACCACTTTCAGTAGTAGGGGAAAAC
21274 AGGTTTCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (33 bp):
ACAGAAACCACTTTCAGTAGTAGGGGAAAACTG
Found at i:26262 original size:33 final size:33
Alignment explanation
Indices: 26220--26285 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
26210 GTGGCAGAAG
*
26220 AACAGGAACCACTTTCAGTAGTAGTGGAAAACT
1 AACAGGAACCACTTTCAGTAGTAGGGGAAAACT
*
26253 AACAGGAACCACTTTCATTAGTAGGGGAAAACT
1 AACAGGAACCACTTTCAGTAGTAGGGGAAAACT
26286 GGTTTCAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (33 bp):
AACAGGAACCACTTTCAGTAGTAGGGGAAAACT
Found at i:38117 original size:1 final size:1
Alignment explanation
Indices: 38111--38200 Score: 72
Period size: 1 Copynumber: 90.0 Consensus size: 1
38101 AAATCTTCAC
* * ** * * * **
38111 TTTTTTTTTTTGTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
38176 TTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
38201 CCAATTGCCA
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:38155 original size:33 final size:33
Alignment explanation
Indices: 38111--38199 Score: 155
Period size: 32 Copynumber: 2.7 Consensus size: 33
38101 AAATCTTCAC
38111 TTTTTTT-TTTTGTTTTTTTTTTTCTTTTTCCT
1 TTTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCT
38143 TTTTTTTGTTTTG-TTTTTTTTTTCTTTTTCCT
1 TTTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCT
38175 TTTTTTTGTTTTGTTTTTTTCTTTT
1 TTTTTTTGTTTTGTTTTTTT-TTTT
38200 TCCAATTGCC
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
32 39 0.72
33 11 0.20
34 4 0.07
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.87
Consensus pattern (33 bp):
TTTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCT
Found at i:49538 original size:52 final size:52
Alignment explanation
Indices: 49460--49588 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
49450 CGAAATATGA
* *
49460 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
* *
49512 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATATATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
49564 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
49589 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
Found at i:49601 original size:52 final size:51
Alignment explanation
Indices: 49460--49608 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 51
49450 CGAAATATGA
*
49460 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
* * *
49512 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATATATCTAGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
*
49564 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
49609 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGC
Found at i:49615 original size:13 final size:13
Alignment explanation
Indices: 49597--49621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49587 CAAAGATCAG
49597 TGTATCGATACAA
1 TGTATCGATACAA
49610 TGTATCGATACA
1 TGTATCGATACA
49622 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:49699 original size:33 final size:33
Alignment explanation
Indices: 49662--49728 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
49652 AGTAGCTTAA
49662 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
49695 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
49728 A
1 A
49729 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:49702 original size:13 final size:13
Alignment explanation
Indices: 49684--49708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49674 CAAAAAAATA
49684 TGTATCGATACAT
1 TGTATCGATACAT
49697 TGTATCGATACA
1 TGTATCGATACA
49709 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50686 original size:92 final size:93
Alignment explanation
Indices: 50495--51469 Score: 1125
Period size: 92 Copynumber: 10.5 Consensus size: 93
50485 AAGATGGAAA
* * *
50495 AGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAAGGTGCCAATATG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATG
* *
50560 TTGATTCAAGGCCAGCGATATTGGACTTAA-
63 CTGATTCAAGGCCAGCTATATTGGACTTAAG
* * *
50590 AGGTGCCAATGTGCTGATTCAAGACCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGTTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTG
*
50655 ATTCAAGGCCAGCTATATTGGGCTT-AG
66 ATTCAAGGCCAGCTATATTGGACTTAAG
* * *
50682 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAAGTGCCAATATGCTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTG
* * *
50747 ATTCAAGGTCAGCGATATTGGATTTAA-
66 ATTCAAGGCCAGCTATATTGGACTTAAG
* * *
50774 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAATTAAAGAAGAAGGTGCCAATATGCTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTG
*
50839 ATTCAAGGCCAGCGATATTGGACTTAA-
66 ATTCAAGGCCAGCTATATTGGACTTAAG
*
50866 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTG
*
50931 ATTCAAGGCCAGCTATATTGAACTTAA-
66 ATTCAAGGCCAGCTATATTGGACTTAAG
* * *
50958 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGCTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTG
*
51022 ATTCAAGGCCAGCTACATTGGACTTAAAG
66 ATTCAAGGCCAGCTATATTGGACTT-AAG
* * * *
51051 ATAACGGTGCCAATATGCTGATTCAGGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGT
1 ---A-GGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAT
*
51110 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
62 GCTGATTCAAGGCCAGCTATATTGGACTT----AAG
* * * *
51146 AAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTT----A--AAGGTGCCAATGTGCT
1 -AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCT
*
51205 GATTCAAGGCCAGCTACATTGGACTTAAAGAAG
65 GATTCAAGGCCAGCTATATTGGACTT----AAG
* * *
51238 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTT----A--AAGGTGCCAATGTGCT
1 -AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCT
*
51297 GATTCAAGGCCAGCTACATTGGACTTAAAGGTG
65 GATTCAAGGCCAGCTATATTGGACTT-AA---G
* *
51330 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTG
* * *
51395 ATTTAGGGCCAGCGATATTGGACTTAAAG
66 ATTCAAGGCCAGCTATATTGGACTT-AAG
* *
51424 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 ----AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
51470 GAAGGGTTGC
Statistics
Matches: 803, Mismatches: 52, Indels: 47
0.89 0.06 0.05
Matches are distributed among these distances:
89 2 0.00
91 77 0.10
92 557 0.69
93 3 0.00
94 2 0.00
95 46 0.06
96 1 0.00
97 76 0.09
98 39 0.05
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (93 bp):
AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTG
ATTCAAGGCCAGCTATATTGGACTTAAG
Found at i:50889 original size:21 final size:21
Alignment explanation
Indices: 50822--50889 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
50812 ATTAAAGAAG
50822 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
*
50843 AA-G-GCCAGCGATAT--TGGACTTA
1 AAGGTGCCA---ATATGCT-GA-TTC
50865 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
50886 AAGG
1 AAGG
50890 CCAGCTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 14 0.39
22 10 0.28
23 2 0.06
24 4 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:51086 original size:324 final size:324
Alignment explanation
Indices: 50440--51464 Score: 1482
Period size: 324 Copynumber: 3.1 Consensus size: 324
50430 AAGATGAGAA
* * *
50440 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATT-GAACTTAAAGATGGAAAAGGTGCCGA
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAA-TTAAAGA---AGAAGGTGCCAA
* *
50504 TATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAAGGTGCCAATATGTTGATTCAA
61 TATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---AAAGGTGCCAATATGCTGATTCAA
* * * * * *
50569 GGCCAGCGATATTGGACTT-----A-AAGGTGCCAATGTGCTGATTCAAGACCAGCTACATTGGA
117 GGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAA
* * * *
50628 CTTAAAGATGAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGGCTT--A---GAGGTGC
182 CTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAGGTGC
*
50688 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAAGTGCCAATATGCTGATTCA
241 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
* *
50752 AGGTCAGCGATATTGGATTT
305 GGGCCAGCGATATTGGATTT
50772 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAATTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAATTAAAGAAGAAGGTGCCAATATGC
50837 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
66 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
50902 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGGTGCCAA
131 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGGTGCCAA
50967 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAGGTGCCAATGTGCTGATTCAAGGCC
196 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAGGTGCCAATGTGCTGATTCAAGGCC
* *
51032 AGCTACATTGGACTTAAAGATAACGGTGCCAATATGCTGATTCAGGGCCAGCGATATTGGACTT
261 AGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAGGGCCAGCGATATTGGATTT
*
51096 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAATTAAAGAAGAAGGTGCCAATATGC
* *
51161 TGATTCAAGGCTAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
66 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
51226 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGGTGCCAA
131 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGGTGCCAA
51291 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAGGTGCCAATGTGCTGATTCAAGGCC
196 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAGGTGCCAATGTGCTGATTCAAGGCC
*
51356 AGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTTAGGGCCAGCGATATTGGACTTA
261 AGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAGGGCCAGCGATATTGGA-TT-
51421 AAGAT
324 ----T
* *
51426 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
51465 GCTTAGAAGG
Statistics
Matches: 646, Mismatches: 28, Indels: 40
0.90 0.04 0.06
Matches are distributed among these distances:
319 78 0.12
321 2 0.00
322 1 0.00
324 401 0.62
325 40 0.06
327 1 0.00
328 39 0.06
330 38 0.06
331 38 0.06
332 8 0.01
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (324 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAATTAAAGAAGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGGTGCCAA
TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAGGTGCCAATGTGCTGATTCAAGGCC
AGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAGGGCCAGCGATATTGGATTT
Found at i:51213 original size:21 final size:20
Alignment explanation
Indices: 51146--51213 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
51136 CTTAAAGAAG
51146 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
* *
51167 AAGGCTAGCGATATTG--GACTTA
1 AAGG-T-GCCA-ATTGCTGA-TTC
51189 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
51210 AAGG
1 AAGG
51214 CCAGCTACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (20 bp):
AAGGTGCCAATTGCTGATTC
Found at i:51496 original size:30 final size:31
Alignment explanation
Indices: 51462--51587 Score: 141
Period size: 33 Copynumber: 4.0 Consensus size: 31
51452 CCAGCTATAT
51462 TGGGC-TTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
*
51492 TGGGCTTTAGAGAATGGTTGCCACCGACTTGTG
1 TGGGCTTT--AGAAGGGTTGCCACCGACTTGTG
*
51525 TGGGCTCT-GAAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAG-AAG--GGTTGCCACCGACTTGTG
* * *
51558 TGGGCTTTAGGAGGG-TGCCACGGAGTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
51588 GACTTAAAAG
Statistics
Matches: 82, Mismatches: 7, Indels: 14
0.80 0.07 0.14
Matches are distributed among these distances:
30 19 0.23
31 6 0.07
33 56 0.68
34 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.27
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:51513 original size:33 final size:32
Alignment explanation
Indices: 51462--51567 Score: 153
Period size: 33 Copynumber: 3.3 Consensus size: 32
51452 CCAGCTATAT
*
51462 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAAGGTTGCCACCGACTTGTG
51492 TGGGCTTTAGAGAATGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAA-GGTTGCCACCGACTTGTG
* *
51525 TGGGCTCTGAAAGAAGGTTGCCACCGACTTGTG
1 TGGGCT-TTAGAGAAGGTTGCCACCGACTTGTG
51558 TGGGCTTTAG
1 TGGGCTTTAG
51568 GAGGGTGCCA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.07
31 5 0.07
32 3 0.04
33 48 0.72
34 6 0.09
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.28
Consensus pattern (32 bp):
TGGGCTTTAGAGAAGGTTGCCACCGACTTGTG
Found at i:51640 original size:34 final size:34
Alignment explanation
Indices: 51571--52245 Score: 735
Period size: 34 Copynumber: 20.0 Consensus size: 34
51561 GCTTTAGGAG
* * *
51571 GGTGCCACGGAGTTGTGGAC-TTAAAAGGAACAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
*
51604 GGTGCCACGGAGTTTTGGGCTTTAAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
* *
51638 GGTGCGACGGAGTTGTGGGCTTTGAAAAGGGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAAAAA
*
51674 GAGCGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAA
1 G-GTGCCACGGAGTTGTGGGCTTTAAAAA--GAAAAA
51711 GAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
1 G-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
***
51746 GGTGCCACGGAGTTGTGGGCTTTGTGAAGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
* *
51780 GGTTGCCACAGAATTGTGGGCTTT-AAAAG-----
1 GG-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
* * * *
51809 GGTGCCACAGAGTTGTGGAC-TTAAAAGGAACAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
*
51842 GGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAA-AG-AAAAA
*
51879 AGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
* *
51913 GGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
*
51947 GGTTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAA
1 GG-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
* *
51982 GGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
*
52016 GGTTGCCACGGAATTGTGGGCTTT-AAAAG-----
1 GG-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
52045 GGTGCCACGGAGTTGTGGGCTTTGAAAAAGGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAAA-GAAAAA
52081 GAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
1 G-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
** * *
52116 GGTGCCATTGAGTTGTGGGCTTTGAGAAGAAAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAG-AAAAA
* * *
52151 GGTTGCCGCGAAATTGTGGGCTTT-AAAAG-----
1 GG-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
* * *
52180 GGTGCCACGGAGTTGTGGAC-TTAAAAGGAACAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
*
52213 GGTGCCACGGAGTTGTGGGCTTTAAAGAGAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
52246 TGCCACTGAG
Statistics
Matches: 548, Mismatches: 57, Indels: 73
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.01
28 58 0.11
29 6 0.01
30 4 0.01
31 1 0.00
33 55 0.10
34 175 0.32
35 104 0.19
36 39 0.07
37 102 0.19
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.21
Consensus pattern (34 bp):
GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
Found at i:51801 original size:69 final size:68
Alignment explanation
Indices: 51571--52245 Score: 735
Period size: 69 Copynumber: 10.0 Consensus size: 68
51561 GCTTTAGGAG
* * * *
51571 GGTGCCACGGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTTTGGGCTTTAAAAAGAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
51635 AAA
66 AAA
* * *
51638 GGTGCGACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGCGCCACGGAGTTGTGGGCTTTAAAAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAA
51703 GGGAAAAA
63 --GAAAAA
***
51711 GAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGTGAAGA
1 G-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
51776 AAAA
65 AAAA
* * * * *
51780 GGTTGCCACAGAATTGTGGGCTTT-AAAAG-----GGTGCCACAGAGTTGTGGAC-TTAAAAGGA
1 GG-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
*
51838 ACAA
65 AAAA
* *
51842 GGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAA-AG-AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
51907 GAAAAA
63 GAAAAA
* * *
51913 GGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAAGGTTGCCATGGAGTTGTGGGCTTTAAAAAGA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG-TGCCACGGAGTTGTGGGCTTTAAAAAGA
51978 AAAA
65 AAAA
* * *
51982 GGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAAGGTTGCCACGGAATTGTGGGCTTT-AAAAG-
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG-TGCCACGGAGTTGTGGGCTTTAAAAAGA
52045 ----
65 AAAA
52045 GGTGCCACGGAGTTGTGGGCTTTGAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAAA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAA
52110 GAAAAA
63 GAAAAA
** * * * * *
52116 GGTGCCATTGAGTTGTGGGCTTTGAGAAGAAAAAAGGTTGCCGCGAAATTGTGGGCTTT-AAAAG
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAG-AAAAAGG-TGCCACGGAGTTGTGGGCTTTAAAAAG
52180 -----
64 AAAAA
* * * *
52180 GGTGCCACGGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAGAGAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
52244 AA
66 AA
52246 TGCCACTGAG
Statistics
Matches: 517, Mismatches: 56, Indels: 71
0.80 0.09 0.11
Matches are distributed among these distances:
61 37 0.07
62 20 0.04
63 49 0.09
64 21 0.04
65 27 0.05
66 6 0.01
67 18 0.03
68 19 0.04
69 125 0.24
70 53 0.10
71 103 0.20
72 7 0.01
73 11 0.02
74 21 0.04
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.21
Consensus pattern (68 bp):
GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
AAA
Found at i:51808 original size:28 final size:27
Alignment explanation
Indices: 51776--51836 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
51766 TTTGTGAAGA
* *
51776 AAAAGGTTGCCACAGAATTGTGGGCTTT
1 AAAAGGGTGCCACAGAATTGTGGAC-TT
*
51804 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAATTGTGGACTT
51831 AAAAGG
1 AAAAGG
51837 AACAAGGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAATTGTGGACTT
Found at i:51862 original size:167 final size:169
Alignment explanation
Indices: 51571--52270 Score: 684
Period size: 167 Copynumber: 4.2 Consensus size: 169
51561 GCTTTAGGAG
* * * ** *
51571 GGTGCCACGGAGTTGTGGAC-TT-AAAAGGAACAAGG-TGCCACGGAGTTTTGGGCTTTAAAAAG
1 GGTGCCACGGAGTTGTGGGCTTTGAGAA-GAAAAAGGTTGCCATAGAGTTGTGGGCTTTAAAAAG
* *
51633 AAAAAGGTGCGACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGCGCCACGGAGTTGTGGGCTTT
65 -----GGTGCCACGGAGTTGTGGGCTTTGAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTT
51698 AAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
123 -AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
* * *
51746 GGTGCCACGGAGTTGTGGGCTTTGTGAAGAAAAAGGTTGCCACAGAATTGTGGGCTTT-AAAAGG
1 GGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAAGGTTGCCATAGAGTTGTGGGCTTTAAAAAGG
* * *
51810 GTGCCACAGAGTTGTGGAC-TT-AAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
66 GTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGG
*
51873 AAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
130 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
*
51913 GGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAAGGTTGCCATGGAGTTGTGGGCTTTAAAAAGA
1 GGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAAGGTTGCCATAGAGTTGTGGGCTTTAAAAAG-
* *
51978 AAAAGGTGCCACGGAGTTGTGGGCTTTGAGAA-GAAAAAGGTTGCCACGGAATTGTGGGCTTTAA
65 ----GGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGG-TGCCACGGAGTTGTGGGCTTTAA
52042 AA--G-----G-GTGCCACGGAGTTGTGGGCTTTGAAAAAGGAAAAA
125 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAA-GAAAAA
* * *
52081 GAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG-TGCCATTGAGTTGTGGGCTTTGAGAAG
1 G-GTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAAGGTTGCCATAGAGTTGTGGGCTTT------
* * * * *
52145 AAAAAAGGTTGCCGCGAAATTGTGGGCTTT-AAAA-G-----GGTGCCACGGAGTTGTGGAC-TT
59 -AAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT
* *
52202 AAAA-GGAACAAG-GTGCCACGGAGTTGTGGGCTTTAAAGAG-AAAA
123 AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
* * *
52246 --TGCCACTGAGTCGTGGACTTTGAGA
1 GGTGCCACGGAGTTGTGGGCTTTGAGA
52271 CAAAATGCCA
Statistics
Matches: 457, Mismatches: 40, Indels: 69
0.81 0.07 0.12
Matches are distributed among these distances:
162 26 0.06
163 17 0.04
164 2 0.00
165 4 0.01
166 23 0.05
167 130 0.28
168 62 0.14
169 41 0.09
170 21 0.05
171 17 0.04
172 1 0.00
173 18 0.04
174 13 0.03
175 48 0.11
176 14 0.03
177 20 0.04
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.22
Consensus pattern (169 bp):
GGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAAGGTTGCCATAGAGTTGTGGGCTTTAAAAAGG
GTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGA
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
Found at i:52052 original size:28 final size:29
Alignment explanation
Indices: 51976--52072 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 29
51966 GCTTTAAAAA
* *
51976 GAAAAAGGTGCCACGGAGTTGTGGGCTTT
1 GAAAAGGGTGCCACGGAATTGTGGGCTTT
*
52005 GAGAAGAAAAAGGTTGCCACGGAATTGTGGGCTTT
1 -----G-AAAAGGGTGCCACGGAATTGTGGGCTTT
*
52040 -AAAAGGGTGCCACGGAGTTGTGGGCTTT
1 GAAAAGGGTGCCACGGAATTGTGGGCTTT
52068 GAAAA
1 GAAAA
52073 AGGAAAAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
28 26 0.46
29 4 0.07
34 1 0.02
35 25 0.45
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.23
Consensus pattern (29 bp):
GAAAAGGGTGCCACGGAATTGTGGGCTTT
Found at i:52179 original size:28 final size:27
Alignment explanation
Indices: 52147--52207 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
52137 TTGAGAAGAA
* * *
52147 AAAAGGTTGCCGCGAAATTGTGGGCTTT
1 AAAAGGGTGCCACGAAATTGTGGAC-TT
* *
52175 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGAAATTGTGGACTT
52202 AAAAGG
1 AAAAGG
52208 AACAAGGTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.30, C:0.13, G:0.34, T:0.23
Consensus pattern (27 bp):
AAAAGGGTGCCACGAAATTGTGGACTT
Found at i:52277 original size:30 final size:29
Alignment explanation
Indices: 52215--52394 Score: 216
Period size: 30 Copynumber: 5.9 Consensus size: 29
52205 AGGAACAAGG
* * * *
52215 TGCCACGGAGTTGTGGGCTTTAAAGAGAAAA
1 TGCCACTGAGTCGTGGACTTT-GAGA-AAAA
52246 TGCCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGA-AAAA
52276 TGCCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGA-AAAA
52306 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTTG-AGAAAA--A
* *
52338 TGCCACTGAGTCATGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAA-A-AA
*
52369 TGCCACTGAGTCGTGGGCTTTGAGAA
1 TGCCACTGAGTCGTGGACTTTGAGAA
52395 GAGATTTGAA
Statistics
Matches: 135, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
30 62 0.46
31 49 0.36
32 23 0.17
33 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (29 bp):
TGCCACTGAGTCGTGGACTTTGAGAAAAA
Found at i:60679 original size:52 final size:52
Alignment explanation
Indices: 60601--60729 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
60591 CGAAATATGA
* *
60601 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
* * *
60653 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
60705 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
60730 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
Found at i:60742 original size:52 final size:51
Alignment explanation
Indices: 60601--60749 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
60591 CGAAATATGA
*
60601 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
* * * *
60653 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
*
60705 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
60750 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGC
Found at i:60756 original size:13 final size:13
Alignment explanation
Indices: 60738--60762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60728 CAAAGATCAG
60738 TGTATCGATACAA
1 TGTATCGATACAA
60751 TGTATCGATACA
1 TGTATCGATACA
60763 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:60840 original size:33 final size:33
Alignment explanation
Indices: 60803--60869 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
60793 AGTAGCTTAA
60803 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
60836 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
60869 A
1 A
60870 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:60843 original size:13 final size:13
Alignment explanation
Indices: 60825--60849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60815 CAAAAAAATA
60825 TGTATCGATACAT
1 TGTATCGATACAT
60838 TGTATCGATACA
1 TGTATCGATACA
60850 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:63021 original size:21 final size:21
Alignment explanation
Indices: 62995--63046 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
62985 ATTAATACTG
* *
62995 TATTGATACATTTGTGT-GATA
1 TATTGATACA-TTGGGTAAATA
*
63016 TATTGATATATTGGGTAAATA
1 TATTGATACATTGGGTAAATA
63037 TATTGATACA
1 TATTGATACA
63047 AAGTTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (21 bp):
TATTGATACATTGGGTAAATA
Found at i:65132 original size:21 final size:21
Alignment explanation
Indices: 65107--65153 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
65097 TTCAAAAATT
*
65107 ATTTTCTCCTGGAAGGAGATA
1 ATTTTCTCCTAGAAGGAGATA
*
65128 ATTTTCTCCTAGAAGGAGATT
1 ATTTTCTCCTAGAAGGAGATA
65149 ATTTT
1 ATTTT
65154 GGATTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (21 bp):
ATTTTCTCCTAGAAGGAGATA
Found at i:69081 original size:61 final size:61
Alignment explanation
Indices: 69010--69130 Score: 224
Period size: 61 Copynumber: 2.0 Consensus size: 61
69000 ACAAGTAGCA
69010 TTTGATTCATGAAAATAGGTTTACTATCTTCAGCTACAAAGGGAAAAGGACAAGGTAACTC
1 TTTGATTCATGAAAATAGGTTTACTATCTTCAGCTACAAAGGGAAAAGGACAAGGTAACTC
* *
69071 TTTGATTCATGAAAATAGGTTTACTATTTTGAGCTACAAAGGGAAAAGGACAAGGTAACT
1 TTTGATTCATGAAAATAGGTTTACTATCTTCAGCTACAAAGGGAAAAGGACAAGGTAACT
69131 TTGGGCTAAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (61 bp):
TTTGATTCATGAAAATAGGTTTACTATCTTCAGCTACAAAGGGAAAAGGACAAGGTAACTC
Found at i:75628 original size:23 final size:23
Alignment explanation
Indices: 75578--75628 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
75568 CATATAATTC
*
75578 TTATTTTTTTCAATTTTTTCTTT
1 TTATTTTTTCCAATTTTTTCTTT
* *
75601 ATATTTTTTCCACTTTTCTT-TTT
1 TTATTTTTTCCAATTTT-TTCTTT
75624 TTATT
1 TTATT
75629 ATTATTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTTTTTCCAATTTTTTCTTT
Found at i:76633 original size:20 final size:21
Alignment explanation
Indices: 76593--76643 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
76583 TTTTACAATT
*
76593 TGTATTAATACAATAAGTGAA
1 TGTATTGATACAATAAGTGAA
*
76614 TGTATTGATAC-ATTAGTGAA
1 TGTATTGATACAATAAGTGAA
*
76634 TGTATCGATA
1 TGTATTGATA
76644 GACATCTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (21 bp):
TGTATTGATACAATAAGTGAA
Found at i:76799 original size:52 final size:51
Alignment explanation
Indices: 76707--76820 Score: 165
Period size: 52 Copynumber: 2.2 Consensus size: 51
76697 AATGAAAATT
* * *
76707 TATCGATACATTCTAGGTTTTGACCTAAATGTATCGATACATTTTTCAATA
1 TATCGATACATTCTAGGTTTTGACCCAAATGTATCAATACATTCTTCAATA
* *
76758 TATCGATACATTCTAGGTTTTTGACCCAAATGTATTAATACATTCTTCAATG
1 TATCGATACATTCTAGG-TTTTGACCCAAATGTATCAATACATTCTTCAATA
*
76810 TACCGATACAT
1 TATCGATACAT
76821 GCAAGCAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
51 17 0.30
52 39 0.70
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (51 bp):
TATCGATACATTCTAGGTTTTGACCCAAATGTATCAATACATTCTTCAATA
Found at i:84853 original size:33 final size:33
Alignment explanation
Indices: 84816--84882 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
84806 TTCAACGATC
84816 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
84849 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
84882 T
1 T
84883 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:84854 original size:13 final size:13
Alignment explanation
Indices: 84836--84860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84826 CATAAAATGT
84836 TGTATCGATACAA
1 TGTATCGATACAA
84849 TGTATCGATACA
1 TGTATCGATACA
84861 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:84944 original size:13 final size:13
Alignment explanation
Indices: 84926--84950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84916 ATTACTCACA
84926 TGTATCGATACAT
1 TGTATCGATACAT
84939 TGTATCGATACA
1 TGTATCGATACA
84951 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:85087 original size:52 final size:52
Alignment explanation
Indices: 84959--85079 Score: 197
Period size: 52 Copynumber: 2.3 Consensus size: 52
84949 CACTGATCTT
* * *
84959 TGTATCGATACATGCAGGCAATTTTGCCTAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
85011 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
85063 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
85080 ATAAATTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:94550 original size:27 final size:25
Alignment explanation
Indices: 94520--94611 Score: 69
Period size: 27 Copynumber: 3.4 Consensus size: 25
94510 CATCCTATGT
94520 AAAAAAAAAATCAAATCAAATCAAA
1 AAAAAAAAAATCAAATCAAATCAAA
*
94545 TGAAAAAAAAACA-AAAATCAAAATCAAA
1 --AAAAAAAAA-ATCAAATC-AAATCAAA
** *
94573 AATCAAAAAATCAAAATCAAAAATAAAA
1 AAAAAAAAAATC-AAATC--AAATCAAA
94601 AAAGAAAAAAA
1 AAA-AAAAAAA
94612 AAGGTCGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
25 1 0.02
26 7 0.13
27 19 0.37
28 19 0.37
29 6 0.12
ACGTcount: A:0.77, C:0.10, G:0.02, T:0.11
Consensus pattern (25 bp):
AAAAAAAAAATCAAATCAAATCAAA
Found at i:94566 original size:7 final size:7
Alignment explanation
Indices: 94550--94601 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 7
94540 TCAAATGAAA
*
94550 AAAAAAC
1 AAAAATC
94557 AAAAATC
1 AAAAATC
94564 -AAAATC
1 AAAAATC
94570 AAAAATC
1 AAAAATC
94577 AAAAAATC
1 -AAAAATC
94585 -AAAATC
1 AAAAATC
94591 AAAAAT-
1 AAAAATC
94597 AAAAA
1 AAAAA
94602 AAGAAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
6 17 0.41
7 17 0.41
8 7 0.17
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATC
Found at i:94574 original size:14 final size:15
Alignment explanation
Indices: 94549--94595 Score: 64
Period size: 13 Copynumber: 3.3 Consensus size: 15
94539 ATCAAATGAA
*
94549 AAAAAAACAAAAATC
1 AAAAAATCAAAAATC
94564 --AAAATCAAAAATC
1 AAAAAATCAAAAATC
94577 AAAAAATC-AAAATC
1 AAAAAATCAAAAATC
94591 AAAAA
1 AAAAA
94596 TAAAAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 12 0.41
14 11 0.38
15 6 0.21
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAATCAAAAATC
Found at i:94581 original size:21 final size:21
Alignment explanation
Indices: 94548--94603 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
94538 AATCAAATGA
*
94548 AAAAAAAACAAAAATCAAAATC
1 AAAAATAA-AAAAATCAAAATC
*
94570 AAAAATCAAAAAATCAAAATC
1 AAAAATAAAAAAATCAAAATC
94591 AAAAATAAAAAAA
1 AAAAATAAAAAAA
94604 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (21 bp):
AAAAATAAAAAAATCAAAATC
Found at i:94609 original size:21 final size:21
Alignment explanation
Indices: 94564--94609 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
94554 AACAAAAATC
* **
94564 AAAATCAAAAATCAAAAAATC
1 AAAATCAAAAATAAAAAAAGA
94585 AAAATCAAAAATAAAAAAAGA
1 AAAATCAAAAATAAAAAAAGA
94606 AAAA
1 AAAA
94610 AAAAGGTCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.78, C:0.09, G:0.02, T:0.11
Consensus pattern (21 bp):
AAAATCAAAAATAAAAAAAGA
Found at i:94938 original size:21 final size:22
Alignment explanation
Indices: 94921--94985 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
94911 CCTTTTTTTC
* *
94921 TTTTTTTATTTTGATTTTGA-T
1 TTTTTTTTTTTTCATTTTGATT
** *
94942 TTTTTGATTTTTGATTTTGATT
1 TTTTTTTTTTTTCATTTTGATT
94964 TTTTTTTTTTTTCA-TTTGATT
1 TTTTTTTTTTTTCATTTTGATT
94985 T
1 T
94986 GATTTGATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (22 bp):
TTTTTTTTTTTTCATTTTGATT
Found at i:94971 original size:27 final size:27
Alignment explanation
Indices: 94913--94973 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
94903 TCATCCGACC
* *
94913 TTTTTTTCTTTTTTTATTTTGATTTTG
1 TTTTTTTCATTTTTGATTTTGATTTTG
* * *
94940 ATTTTTTGATTTTTGATTTTGATTTTT
1 TTTTTTTCATTTTTGATTTTGATTTTG
94967 TTTTTTT
1 TTTTTTT
94974 TTCATTTGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.10, C:0.02, G:0.08, T:0.80
Consensus pattern (27 bp):
TTTTTTTCATTTTTGATTTTGATTTTG
Found at i:94981 original size:27 final size:27
Alignment explanation
Indices: 94930--95002 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
94920 CTTTTTTTAT
**
94930 TTTGATTTTGATTTTTTGATT--TTTGA
1 TTTGA-TTTGATTTTTTTTTTCATTTGA
*
94956 TTTTGATTT-TTTTTTTTTTTCATTTGA
1 -TTTGATTTGATTTTTTTTTTCATTTGA
94983 TTTGATTTGATTTTTTTTTT
1 TTTGATTTGATTTTTTTTTT
95003 ACATAGGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 8 0.21
26 11 0.28
27 20 0.51
ACGTcount: A:0.12, C:0.01, G:0.11, T:0.75
Consensus pattern (27 bp):
TTTGATTTGATTTTTTTTTTCATTTGA
Found at i:101655 original size:16 final size:17
Alignment explanation
Indices: 101629--101662 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
101619 ATATTGGTTG
*
101629 CATTGATTTTGATTTAT
1 CATTGATTTTGATATAT
101646 CATT-ATTTTGATATAT
1 CATTGATTTTGATATAT
101662 C
1 C
101663 CCTTTGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (17 bp):
CATTGATTTTGATATAT
Found at i:104363 original size:49 final size:52
Alignment explanation
Indices: 104289--104402 Score: 155
Period size: 49 Copynumber: 2.3 Consensus size: 52
104279 AATTTATCTG
* * *
104289 CATGTATCGA-ACATTTAATAGTGTATCGATACATCTGGGC-AAATT-TCTA
1 CATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAATTGCCTA
* *
104338 CATGTATCGATAC-TTTTATAATGTATCGATACATCTAGGCAAAATTGCCTG
1 CATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAATTGCCTA
104389 CATGTATCGATACA
1 CATGTATCGATACA
104403 AAGATCAGTG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
49 34 0.61
50 7 0.12
51 15 0.27
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (52 bp):
CATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAATTGCCTA
Found at i:104429 original size:13 final size:13
Alignment explanation
Indices: 104411--104435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104401 CAAAGATCAG
104411 TGTATCGATACAA
1 TGTATCGATACAA
104424 TGTATCGATACA
1 TGTATCGATACA
104436 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.