Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007770.1 Hibiscus syriacus cultivar Beakdansim tig00110050_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1450453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1238602 original size:19 final size:19
Alignment explanation
Indices: 1238580--1238710 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
1238570 GGAAATTACT
1238580 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1238599 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1238613 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1238632 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1238646 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1238665 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
1238679 ATCTCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1238698 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1238711 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1238622 original size:33 final size:33
Alignment explanation
Indices: 1238580--1238706 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1238570 GGAAATTACT
1238580 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1238613 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1238645 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1238679 ATCTCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1238707 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1238687 original size:66 final size:66
Alignment explanation
Indices: 1238581--1238713 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1238571 GAAATTACTA
*
1238581 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1238646 T
66 T
* *
1238647 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCTCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1238712 T
66 T
1238713 T
1 T
1238714 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1238728 original size:19 final size:20
Alignment explanation
Indices: 1238706--1238748 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1238696 AAATCGCAAC
1238706 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1238725 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1238745 GCGA
1 GCGA
1238749 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1238733 original size:14 final size:14
Alignment explanation
Indices: 1238734--1238767 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1238724 TGCGATTTTC
1238734 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1238748 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1238762 ATTTTC
1 ATTTTC
1238768 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1238908 original size:14 final size:14
Alignment explanation
Indices: 1238889--1238925 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1238879 CATCAATTAA
1238889 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1238903 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1238917 ACAAATCAA
1 ACAAATCAA
1238926 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1240349 original size:21 final size:21
Alignment explanation
Indices: 1240283--1240349 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1240273 GTGAATCGGG
*
1240283 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1240303 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1240325 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1240346 CTCT
1 CTCT
1240350 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1240368 original size:42 final size:41
Alignment explanation
Indices: 1240283--1240405 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1240273 GTGAATCGGG
* * * * *
1240283 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1240325 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1240367 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1240406 TGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1242437 original size:20 final size:19
Alignment explanation
Indices: 1242406--1242466 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1242396 TCTTTTGGTT
1242406 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1242425 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1242446 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
1242465 GA
1 GA
1242467 GAATCACAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1242485 original size:33 final size:33
Alignment explanation
Indices: 1242431--1242529 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
1242421 ACGAGATAAT
*
1242431 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* * *
1242465 GAGAATCACAATGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1242498 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1242530 GCGAAATAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 43 0.78
34 12 0.22
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1242523 original size:19 final size:19
Alignment explanation
Indices: 1242501--1242590 Score: 153
Period size: 19 Copynumber: 4.7 Consensus size: 19
1242491 GCGACCAGAC
1242501 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1242520 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
1242540 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1242559 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1242578 AATCGCAATGCGA
1 AATCGCAACGCGA
1242591 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1242544 original size:39 final size:38
Alignment explanation
Indices: 1242501--1242590 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
1242491 GCGACCAGAC
1242501 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
1242540 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
1242578 AATCGCAATGCGA
1 AATCGCAACGCGA
1242591 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:1242619 original size:19 final size:19
Alignment explanation
Indices: 1242586--1242652 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1242576 AAAATCGCAA
**
1242586 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1242605 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1242624 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1242644 TGCGATTTT
1 TGCGATTTT
1242653 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1243195 original size:20 final size:20
Alignment explanation
Indices: 1243170--1243222 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1243160 GCGCTATGTA
*
1243170 AATCGCGTTGCGAAAGTTAG
1 AATCGCGTTGCGAAAGTCAG
1243190 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1243210 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1243223 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1243256 original size:20 final size:20
Alignment explanation
Indices: 1243231--1243284 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1243221 GATTTTGTAT
1243231 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1243251 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1243271 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1243285 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1243269 original size:61 final size:61
Alignment explanation
Indices: 1243171--1243287 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1243161 CGCTATGTAA
* * * * *
1243171 ATCGCGTTGCGAAAGTTAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1243232 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1243288 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1243303 original size:61 final size:61
Alignment explanation
Indices: 1243171--1243305 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1243161 CGCTATGTAA
* * * * * ** *
1243171 ATCGCGTTGCGAAAGTTAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1243232 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1243294 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1243306 TTGCTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1243395 original size:21 final size:21
Alignment explanation
Indices: 1243355--1243395 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1243345 ATTGTATACC
**
1243355 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1243376 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1243396 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1246978 original size:31 final size:31
Alignment explanation
Indices: 1246940--1247021 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
1246930 GATGAGCTCG
* **
1246940 ACTCGACTCGACTCGAAAACCTTAAAATGGA
1 ACTCGACTCGACTCGAAAACCCTAAAATAAA
*
1246971 ACTCGACTCGACTCAAAAACCCTAAAATAAA
1 ACTCGACTCGACTCGAAAACCCTAAAATAAA
*
1247002 ACTCGACTCGACTTGAAAAC
1 ACTCGACTCGACTCGAAAAC
1247022 TCACGAGCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.18
Consensus pattern (31 bp):
ACTCGACTCGACTCGAAAACCCTAAAATAAA
Found at i:1248345 original size:16 final size:16
Alignment explanation
Indices: 1248307--1248360 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
1248297 AAATTTCAGT
1248307 GAGCTTAACGAGCAA-
1 GAGCTTAACGAGCAAC
* *
1248322 TAGACTTAATGAGCAAC
1 GAG-CTTAACGAGCAAC
1248339 GAGCTTAACGAGC-AC
1 GAGCTTAACGAGCAAC
1248354 GAG-TTAA
1 GAGCTTAA
1248361 GCAAAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 4 0.12
15 7 0.21
16 20 0.61
17 2 0.06
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (16 bp):
GAGCTTAACGAGCAAC
Found at i:1250877 original size:21 final size:20
Alignment explanation
Indices: 1250847--1250891 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
1250837 ATTGGTCTCT
1250847 ATACTGATGGACTGATATCC
1 ATACTGATGGACTGATATCC
* *
1250867 ATACTAGATGGATTGGTATCC
1 ATACT-GATGGACTGATATCC
1250888 ATAC
1 ATAC
1250892 CGAAGGCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (20 bp):
ATACTGATGGACTGATATCC
Found at i:1254558 original size:20 final size:20
Alignment explanation
Indices: 1254535--1254709 Score: 147
Period size: 20 Copynumber: 8.7 Consensus size: 20
1254525 GTTTCCAGAT
* *
1254535 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* * *
1254555 TCGCATTGCAATTTTCCGACTA
1 TCGCAATGCGATTAT--GACTA
* *
1254577 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
*
1254597 TCGCAATGCGAGTATGACTA
1 TCGCAATGCGATTATGACTA
* * *
1254617 TCGCAACGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
*
1254637 TCGCAATGTGATTATGACTA
1 TCGCAATGCGATTATGACTA
* *
1254657 TCGCAATGCAATTCTGACTA
1 TCGCAATGCGATTATGACTA
* * *
1254677 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTATGACTA
1254697 TCGCAATGCGATT
1 TCGCAATGCGATT
1254710 TTCAAAGCGC
Statistics
Matches: 124, Mismatches: 25, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.02
20 104 0.84
21 2 0.02
22 16 0.13
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTATGACTA
Found at i:1254680 original size:40 final size:40
Alignment explanation
Indices: 1254572--1254707 Score: 168
Period size: 40 Copynumber: 3.4 Consensus size: 40
1254562 GCAATTTTCC
*
1254572 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
* *
1254612 GACTATCGCAACGCGAATATGTAAATCGCAATGTGATTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
* * * *
1254652 GACTATCGCAATGC-AAT-TCTGACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGAATATGT-A-AATCGCAATGCGATTAT
*
1254692 GACTGTCGCAATGCGA
1 GACTATCGCAATGCGA
1254708 TTTTCAAAGC
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.02
39 4 0.05
40 76 0.92
41 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
Found at i:1254909 original size:22 final size:22
Alignment explanation
Indices: 1254884--1254926 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1254874 GGCGACATCC
1254884 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1254906 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
1254927 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1255335 original size:19 final size:19
Alignment explanation
Indices: 1255313--1255352 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1255303 AGAATCGCAA
1255313 TGTGATTTTAGTTTCGCGT
1 TGTGATTTTAGTTTCGCGT
*
1255332 TGTGATTTTTGTTTCGCGT
1 TGTGATTTTAGTTTCGCGT
1255351 TG
1 TG
1255353 CGATAGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.07, C:0.10, G:0.28, T:0.55
Consensus pattern (19 bp):
TGTGATTTTAGTTTCGCGT
Found at i:1255369 original size:20 final size:20
Alignment explanation
Indices: 1255344--1255396 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1255334 TGATTTTTGT
1255344 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
* **
1255364 TTCGCGTTACGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
1255384 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
1255397 TTTCATTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:1255402 original size:20 final size:20
Alignment explanation
Indices: 1255379--1255419 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1255369 GTTACGATAG
1255379 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
1255399 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
1255419 T
1 T
1255420 AAGTTTCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:1255426 original size:20 final size:20
Alignment explanation
Indices: 1255383--1255426 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1255373 CGATAGTCAT
* *
1255383 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1255403 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1255423 TTTC
1 TTTC
1255427 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1257177 original size:18 final size:18
Alignment explanation
Indices: 1257154--1257203 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1257144 TTTACTCGTA
1257154 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1257172 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1257190 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1257204 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1257372 original size:20 final size:20
Alignment explanation
Indices: 1257347--1257413 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
1257337 TAGTTTACTT
1257347 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
1257367 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
1257387 TCACAACGC-GAATTTGACTA
1 TCGCAACGCGGAA-ATGACTA
1257407 TCGCAAC
1 TCGCAAC
1257414 AAGAGAATCG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 2 0.05
20 37 0.95
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1257511 original size:20 final size:20
Alignment explanation
Indices: 1257459--1257512 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1257449 GATTCTCTCG
** *
1257459 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCA
*
1257479 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
1257499 TTGCGATAGTCATT
1 TTGCGATAGTCATT
1257513 CGTGTTACGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1259573 original size:36 final size:30
Alignment explanation
Indices: 1259493--1259558 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
1259483 ATAAAAGTTG
1259493 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
1259523 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
1259553 ATTTGT
1 ATTTGT
1259559 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:1259737 original size:20 final size:20
Alignment explanation
Indices: 1259708--1259952 Score: 172
Period size: 20 Copynumber: 12.8 Consensus size: 20
1259698 GCGATTTTCT
*
1259708 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* * *
1259728 CGTTGTGATAATCAAATTTG
1 CGTTGCGATAGTCAAATTCG
1259748 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1259768 AGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
**
1259788 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* ** *
1259808 CATTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCG
* *
1259828 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
1259842 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* ** *
1259862 TGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCG
* *
1259882 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* * *
1259896 CGTTGTGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* * *
1259916 TGTTGTGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
1259936 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
1259953 GAATGTGTAA
Statistics
Matches: 176, Mismatches: 37, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
14 17 0.10
16 2 0.01
18 2 0.01
19 2 0.01
20 153 0.87
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1259870 original size:54 final size:54
Alignment explanation
Indices: 1259788--1259944 Score: 215
Period size: 54 Copynumber: 2.9 Consensus size: 54
1259778 GTCATATTCG
** **
1259788 CGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTTGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCATTTTTGCATTGCGATTATCC
1259842 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCATTTTTGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCATTTTTGCATTGCGATTATCC
* * * * * * *
1259896 CGTTGTGATATTCAAATTCATGTTGTGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCATTTTTGCATTGCGAT
1259945 AGTCAAATGA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCATTTTTGCATTGCGATTATCC
Found at i:1259926 original size:74 final size:72
Alignment explanation
Indices: 1259748--1259949 Score: 210
Period size: 74 Copynumber: 2.7 Consensus size: 72
1259738 ATCAAATTTG
* *
1259748 CGTTGCGATAGTCAAATTCGAGTTGCGATAGTCATATTCGCGTTGCGATAGTCATTTTCGCATTG
1 CGTTGTGATATTCAAATTC-AGTTGCGATAGTCATATTCGCGTTGCGATAGTCATTTTCGCATTG
1259813 CGATAGTC
65 CGATAGTC
** * * * * * * * *
1259821 ATTTTTGCAT-TGCGATTATCCCGTTGCGATAGTCAAATTCGTGTTGCGATAGTCATTTTTGCAT
1 CGTTGTG-ATATTC-A-AATTCAGTTGCGATAGTCATATTCGCGTTGCGATAGTCATTTTCGCAT
1259885 TGCGATTA-TCC
63 TGCGA-TAGT-C
*
1259896 CGTTGTGATATTCAAATTCATGTTGTGATAGTCATATTCGCGTTGCGATAGTCA
1 CGTTGTGATATTCAAATTCA-GTTGCGATAGTCATATTCGCGTTGCGATAGTCA
1259950 AATGAATGTG
Statistics
Matches: 100, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
73 7 0.07
74 81 0.81
75 12 0.12
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (72 bp):
CGTTGTGATATTCAAATTCAGTTGCGATAGTCATATTCGCGTTGCGATAGTCATTTTCGCATTGC
GATAGTC
Found at i:1260151 original size:18 final size:18
Alignment explanation
Indices: 1260128--1260162 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1260118 AAGCCGGTTG
*
1260128 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1260146 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1260163 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1263342 original size:20 final size:20
Alignment explanation
Indices: 1263297--1263365 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1263287 TGAAATTCAG
*
1263297 CATTGCGACAGTCAGAATCGA
1 CATTGCGATAGTCAGAATC-A
*
1263318 -GTTGCGATAGTCAGAATCA
1 CATTGCGATAGTCAGAATCA
* *
1263337 CATTGCGATAGTCATAATCG
1 CATTGCGATAGTCAGAATCA
1263357 CATTGCGAT
1 CATTGCGAT
1263366 TTACATATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.02
20 41 0.98
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (20 bp):
CATTGCGATAGTCAGAATCA
Found at i:1263372 original size:20 final size:20
Alignment explanation
Indices: 1263349--1263425 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1263339 TTGCGATAGT
*
1263349 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
* *
1263369 CATATTCGCGTTGCGATAGT-
1 CATATTCGCATTGCGAT-TTA
*
1263389 CATACTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
1263409 CATATTCGCATTGCGAT
1 CATATTCGCATTGCGAT
1263426 AGTCGGAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:1263383 original size:40 final size:40
Alignment explanation
Indices: 1263337--1263429 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
1263327 GTCAGAATCA
1263337 CATTGCGATAGTCATAATCGCATTGCGATTTACATATTCG
1 CATTGCGATAGTCATAATCGCATTGCGATTTACATATTCG
* *
1263377 CGTTGCGATAGTCATACTCGCATTGCGATTTACATATTCG
1 CATTGCGATAGTCATAATCGCATTGCGATTTACATATTCG
1263417 CATTGCGATAGTC
1 CATTGCGATAGTC
1263430 GGAAAATCGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (40 bp):
CATTGCGATAGTCATAATCGCATTGCGATTTACATATTCG
Found at i:1263658 original size:22 final size:22
Alignment explanation
Indices: 1263633--1263677 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1263623 CTATTTTTTC
1263633 AAATTTATATATACATTTGATA
1 AAATTTATATATACATTTGATA
*
1263655 AAATTTATATATACATTTTATA
1 AAATTTATATATACATTTGATA
1263677 A
1 A
1263678 TATATACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATTTATATATACATTTGATA
Found at i:1263683 original size:20 final size:21
Alignment explanation
Indices: 1263633--1263683 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1263623 CTATTTTTTC
*
1263633 AAATTTATATATACATTTGATA
1 AAATATATATATACATTT-ATA
*
1263655 AAATTTATATATACATTT-TA
1 AAATATATATATACATTTATA
*
1263675 TAATATATA
1 AAATATATA
1263684 CTATTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 9 0.33
22 18 0.67
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATATATATATACATTTATA
Found at i:1267128 original size:54 final size:55
Alignment explanation
Indices: 1267008--1267150 Score: 189
Period size: 54 Copynumber: 2.6 Consensus size: 55
1266998 ATTGTATGAG
* * * **
1267008 TGTGTATCGGTACACTAAGGAGTTTATCGGTACACTCAAAACATCAAATGTTATT
1 TGTGTATCGGTACACTGAGGAGTATATCGATACACTCAAAACATCAAATGCAATT
* * *
1267063 TGTGTATCGGTACACTGAGTAGTATATCGATACCCTC-AAACATCGAATGCAATT
1 TGTGTATCGGTACACTGAGGAGTATATCGATACACTCAAAACATCAAATGCAATT
* *
1267117 TGTGTATCGGTACATTGAGGAGTGTATCGATACA
1 TGTGTATCGGTACACTGAGGAGTATATCGATACA
1267151 TTGAGGAGTG
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
54 44 0.58
55 32 0.42
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTATATCGATACACTCAAAACATCAAATGCAATT
Found at i:1267143 original size:20 final size:20
Alignment explanation
Indices: 1267118--1267169 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1267108 AATGCAATTT
*
1267118 GTGTATCGGTACATTGAGGA
1 GTGTATCGATACATTGAGGA
1267138 GTGTATCGATACATTGAGGA
1 GTGTATCGATACATTGAGGA
1267158 GTGTATCGATAC
1 GTGTATCGATAC
1267170 CCCAGTTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.31
Consensus pattern (20 bp):
GTGTATCGATACATTGAGGA
Found at i:1268055 original size:18 final size:18
Alignment explanation
Indices: 1268032--1268066 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1268022 ATGTGTTATA
*
1268032 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTACGGGACAT
1268050 AGTGGTCCTACGGGACA
1 AGTGGTCCTACGGGACA
1268067 AATTCTACGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:1271200 original size:15 final size:15
Alignment explanation
Indices: 1271180--1271213 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1271170 CTATGGTATG
1271180 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1271195 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1271210 AATT
1 AATT
1271214 AGAATTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1274520 original size:18 final size:18
Alignment explanation
Indices: 1274492--1274539 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1274482 TAAGTATATG
1274492 ATTATATGATAA-AAAAGGA
1 ATTA-ATGATAATAAAA-GA
*
1274511 ATTAATGATAATAAAATA
1 ATTAATGATAATAAAAGA
*
1274529 AGTAATGATAA
1 ATTAATGATAA
1274540 GCATGTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.29
Consensus pattern (18 bp):
ATTAATGATAATAAAAGA
Found at i:1278753 original size:27 final size:27
Alignment explanation
Indices: 1278723--1278780 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
1278713 AAAAATCTTT
1278723 ATTTACTAATGTTGATCTCAATCATTC
1 ATTTACTAATGTTGATCTCAATCATTC
1278750 ATTTACTAATGTTGATCTCAATCATTC
1 ATTTACTAATGTTGATCTCAATCATTC
1278777 ATTT
1 ATTT
1278781 TCATTCATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (27 bp):
ATTTACTAATGTTGATCTCAATCATTC
Found at i:1284556 original size:11 final size:11
Alignment explanation
Indices: 1284542--1284575 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1284532 ACAAAACACG
1284542 TAAAAAAATAA
1 TAAAAAAATAA
*
1284553 TAAAATAATAA
1 TAAAAAAATAA
1284564 TAATAAAAATAA
1 TAA-AAAAATAA
1284576 ACAAAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAAAAAATAA
Found at i:1284957 original size:14 final size:14
Alignment explanation
Indices: 1284949--1285002 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
1284939 TATAAGATAT
1284949 ATATAATAAAAATA
1 ATATAATAAAAATA
*
1284963 ATATAATATAAATA
1 ATATAATAAAAATA
*
1284977 A-ATAAATAAAAGAGGA
1 ATAT-AATAAAA-A-TA
1284993 ATATAATAAA
1 ATATAATAAA
1285003 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.06
14 20 0.61
15 1 0.03
16 8 0.24
17 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (14 bp):
ATATAATAAAAATA
Found at i:1284966 original size:25 final size:25
Alignment explanation
Indices: 1284918--1284982 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
1284908 ACATCTATAC
* *
1284918 ATATATATATATATATAATGATATAAG
1 ATATATATA-ATA-AAAATAATATAAG
*
1284945 ATATATATAATAAAAATAATATAAT
1 ATATATATAATAAAAATAATATAAG
*
1284970 ATAAATA-AATAAA
1 ATATATATAATAAA
1284983 TAAAAGAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.18
25 16 0.47
26 3 0.09
27 9 0.26
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (25 bp):
ATATATATAATAAAAATAATATAAG
Found at i:1285024 original size:24 final size:24
Alignment explanation
Indices: 1284951--1285024 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
1284941 TAAGATATAT
1284951 ATAATAAAAATAATATAATATAAATAA
1 ATAA-AAAAA-AATATAAT-TAAATAA
* **
1284978 ATAAATAAAAGA-GGAA-TATAATAA
1 ATAAA-AAAAAATATAATTA-AATAA
1285002 ATAAAAAAAAATATAATTAAATA
1 ATAAAAAAAAATATAATTAAATA
1285025 TATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
23 7 0.19
24 16 0.43
25 4 0.11
26 2 0.05
27 8 0.22
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
ATAAAAAAAAATATAATTAAATAA
Found at i:1287416 original size:36 final size:36
Alignment explanation
Indices: 1287371--1287594 Score: 223
Period size: 36 Copynumber: 6.4 Consensus size: 36
1287361 GAAGATTTTG
1287371 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
*
1287407 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TT
* * * * *
1287444 AGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
* * *
1287480 TGTTTCAA-ATAAAACATAT-TC---A-A-A--TAATT
1 TGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACGAAATT
* *
1287509 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
* *
1287545 TGTTTCAAGGGAAACTGTCTTAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
* *
1287581 TATTTCAAGGGAAA
1 TGTTTCAAGAGAAA
1287595 TGTTTTCAAT
Statistics
Matches: 156, Mismatches: 20, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 98 0.63
37 32 0.21
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
Found at i:1287466 original size:37 final size:36
Alignment explanation
Indices: 1287380--1287472 Score: 132
Period size: 37 Copynumber: 2.6 Consensus size: 36
1287370 GTGTTTCAAG
* * * *
1287380 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
1287416 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
1 AGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAA
*
1287453 AGAAACTGTCTCAAGGGAGA
1 AGAAACTGTCTCAAGAGAGA
1287473 TGAAATTTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 24 0.47
37 27 0.53
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (36 bp):
AGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
Found at i:1287624 original size:101 final size:102
Alignment explanation
Indices: 1287403--1287675 Score: 316
Period size: 101 Copynumber: 2.7 Consensus size: 102
1287393 AGAGAGACGA
* * * **
1287403 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
1 AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
* * * *
1287468 GGAGATGAAATTTGTTTCAAATAAAACATATTCAAAT
66 AGAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
* * *
1287505 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTTAAG
1 AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
* * ** *
1287569 AGAGACGAAATTTATTTCAAGGGAAATGTTTTC-AAT
66 AGAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
** * * *
1287605 GTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
1 AATT-TATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAA
*
1287670 GCGAGA
65 GAGAGA
1287676 TAAAATCTTC
Statistics
Matches: 146, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
100 5 0.03
101 76 0.52
102 65 0.45
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (102 bp):
AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
AGAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
Found at i:1289367 original size:13 final size:13
Alignment explanation
Indices: 1289337--1289389 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
1289327 TTTTTCTTCA
1289337 ATTTTC-CTTTTGT
1 ATTTTCTCTTTT-T
*
1289350 TTTTTCTCTTTTT
1 ATTTTCTCTTTTT
1289363 ATTTTCTCTTTGATT
1 ATTTTCTCTTT--TT
1289378 -TTTTCTCTTTTT
1 ATTTTCTCTTTTT
1289390 TCTCTTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
12 2 0.06
13 16 0.46
14 15 0.43
15 2 0.06
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (13 bp):
ATTTTCTCTTTTT
Found at i:1289381 original size:27 final size:26
Alignment explanation
Indices: 1289337--1289389 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
1289327 TTTTTCTTCA
1289337 ATTTTCCTTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTTGTTTTTTCTCTTTTT
1289363 ATTTT-CTCTTTGATTTTTTCTCTTTTT
1 ATTTTCCT-TTTG-TTTTTTCTCTTTTT
1289390 TCTCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 2 0.08
26 9 0.36
27 14 0.56
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (26 bp):
ATTTTCCTTTTGTTTTTTCTCTTTTT
Found at i:1290682 original size:14 final size:14
Alignment explanation
Indices: 1290658--1290692 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
1290648 GATGCATATG
1290658 ATAATAATAATGAAA
1 ATAA-AATAATGAAA
1290673 ATAAAATAATGAAA
1 ATAAAATAATGAAA
1290687 ATAAAA
1 ATAAAA
1290693 GATCCTACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (14 bp):
ATAAAATAATGAAA
Found at i:1291786 original size:24 final size:23
Alignment explanation
Indices: 1291759--1291822 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
1291749 AAAAATAGAA
*
1291759 AATAACAAAATACGTAAAAAAAAT
1 AATAACAAAATA-ATAAAAAAAAT
* *
1291783 AATAATAAAATAATAATAAAAAT
1 AATAACAAAATAATAAAAAAAAT
1291806 -A-AACAAAATGAATAAAA
1 AATAACAAAAT-AATAAAA
1291823 TGTTAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.21
22 7 0.21
23 9 0.26
24 11 0.32
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (23 bp):
AATAACAAAATAATAAAAAAAAT
Found at i:1291792 original size:11 final size:11
Alignment explanation
Indices: 1291778--1291803 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1291768 ATACGTAAAA
1291778 AAAATAATAAT
1 AAAATAATAAT
1291789 AAAATAATAAT
1 AAAATAATAAT
1291800 AAAA
1 AAAA
1291804 ATAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:1291806 original size:17 final size:19
Alignment explanation
Indices: 1291780--1291822 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
1291770 ACGTAAAAAA
* *
1291780 AATAATAATAAA-ATAAT-
1 AATAAAAATAAACAAAATG
1291797 AATAAAAATAAACAAAATG
1 AATAAAAATAAACAAAATG
1291816 AATAAAA
1 AATAAAA
1291823 TGTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 4 0.18
19 7 0.32
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAACAAAATG
Found at i:1292145 original size:8 final size:8
Alignment explanation
Indices: 1292132--1292181 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
1292122 ATAAAAAATA
*
1292132 ATACATCT
1 ATACATAT
1292140 ATACATAT
1 ATACATAT
*
1292148 ATATATAT
1 ATACATAT
*
1292156 ATATATAT
1 ATACATAT
*
1292164 ATATATAT
1 ATACATAT
*
1292172 ATATATAT
1 ATACATAT
1292180 AT
1 AT
1292182 GATATAAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (8 bp):
ATACATAT
Found at i:1292151 original size:2 final size:2
Alignment explanation
Indices: 1292139--1292196 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
1292129 ATAATACATC
*
1292139 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1292181 TGA TA TA -A GA TA TA TA
1 T-A TA TA TA TA TA TA TA
1292197 ACAAAATAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1302200 original size:2 final size:2
Alignment explanation
Indices: 1302195--1302235 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1302185 GGTGGACGTG
1302195 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1302236 TAATAACATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1304328 original size:13 final size:13
Alignment explanation
Indices: 1304310--1304358 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1304300 ATTAAAAGGA
*
1304310 ATCTAAAATAATG
1 ATCTAAAATAAAG
*
1304323 ATCTAAAACTAAAA
1 ATCTAAAA-TAAAG
*
1304337 ACCTAAAATAAAG
1 ATCTAAAATAAAG
*
1304350 AACTAAAAT
1 ATCTAAAAT
1304359 GCATAAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.61, C:0.12, G:0.04, T:0.22
Consensus pattern (13 bp):
ATCTAAAATAAAG
Found at i:1316598 original size:20 final size:20
Alignment explanation
Indices: 1316573--1316614 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1316563 CACCCTTTGA
1316573 ACAATACATTTTAGCATAGG
1 ACAATACATTTTAGCATAGG
1316593 ACAATACATTTTAGCATAGG
1 ACAATACATTTTAGCATAGG
1316613 AC
1 AC
1316615 TCAAACATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (20 bp):
ACAATACATTTTAGCATAGG
Found at i:1334532 original size:3 final size:3
Alignment explanation
Indices: 1334524--1334548 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1334514 TGTAAAAACA
1334524 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1334549 GCAAGACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1334992 original size:129 final size:133
Alignment explanation
Indices: 1334670--1334996 Score: 473
Period size: 134 Copynumber: 2.5 Consensus size: 133
1334660 TGGAATATGA
* * *
1334670 TGAGGGAATATCAGATCTGGGGACGTTGATCCATTCCACTGTCACTTAGGGAAGATTGAATCGAG
1 TGAGGGAATATCAGATCTGGGG-CGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGAG
* * * *
1334735 GTAGACTTGTTCAAATGTTACTCAGGGAATATCAAATCTTGGAAGAGAGGGATATATTTCGTTTC
65 GCAGACTTGTTCAAATGTTACTCAGAGAATATCAAATCTTGGAAGAGAGGGATATAGTTCGCTTC
1334800 TTCT
130 TTCT
* * * * *
1334804 GGAGGGAATACCAGATCTAGGGACGTTGATTCATTTCGCTGTCACTCAAGGAAGATTGAATCGAG
1 TGAGGGAATATCAGATCT-GGGGCGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGAG
*
1334869 GCAGACTTGTTC-ATTGTTACTCAGAGAATATCAAATCTTGGAAGAGAGGGATAT-GTTCGCTTC
65 GCAGACTTGTTCAAATGTTACTCAGAGAATATCAAATCTTGGAAGAGAGGGATATAGTTCGCTTC
1334932 -TCT
130 TTCT
* *
1334935 TGAGGGAA-ATCAGATATGGGGTGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGA
1 TGAGGGAATATCAGATCTGGGGCGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGA
1334997 CTTCGATTCG
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
129 41 0.24
130 7 0.04
131 10 0.06
132 7 0.04
133 40 0.23
134 64 0.37
135 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (133 bp):
TGAGGGAATATCAGATCTGGGGCGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGAGG
CAGACTTGTTCAAATGTTACTCAGAGAATATCAAATCTTGGAAGAGAGGGATATAGTTCGCTTCT
TCT
Found at i:1335657 original size:42 final size:41
Alignment explanation
Indices: 1335561--1335657 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
1335551 AGGTCTTATG
* * * *
1335561 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTTCA
1 GATGGCCCGAAGGACTTAACATCATGCTCAAAAGACTTACA
* * * *
1335602 GATGACCTGAAGGATTTAAACATCATGCTCAAAAGACTTACT
1 GATGGCCCGAAGGACTT-AACATCATGCTCAAAAGACTTACA
*
1335644 GATGGCCCAAAGGA
1 GATGGCCCGAAGGA
1335658 ATTCCCAATT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 14 0.32
42 30 0.68
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAACATCATGCTCAAAAGACTTACA
Found at i:1335796 original size:233 final size:230
Alignment explanation
Indices: 1335278--1336071 Score: 1002
Period size: 231 Copynumber: 3.4 Consensus size: 230
1335268 TGGAAATTGT
* * * * * * *** *
1335278 TTTCTCATTTTTCAAAAAATCATGCGAAAATATCATACCCTAATAACTTATGGATGGACCGAAGG
1 TTTCTCATTTTTCAAAAAA-CATGTGAAAACATCCTGCACAAAGGTCTTATGGATGGCCCGAAGG
* * **
1335343 ACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAGGCATCATGCTCGAAAGAC
65 ACTTATCATCTTGCTCGAAAGACTTACAGATGACCTGAAGGATTTAAACATCATGCTCGAAAGAC
* * * * *
1335408 TTACTGATTGTCCAAAGGAATTACCAACTCGGAAATAGTTTACTAGGAAAAAACCTTCCTTACTT
130 TTACTGATGGCCCAAAGGAATTACCAAATTGGAAATAGTTTACTAGTAAAAAACCTTCCTTAC-T
* *
1335473 TTTC-AAAATTTCAATTTCCAGATTTAAATGAGAATTC
194 TTTCAAAAATTTCAATTTTCAGATTTAAATGAGAA-AC
* *
1335510 TTTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGA
1 TTTCTCATTTTTCAAAAAACATGTGAAAACATCCTGCACAAAGGTCTTATGGATGGCCCGAAGGA
* *
1335575 CTTATCATCTTGCTCGAAAGACTTTCAGATGACCTGAAGGATTTAAACATCATGCTCAAAAGACT
66 CTTATCATCTTGCTCGAAAGACTTACAGATGACCTGAAGGATTTAAACATCATGCTCGAAAGACT
* *
1335640 TACTGATGGCCCAAAGGAATTCCCAATTTTGGAAATAGTTTACTAGTTAAAAAACCTTCCTTACT
131 TACTGATGGCCCAAAGGAATTACCAA-ATTGGAAATAGTTTACTAG-TAAAAAACCTTCCTTACT
*
1335705 TTTCAAAAATTTCAATTTTCAGATTTAGATGAGAAAC
194 TTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAC
* *
1335742 ATTTCTTATTTTTCAAAAAACTTGTGAAAACATCCTGCACAAAGGTCTTATGGATGGCCCGAAGG
1 -TTTCTCATTTTTCAAAAAACATGTGAAAACATCCTGCACAAAGGTCTTATGGATGGCCCGAAGG
* * * * *
1335807 ACTTACCATCTTACTCGAAAGACTTACAGATGA-CTCGAATGATTTAAACATCATGTTTGAAAGA
65 ACTTATCATCTTGCTCGAAAGACTTACAGATGACCT-GAAGGATTTAAACATCATGCTCGAAAGA
* * * * *
1335871 C--ACTGATGGCCCAAAGGATTTACCAAATTCGAGAATAGTTTACTAGGTAAGAAACTTTACTTA
129 CTTACTGATGGCCCAAAGGAATTACCAAATTGGA-AATAGTTTACTA-GTAAAAAACCTTCCTTA
*
1335934 CTTTTCAAAAAATTTTAATTTTCAGATTTAAATGAGAAATC
192 CTTTTC-AAAAATTTCAATTTTCAGATTTAAATGAGAAA-C
* * * * * * * *
1335975 TTTCTCATTTTTCAAGAGACGTGTGAAAATATCTTGCTCGAATGTCTTATGGATGGCCCGAAGGA
1 TTTCTCATTTTTCAAAAAACATGTGAAAACATCCTGCACAAAGGTCTTATGGATGGCCCGAAGGA
* *
1336040 CTTATCATCTTGCTCAAAAGACTTATAGATGA
66 CTTATCATCTTGCTCGAAAGACTTACAGATGA
1336072 TCTTTCTTAC
Statistics
Matches: 495, Mismatches: 58, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
230 4 0.01
231 173 0.35
232 158 0.32
233 160 0.32
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (230 bp):
TTTCTCATTTTTCAAAAAACATGTGAAAACATCCTGCACAAAGGTCTTATGGATGGCCCGAAGGA
CTTATCATCTTGCTCGAAAGACTTACAGATGACCTGAAGGATTTAAACATCATGCTCGAAAGACT
TACTGATGGCCCAAAGGAATTACCAAATTGGAAATAGTTTACTAGTAAAAAACCTTCCTTACTTT
TCAAAAATTTCAATTTTCAGATTTAAATGAGAAAC
Found at i:1336036 original size:232 final size:230
Alignment explanation
Indices: 1335324--1336071 Score: 1004
Period size: 233 Copynumber: 3.2 Consensus size: 230
1335314 ACCCTAATAA
* *
1335324 CTTATGGATGGACCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTA
1 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGA-CCGAAGGATTTA
** * * *
1335389 GGCATCATGCTCGAAAGACTTACTGATTGTCCAAAGGAATTACC-AACTCGGAAATAGTTTACTA
65 AACATCATGCTCGAAAGAC-TACTGATGGCCCAAAGGAATTACCAAATTCGGAAATAGTTTACTA
* *
1335453 GG-AAAAAACCTTCCTTACTTTTTC-AAAATTTCAATTTCCAGATTTAAATGAGAATTCTTTCTC
129 GGTAAAAAACCTTCCTTAC-TTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATCTTTCTC
*
1335516 ATTTTTCGAAAAACATGTGAAAACATCCTGCCCAAAGGT
193 ATTTTTC-AAAAACATGTGAAAACATCCTGCACAAAGGT
*
1335555 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTTCAGATGACCTGAAGGATTTA
1 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACC-GAAGGATTTA
* * * *
1335620 AACATCATGCTCAAAAGACTTACTGATGGCCCAAAGGAATTCCCAATTTTGGAAATAGTTTACTA
65 AACATCATGCTCGAAAGAC-TACTGATGGCCCAAAGGAATTACCAAATTCGGAAATAGTTTACTA
* * *
1335685 GTTAAAAAACCTTCCTTACTTTTCAAAAATTTCAATTTTCAGATTTAGATGAGAAA-CATTTCTT
129 GGTAAAAAACCTTCCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATC-TTTCTC
*
1335749 ATTTTTCAAAAAACTTGTGAAAACATCCTGCACAAAGGT
193 ATTTTTC-AAAAACATGTGAAAACATCCTGCACAAAGGT
* * *
1335788 CTTATGGATGGCCCGAAGGACTTACCATCTTACTCGAAAGACTTACAGATGACTCGAATGATTTA
1 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGAC-CGAAGGATTTA
* * *
1335853 AACATCATGTTTGAAAGAC-ACTGATGGCCCAAAGGATTTACCAAATTC-GAGAATAGTTTACTA
65 AACATCATGCTCGAAAGACTACTGATGGCCCAAAGGAATTACCAAATTCGGA-AATAGTTTACTA
* * * *
1335916 GGTAAGAAACTTTACTTACTTTTCAAAAAATTTTAATTTTCAGATTTAAATGAGAAATCTTTCTC
129 GGTAAAAAACCTTCCTTACTTTTC-AAAAATTTCAATTTTCAGATTTAAATGAGAAATCTTTCTC
* * * * * * *
1335981 ATTTTTCAAGAGACGTGTGAAAATATCTTGCTCGAATGT
193 ATTTTTCAA-AAACATGTGAAAACATCCTGCACAAAGGT
* *
1336020 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGA
1 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGA
1336072 TCTTTCTTAC
Statistics
Matches: 458, Mismatches: 49, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
230 4 0.01
231 156 0.34
232 136 0.30
233 161 0.35
234 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (230 bp):
CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCGAAGGATTTAA
ACATCATGCTCGAAAGACTACTGATGGCCCAAAGGAATTACCAAATTCGGAAATAGTTTACTAGG
TAAAAAACCTTCCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATCTTTCTCATT
TTTCAAAAACATGTGAAAACATCCTGCACAAAGGT
Found at i:1338563 original size:30 final size:30
Alignment explanation
Indices: 1338524--1338620 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 30
1338514 GAAAGACCTA
* * *
1338524 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTC-TAAAGAACCTAGGTAAACTG
*
1338554 TCCATAGGTCTGAAGAACCTAGGTAAACTG
1 TCCATAGGTCTAAAGAACCTAGGTAAACTG
* * * *
1338584 TCCATATGTTCCT-TAGAACATAGGTATACTG
1 TCCATA-GGT-CTAAAGAACCTAGGTAAACTG
1338615 TCCATA
1 TCCATA
1338621 TGTCCCGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 11 0.20
30 20 0.36
31 23 0.41
32 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (30 bp):
TCCATAGGTCTAAAGAACCTAGGTAAACTG
Found at i:1338653 original size:32 final size:32
Alignment explanation
Indices: 1338550--1338673 Score: 130
Period size: 31 Copynumber: 4.0 Consensus size: 32
1338540 AACCTCGGCA
* * *
1338550 ACTGTCCATAGGT-CTGAAGAACCTAGGTAA-
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAT
* **
1338580 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAT
1338611 ACTGTCCATATGTCCCGAA-AGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGTAAT
* * *
1338643 TCTGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTCCCGAAGAACATAGGTAA
1338674 ACCCTCGACT
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
30 14 0.18
31 35 0.45
32 28 0.36
33 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (32 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:1339256 original size:16 final size:16
Alignment explanation
Indices: 1339231--1339263 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1339221 TACTCTTATG
*
1339231 TATTCTCATATACATA
1 TATTCACATATACATA
1339247 TATTCACATATACATA
1 TATTCACATATACATA
1339263 T
1 T
1339264 CATTTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTCACATATACATA
Found at i:1341058 original size:32 final size:32
Alignment explanation
Indices: 1341022--1341093 Score: 144
Period size: 32 Copynumber: 2.2 Consensus size: 32
1341012 TCTAGACTAC
1341022 CCATTTTTGAGTTTTCACCCTAGATTTCATCT
1 CCATTTTTGAGTTTTCACCCTAGATTTCATCT
1341054 CCATTTTTGAGTTTTCACCCTAGATTTCATCT
1 CCATTTTTGAGTTTTCACCCTAGATTTCATCT
1341086 CCATTTTT
1 CCATTTTT
1341094 TATATCTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.18, C:0.25, G:0.08, T:0.49
Consensus pattern (32 bp):
CCATTTTTGAGTTTTCACCCTAGATTTCATCT
Found at i:1341236 original size:14 final size:14
Alignment explanation
Indices: 1341217--1341315 Score: 83
Period size: 16 Copynumber: 6.6 Consensus size: 14
1341207 TTATTTTCTC
1341217 TCTTTTTTCTTTTT
1 TCTTTTTTCTTTTT
1341231 TCTTTTTTCTTTTT
1 TCTTTTTTCTTTTT
* *
1341245 CCTCTTTTTCTCTTCT
1 TCT-TTTTTCT-TTTT
* *
1341261 TATTTTTCTATCTTTT
1 TCTTTTT-TCT-TTTT
1341277 TCTTTTCTT-TTTTAT
1 TCTTTT-TTCTTTT-T
1341292 CTCTTTTTTCTTTTT
1 -TCTTTTTTCTTTTT
1341307 ATCTTTTTT
1 -TCTTTTTT
1341316 TTTCCTATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
14 19 0.27
15 24 0.34
16 26 0.37
17 1 0.01
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (14 bp):
TCTTTTTTCTTTTT
Found at i:1341237 original size:24 final size:22
Alignment explanation
Indices: 1341210--1341316 Score: 51
Period size: 23 Copynumber: 4.6 Consensus size: 22
1341200 ATTTGATTTA
*
1341210 TTTTCTCTCTTTTTTCTTTTTTC
1 TTTTTTCTC-TTTTTCTTTTTTC
*
1341233 TTTTTTCT-TTTTCCTCTTTTTC
1 TTTTTTCTCTTTTTCT-TTTTTC
* * *
1341255 TCTTCTTAT-TTTTCTATCTTTTTC
1 T-TTTTTCTCTTTT-TCT-TTTTTC
1341279 TTTTCTT-T-TTTATCTCTTTTTTC
1 TTTT-TTCTCTTT-T-TCTTTTTTC
*
1341302 TTTTTATCTTTTTTT
1 TTTTT-TCTCTTTTT
1341317 TTCCTATTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
21 6 0.09
22 8 0.12
23 34 0.50
24 17 0.25
25 3 0.04
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTCTCTTTTTCTTTTTTC
Found at i:1341282 original size:29 final size:28
Alignment explanation
Indices: 1341250--1341339 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 28
1341240 TTTTTCCTCT
1341250 TTTTCTCTTCTTATTTTTCTATCTTTTTC
1 TTTTCT-TTCTTATTTTTCTATCTTTTTC
* *
1341279 TTTTCTTTTTTATCTCTTT-TTTCTTTTTATC
1 TTTTCTTTCTTAT-T-TTTCTATC-TTTT-TC
* * *
1341310 TTTTTTTTTCCTATTTTTCTATTTTTTTC
1 -TTTTCTTTCTTATTTTTCTATCTTTTTC
1341339 T
1 T
1341340 CTATTATCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
28 7 0.15
29 12 0.25
30 14 0.29
31 5 0.10
32 10 0.21
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTCTTTCTTATTTTTCTATCTTTTTC
Found at i:1341283 original size:38 final size:37
Alignment explanation
Indices: 1341208--1341336 Score: 131
Period size: 37 Copynumber: 3.4 Consensus size: 37
1341198 ATATTTGATT
*
1341208 TATTTTCTCTCTTTTTTCTTT-TTTCTTTTTTCTTTTTCC
1 TATTTT-TCTCTTTTTTCTTTCTATC-TTTTTC-TTTTCC
*
1341247 TCTTTTTCTCTTCTTATT-TTTCTATCTTTTTCTTTT-C
1 TATTTTTCTCTT-TT-TTCTTTCTATCTTTTTCTTTTCC
* *
1341284 TTTTTTATCTCTTTTTTCTTTTTATCTTTTT-TTTTCC
1 TATTTT-TCTCTTTTTTCTTTCTATCTTTTTCTTTTCC
*
1341321 TATTTTTCTATTTTTT
1 TATTTTTCTCTTTTTT
1341337 TCTCTATTAT
Statistics
Matches: 78, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
36 15 0.19
37 26 0.33
38 16 0.21
39 16 0.21
40 5 0.06
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (37 bp):
TATTTTTCTCTTTTTTCTTTCTATCTTTTTCTTTTCC
Found at i:1341316 original size:11 final size:10
Alignment explanation
Indices: 1341219--1341339 Score: 56
Period size: 10 Copynumber: 11.8 Consensus size: 10
1341209 ATTTTCTCTC
1341219 TTTTTTCTTT
1 TTTTTTCTTT
1341229 TTTCTTT-TTT
1 TTT-TTTCTTT
1341239 CTTTTTCCTCTTT
1 -TTTTT--TCTTT
*
1341252 TTCTCTTCTTAT
1 TT-TTTTCTT-T
1341264 TTTTCTATCTTT
1 TTTT-T-TCTTT
1341276 TTCTTTTC-TT
1 TT-TTTTCTTT
* *
1341286 TTTTATC-TC
1 TTTTTTCTTT
1341295 TTTTTTC--T
1 TTTTTTCTTT
*
1341303 TTTTATCTTT
1 TTTTTTCTTT
*
1341313 TTTTTTC-CT
1 TTTTTTCTTT
* *
1341322 ATTTTTCTAT
1 TTTTTTCTTT
1341332 TTTTTTCT
1 TTTTTTCT
1341340 CTATTATCTT
Statistics
Matches: 86, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
8 6 0.07
9 18 0.21
10 27 0.31
11 13 0.15
12 11 0.13
13 11 0.13
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1341335 original size:8 final size:7
Alignment explanation
Indices: 1341217--1341315 Score: 83
Period size: 7 Copynumber: 13.1 Consensus size: 7
1341207 TTATTTTCTC
1341217 TCTTTTT
1 TCTTTTT
1341224 TCTTTTT
1 TCTTTTT
1341231 TCTTTTT
1 TCTTTTT
1341238 TCTTTTT
1 TCTTTTT
*
1341245 CCTCTTTT
1 TCT-TTTT
*
1341253 TCTCTTCT
1 TCT-TTTT
*
1341261 TATTTTT
1 TCTTTTT
*
1341268 CTATCTTTT
1 -TCT-TTTT
1341277 TCTTTTCT
1 TCTTTT-T
1341285 T-TTTTAT
1 TCTTTT-T
1341292 CTCTTTTT
1 -TCTTTTT
1341300 TCTTTTT
1 TCTTTTT
1341307 ATCTTTTT
1 -TCTTTTT
1341315 T
1 T
1341316 TTTCCTATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
7 42 0.54
8 28 0.36
9 8 0.10
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (7 bp):
TCTTTTT
Found at i:1341336 original size:9 final size:8
Alignment explanation
Indices: 1341219--1341316 Score: 67
Period size: 8 Copynumber: 11.8 Consensus size: 8
1341209 ATTTTCTCTC
1341219 TTTTTTC-
1 TTTTTTCT
1341226 TTTTTTC-
1 TTTTTTCT
1341233 TTTTTTCT
1 TTTTTTCT
*
1341241 TTTTCCTCTT
1 TTTT-TTC-T
1341251 TTTCTCTTCT
1 TTT-T-TTCT
1341261 TATTTTTCT
1 T-TTTTTCT
* *
1341270 ATCTTT-T
1 TTTTTTCT
*
1341277 TCTTTTCT
1 TTTTTTCT
1341285 TTTTTATCT
1 TTTTT-TCT
1341294 CTTTTTTCT
1 -TTTTTTCT
*
1341303 TTTTATCT
1 TTTTTTCT
1341311 TTTTTT
1 TTTTTT
1341317 TTCCTATTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
7 18 0.25
8 25 0.34
9 12 0.16
10 12 0.16
11 6 0.08
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1341337 original size:38 final size:37
Alignment explanation
Indices: 1341210--1341363 Score: 120
Period size: 38 Copynumber: 4.1 Consensus size: 37
1341200 ATTTGATTTA
* *
1341210 TTTTCTCTCTTTTTTCTTTTT-TCTTTTTTCTTTTTCCTCT
1 TTTTCTCTTTTTTTTCTTTTTATC--TTTT-TTTTT-CTAT
* * *
1341250 TTTTCTCTTCTTATT-TTTCTATCTTTTTCTTTTCT-T
1 TTTTCTCTTTTTTTTCTTTTTATCTTTTT-TTTTCTAT
* *
1341286 TTTTATCTCTTTTTTCTTTTTATCTTTTTTTTTCCTAT
1 TTTTCTCTTTTTTTTCTTTTTATCTTTTTTTTT-CTAT
* * *
1341324 TTTTCT-ATTTTTTTCTCTATTATCTTTCTTTTT-TAT
1 TTTTCTCTTTTTTTTCT-TTTTATCTTTTTTTTTCTAT
1341360 TTTT
1 TTTT
1341364 TATTTTATGT
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
36 23 0.24
37 25 0.27
38 28 0.30
39 4 0.04
40 14 0.15
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.77
Consensus pattern (37 bp):
TTTTCTCTTTTTTTTCTTTTTATCTTTTTTTTTCTAT
Found at i:1347337 original size:5 final size:6
Alignment explanation
Indices: 1347322--1347346 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1347312 GACAACATGC
1347322 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
1347347 GGACTAAAAC
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:1347494 original size:29 final size:30
Alignment explanation
Indices: 1347455--1347530 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
1347445 TTACAATTAA
1347455 TAAAAATAAATAAAACATG-A-GGACTAAAT
1 TAAAAATAAATAAAACATGCATGG-CTAAAT
*
1347484 TAAAAATAAATTAAAA-TTGCATGGCTAAAT
1 TAAAAATAAA-TAAAACATGCATGGCTAAAT
1347514 T-AAAATAAATAAAACAT
1 TAAAAATAAATAAAACAT
1347531 ACTCGGGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 5 0.12
29 21 0.51
30 13 0.32
31 2 0.05
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.25
Consensus pattern (30 bp):
TAAAAATAAATAAAACATGCATGGCTAAAT
Found at i:1375993 original size:3 final size:3
Alignment explanation
Indices: 1375985--1376012 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1375975 TGTAAAAACA
1375985 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1376013 GCAAGACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1376455 original size:129 final size:133
Alignment explanation
Indices: 1376134--1376460 Score: 473
Period size: 134 Copynumber: 2.5 Consensus size: 133
1376124 TGGAATATGA
* * *
1376134 TGAGGGAATATCAGATCTGGGGACGTTAATCCATTCCACTGTCACTCAGGGAAGATTGAATCGAG
1 TGAGGGAATATCAGATCTGGGG-CGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGAG
* * * * *
1376199 GTAGACTTGTTCAAATGTTACTCAGGGAATATCAAATCTTGGAAGAGAGGGATATATTTCGTTTC
65 GCAGACTTGTTCAAATGTTACTCAGAGAATATCAAATCTTAGAAGAGAGGGATATAGTTCGCTTC
1376264 TTCT
130 TTCT
* * * *
1376268 GGAGGGAATATCAGATCTAGGGACGTTGATTCATTTCGCTGTCACTCAAGGAAGATTGAATCGAG
1 TGAGGGAATATCAGATCT-GGGGCGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGAG
*
1376333 GCAGACTTGTTC-ATTGTTACTCAGAGAATATCAAATCTTAGAAGAGAGGGATAT-GTTCGCTTC
65 GCAGACTTGTTCAAATGTTACTCAGAGAATATCAAATCTTAGAAGAGAGGGATATAGTTCGCTTC
1376396 -TCT
130 TTCT
* *
1376399 TGAGGGAA-ATCAGATATGGGGTGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGA
1 TGAGGGAATATCAGATCTGGGGCGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGA
1376461 CTTCGATTCG
Statistics
Matches: 173, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
129 41 0.24
130 8 0.05
131 10 0.06
132 7 0.04
133 39 0.23
134 65 0.38
135 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (133 bp):
TGAGGGAATATCAGATCTGGGGCGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGAGG
CAGACTTGTTCAAATGTTACTCAGAGAATATCAAATCTTAGAAGAGAGGGATATAGTTCGCTTCT
TCT
Found at i:1376846 original size:41 final size:42
Alignment explanation
Indices: 1376788--1376875 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 42
1376778 TACCCTAATA
* * *
1376788 ACTTATGGATGGACCGAAGGACTTA-TCATCTTGCTCGAAAG
1 ACTTATAGATGGACCGAAGGACTTAGGCATCATGCTCGAAAG
* *
1376829 ACTTATAGAT-GACCCGAAGGATTTAGGCATCATGCTTGAAAG
1 ACTTATAGATGGA-CCGAAGGACTTAGGCATCATGCTCGAAAG
1376871 ACTTA
1 ACTTA
1376876 CTGATTGTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
40 2 0.05
41 20 0.50
42 18 0.45
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (42 bp):
ACTTATAGATGGACCGAAGGACTTAGGCATCATGCTCGAAAG
Found at i:1377470 original size:232 final size:231
Alignment explanation
Indices: 1376969--1377490 Score: 712
Period size: 232 Copynumber: 2.2 Consensus size: 231
1376959 ATTTAAATGA
* *
1376969 GAATTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTTCAGATGACCTGAAGG
1 GAATTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCTGAAGG
* *
1377034 ATTTAAACATCATGCTCAAAAGACTTACTGATGGCCTAAAGGAATTACCAATTTTGGAAATAGTT
66 ATTTAAACATCATGCTCAAAAGAC-TACTGATGGCCCAAAGGAATTACCAAATTTGGAAATAGTT
* * *
1377099 TACTAGTTAAAAAACCTTCCTTACTTTTCAAAAATTTCAATTTTCAGATTTAGATGAGAAACCTT
130 TACTAGGTAAAAAACCTTACTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTT
*
1377164 TCTTATTTTTCAAAAAACATGTGAAAACATCCTGCAC
195 TCTCATTTTTCAAAAAACATGTGAAAACATCCTGCAC
* * *
1377201 AAAGGTCTTATGGATGGCCCGAAA-GACTTACCATCTTGCTCGAAAGACTTACAGATGA-CTCGA
1 GAA-TTCTTATGGATGGCCC-AAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCT-GA
* * ** *
1377264 ATGATTTAAACATCATGTTTGAAAGAC-ACTGATGGCCCAAAGGATTTACCAAATTT-GAGAATA
63 AGGATTTAAACATCATGCTCAAAAGACTACTGATGGCCCAAAGGAATTACCAAATTTGGA-AATA
* *
1377327 GTTTACTAGGTAAGAAACTTTACTTACTTTTCAAAAAAATTT-AATTTTCAGATTTAAATGAGAA
127 GTTTACTAGGTAAAAAACCTTACTTACTTTTC--AAAAATTTCAATTTTCAGATTTAAATGAGAA
* * * * * *
1377391 ATCTTTCTCATTTTTCAAGAGACGTGTGAAAACATCTTGCTC
190 ACCTTTCTCATTTTTCAAAAAACATGTGAAAACATCCTGCAC
*
1377433 GAATATCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGA
1 GAAT-TCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGA
1377491 TCTTTCTAAC
Statistics
Matches: 254, Mismatches: 28, Indels: 16
0.85 0.09 0.05
Matches are distributed among these distances:
230 2 0.01
231 61 0.24
232 109 0.43
233 80 0.31
234 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (231 bp):
GAATTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCTGAAGG
ATTTAAACATCATGCTCAAAAGACTACTGATGGCCCAAAGGAATTACCAAATTTGGAAATAGTTT
ACTAGGTAAAAAACCTTACTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTT
CTCATTTTTCAAAAAACATGTGAAAACATCCTGCAC
Found at i:1379688 original size:6 final size:6
Alignment explanation
Indices: 1379677--1379704 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1379667 AATAAAATGC
1379677 ATACAT ATACAT ATACAT ATACAT ATAC
1 ATACAT ATACAT ATACAT ATACAT ATAC
1379705 CATAATCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACAT
Found at i:1379995 original size:30 final size:30
Alignment explanation
Indices: 1379956--1380052 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 30
1379946 GAAAGACCTA
* * *
1379956 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTC-TAAAGAACCTAGGTAAACTG
*
1379986 TCCATAGGTCTGAAGAACCTAGGTAAACTG
1 TCCATAGGTCTAAAGAACCTAGGTAAACTG
* * * *
1380016 TCCATATGTTCCT-TAGAACATAGGTATACTG
1 TCCATA-GGT-CTAAAGAACCTAGGTAAACTG
1380047 TCCATA
1 TCCATA
1380053 TGTCCCGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 11 0.20
30 20 0.36
31 23 0.41
32 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (30 bp):
TCCATAGGTCTAAAGAACCTAGGTAAACTG
Found at i:1380085 original size:32 final size:32
Alignment explanation
Indices: 1379982--1380105 Score: 130
Period size: 31 Copynumber: 4.0 Consensus size: 32
1379972 AACCTCGGCA
* * *
1379982 ACTGTCCATAGGT-CTGAAGAACCTAGGTAA-
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAT
* **
1380012 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAT
1380043 ACTGTCCATATGTCCCGAA-AGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGTAAT
* * *
1380075 TCTGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTCCCGAAGAACATAGGTAA
1380106 ACCCTCGACT
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
30 14 0.18
31 35 0.45
32 28 0.36
33 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (32 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:1380539 original size:13 final size:13
Alignment explanation
Indices: 1380521--1380557 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1380511 CATAGGCATG
*
1380521 TATTCTCATATTT
1 TATTCTCATATGT
1380534 TATTCTCATATGT
1 TATTCTCATATGT
1380547 TATTCTCATAT
1 TATTCTCATAT
1380558 ATTCACATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.03, T:0.57
Consensus pattern (13 bp):
TATTCTCATATGT
Found at i:1380927 original size:2 final size:2
Alignment explanation
Indices: 1380920--1380979 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1380910 ACTTATATTC
1380920 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
1380962 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1380980 CACACAACAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1382683 original size:9 final size:9
Alignment explanation
Indices: 1382671--1382735 Score: 73
Period size: 9 Copynumber: 7.4 Consensus size: 9
1382661 ATTTGATTTA
1382671 TTTTCTCTT
1 TTTTCTCTT
*
1382680 TTTTTTCTT
1 TTTTCTCTT
*
1382689 TTTCCTC-T
1 TTTTCTCTT
1382697 TTTTCTC-T
1 TTTTCTCTT
1382705 TTTTCTCTT
1 TTTTCTCTT
1382714 TTTTC-CTAT
1 TTTTCTCT-T
*
1382723 TTTTCTATT
1 TTTTCTCTT
1382732 TTTT
1 TTTT
1382736 TTCTCTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
8 17 0.35
9 30 0.62
10 1 0.02
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:1382690 original size:8 final size:8
Alignment explanation
Indices: 1382679--1382735 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
1382669 TATTTTCTCT
1382679 TTTTTTTC
1 TTTTTTTC
*
1382687 TTTTTCCTC
1 TTTTT-TTC
*
1382696 TTTTTCTC
1 TTTTTTTC
*
1382704 TTTTTCTC
1 TTTTTTTC
*
1382712 TTTTTTCC
1 TTTTTTTC
*
1382720 TATTTTTC
1 TTTTTTTC
1382728 TATTTTTT
1 T-TTTTTT
1382736 TTCTCTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
8 29 0.71
9 12 0.29
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1382699 original size:17 final size:16
Alignment explanation
Indices: 1382671--1382763 Score: 75
Period size: 16 Copynumber: 5.8 Consensus size: 16
1382661 ATTTGATTTA
1382671 TTTTCTCTTTTTTTTCT
1 TTTTCTC-TTTTTTTCT
*
1382688 TTTTCCTCTTTTTCTCT
1 TTTT-CTCTTTTTTTCT
*
1382705 TTTTCTCTTTTTTCCT
1 TTTTCTCTTTTTTTCT
*
1382721 ATTTT-TCTATTTTT-T
1 -TTTTCTCTTTTTTTCT
* * *
1382736 TTCTCTATTATCTTTCT
1 TTTTCTCTT-TTTTTCT
1382753 TTTT-TCTTTTT
1 TTTTCTCTTTTT
1382764 CATTTTATGT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
14 3 0.05
15 5 0.08
16 24 0.41
17 24 0.41
18 3 0.05
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTCTTTTTTTCT
Found at i:1382700 original size:26 final size:26
Alignment explanation
Indices: 1382671--1382739 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
1382661 ATTTGATTTA
*
1382671 TTTTCTCTTTTTTTTCTTTTTCCTCT
1 TTTTCTCTTTTTTTTCTTTTTCCTAT
*
1382697 TTTTCTC-TTTTTCTCTTTTTTCCTAT
1 TTTTCTCTTTTTTTTC-TTTTTCCTAT
*
1382723 TTTTCTATTTTTTTTCT
1 TTTTCTCTTTTTTTTCT
1382740 CTATTATCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.19
26 23 0.62
27 7 0.19
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTCTCTTTTTTTTCTTTTTCCTAT
Found at i:1382755 original size:20 final size:22
Alignment explanation
Indices: 1382710--1382759 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
1382700 TCTCTTTTTC
*
1382710 TCTTTTTTC-CTATTTTTCTAT
1 TCTTTTTTCTCTATTTATCTAT
1382731 T-TTTTTTCTCTA-TTATCT-T
1 TCTTTTTTCTCTATTTATCTAT
1382750 TCTTTTTTCT
1 TCTTTTTTCT
1382760 TTTTCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (22 bp):
TCTTTTTTCTCTATTTATCTAT
Found at i:1388719 original size:5 final size:6
Alignment explanation
Indices: 1388704--1388728 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1388694 AACAACATGC
1388704 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
1388729 GGACTAAAAC
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:1388875 original size:29 final size:30
Alignment explanation
Indices: 1388836--1388911 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
1388826 TTACAATTAA
*
1388836 TAAAAATAAATAAAACATG-A-GGACTAAAT
1 TAAAAATAAATAAAACATGCATGG-CCAAAT
*
1388865 TAAAAATAAATTAAAA-TTGCATGGCCAAAT
1 TAAAAATAAA-TAAAACATGCATGGCCAAAT
1388895 T-AAAATAAATAAAACAT
1 TAAAAATAAATAAAACAT
1388912 ACTCAGGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 5 0.12
29 21 0.52
30 12 0.30
31 2 0.05
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (30 bp):
TAAAAATAAATAAAACATGCATGGCCAAAT
Found at i:1405502 original size:21 final size:21
Alignment explanation
Indices: 1405466--1405528 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1405456 ATATAAAATT
* * *
1405466 TGTTCTGAAGGACCTCATGTA
1 TGTTCCGAAAGACCTCATATA
*
1405487 TG-TCTCGAAAGACCTCGTATA
1 TGTTC-CGAAAGACCTCATATA
*
1405508 TGTTCCGAAGGACCTCATATA
1 TGTTCCGAAAGACCTCATATA
1405529 ATCTCTCGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.06
21 30 0.88
22 2 0.06
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (21 bp):
TGTTCCGAAAGACCTCATATA
Found at i:1406762 original size:25 final size:25
Alignment explanation
Indices: 1406734--1406794 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
1406724 ACTTATAAAC
1406734 CTTTCATCTTTAATCCTTCTTAACT
1 CTTTCATCTTTAATCCTTCTTAACT
1406759 CTTTCATCTTTAATCCTTCTTAACT
1 CTTTCATCTTTAATCCTTCTTAACT
1406784 CTTTCATCTTT
1 CTTTCATCTTT
1406795 TGGTTTTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.18, C:0.28, G:0.00, T:0.54
Consensus pattern (25 bp):
CTTTCATCTTTAATCCTTCTTAACT
Found at i:1410254 original size:7 final size:7
Alignment explanation
Indices: 1410242--1410266 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1410232 AAAAACAAAT
1410242 AATAATA
1 AATAATA
1410249 AATAATA
1 AATAATA
1410256 AATAATA
1 AATAATA
1410263 AATA
1 AATA
1410267 GAATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:1413450 original size:18 final size:18
Alignment explanation
Indices: 1413427--1413468 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1413417 AATTCCAGCT
1413427 GTTGCAATGGTTGTTGCC
1 GTTGCAATGGTTGTTGCC
1413445 GTTGCAATGGTTGTTGCC
1 GTTGCAATGGTTGTTGCC
1413463 GTTGCA
1 GTTGCA
1413469 TTTTTCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (18 bp):
GTTGCAATGGTTGTTGCC
Found at i:1420641 original size:230 final size:230
Alignment explanation
Indices: 1420338--1420799 Score: 780
Period size: 230 Copynumber: 2.0 Consensus size: 230
1420328 TGGATCGACG
* *
1420338 AGATTGAAGTTTCGAGGATCGATTTTTGAATTATAGTTTCCAAGTCCCCTACCGACGACAAAGAA
1 AGATTGAAGTTTCGAGGATCGATTTTCGAATTATAGTTTACAAGTCCCCTACCGACGACAAAGAA
* *
1420403 ATTGAATCCATGCAAGTGGATGGTGTTGAAAATTAGTGTGAATGCACCGAATTCCACCGAAAGTA
66 ATTGAATCCATGCAAGTGGATGGTGTTGAAAATTAGTGTGAATGCACCAAATTCCACCGAAAGCA
*
1420468 TTACACCGAAAGTTGCAGCTTGATTTTGTTGAAAATATGGTAATGGGAAAATTGCTCATTTAGTC
131 TTACACCGAAAGTTGCAGCTTCATTTTGTTGAAAATATGGTAATGGGAAAATTGCTCATTTAGTC
*
1420533 TATGAACTTTAGGGTATTTACAAGATTAATCCTTA
196 TATAAACTTTAGGGTATTTACAAGATTAATCCTTA
* * ** *
1420568 AGATTGAAGTTTCGAGGATCGGTTTTCGGATTATAGTTTATGAGTCCCCTACCGACGGCAAAGAA
1 AGATTGAAGTTTCGAGGATCGATTTTCGAATTATAGTTTACAAGTCCCCTACCGACGACAAAGAA
1420633 ATTGAATCCATGCAAGTGGATGGTGTTGAAAATTAGTGTGAATGCACCAAATTCCACCGAAAGCA
66 ATTGAATCCATGCAAGTGGATGGTGTTGAAAATTAGTGTGAATGCACCAAATTCCACCGAAAGCA
* *
1420698 TTACACCGAAAGTTGTAGCTTCATTTTGTTGAAAATATGGTAATGGGAAAATTTCTCATTTAGTC
131 TTACACCGAAAGTTGCAGCTTCATTTTGTTGAAAATATGGTAATGGGAAAATTGCTCATTTAGTC
* * *
1420763 TCTAAACTTTAGGGTATTTATAAGATTAGTCCTTA
196 TATAAACTTTAGGGTATTTACAAGATTAATCCTTA
1420798 AG
1 AG
1420800 CTTCAACACC
Statistics
Matches: 216, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
230 216 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (230 bp):
AGATTGAAGTTTCGAGGATCGATTTTCGAATTATAGTTTACAAGTCCCCTACCGACGACAAAGAA
ATTGAATCCATGCAAGTGGATGGTGTTGAAAATTAGTGTGAATGCACCAAATTCCACCGAAAGCA
TTACACCGAAAGTTGCAGCTTCATTTTGTTGAAAATATGGTAATGGGAAAATTGCTCATTTAGTC
TATAAACTTTAGGGTATTTACAAGATTAATCCTTA
Found at i:1432625 original size:24 final size:24
Alignment explanation
Indices: 1432591--1432697 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1432581 AAACGGAGAT
* *
1432591 ATCAGAAATCAAAATATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
1432615 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1432639 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
1432663 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1432687 ATCAGAAATCA
1 ATCAGAAATCA
1432698 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1432697 original size:48 final size:48
Alignment explanation
Indices: 1432591--1432699 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
1432581 AAACGGAGAT
* * * * *
1432591 ATCAGAAATCAAAATATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
1432639 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1432687 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1432700 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1433839 original size:18 final size:18
Alignment explanation
Indices: 1433818--1433855 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1433808 TCCTTCCATC
*
1433818 CAATCTTATTATTTAATT
1 CAATCTTATCATTTAATT
*
1433836 CAATCTTATCATTTACTT
1 CAATCTTATCATTTAATT
1433854 CA
1 CA
1433856 GTCCTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (18 bp):
CAATCTTATCATTTAATT
Found at i:1435179 original size:8 final size:8
Alignment explanation
Indices: 1435159--1435213 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
1435149 GGTCAACTCC
1435159 GGTCAAC-
1 GGTCAACG
1435166 GGTCAACG
1 GGTCAACG
1435174 GGTCAAC-
1 GGTCAACG
1435181 GGTCAACG
1 GGTCAACG
1435189 GGT---CG
1 GGTCAACG
1435194 GGTCAACG
1 GGTCAACG
1435202 GGTCAACG
1 GGTCAACG
1435210 GGTC
1 GGTC
1435214 GGGTAAATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1435179 original size:15 final size:15
Alignment explanation
Indices: 1435159--1435210 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
1435149 GGTCAACTCC
1435159 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1435174 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1435189 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1435202 GGTCAACGG
1 GGTCAACGG
1435211 GTCGGGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.36
15 21 0.64
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1435207 original size:21 final size:21
Alignment explanation
Indices: 1435172--1435226 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
1435162 CAACGGTCAA
1435172 CGGGTCAAC-GGTCAACGGGT
1 CGGGTCAACGGGTCAACGGGT
1435192 CGGGTCAACGGGTCAACGGGT
1 CGGGTCAACGGGTCAACGGGT
* *
1435213 CGGGTAAATGGGTC
1 CGGGTCAACGGGTC
1435227 GGTTCGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 9 0.28
21 23 0.72
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (21 bp):
CGGGTCAACGGGTCAACGGGT
Found at i:1435235 original size:18 final size:18
Alignment explanation
Indices: 1435187--1435253 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
1435177 CAACGGTCAA
*
1435187 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
1435205 CAACGGGTCGGGTAAATGGGT
1 ---CGGGTCGGGTAAACGGGT
*
1435226 CGGTTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1435244 CGGGTCGGGT
1 CGGGTCGGGT
1435254 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 25 0.61
21 16 0.39
ACGTcount: A:0.15, C:0.18, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1437413 original size:24 final size:24
Alignment explanation
Indices: 1437379--1437485 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1437369 AAACGGAGAT
* *
1437379 ATCAGAAATCAAAATATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
1437403 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1437427 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
1437451 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1437475 ATCAGAAATCA
1 ATCAGAAATCA
1437486 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1437485 original size:48 final size:48
Alignment explanation
Indices: 1437379--1437487 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
1437369 AAACGGAGAT
* * * * *
1437379 ATCAGAAATCAAAATATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
1437427 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1437475 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1437488 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1438630 original size:18 final size:18
Alignment explanation
Indices: 1438609--1438646 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1438599 TCCTTCCATC
*
1438609 CAATCTTATTATTTAATT
1 CAATCTTATCATTTAATT
*
1438627 CAATCTTATCATTTACTT
1 CAATCTTATCATTTAATT
1438645 CA
1 CA
1438647 GTCCTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (18 bp):
CAATCTTATCATTTAATT
Found at i:1439962 original size:7 final size:7
Alignment explanation
Indices: 1439950--1440004 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
1439940 TGGTCAACTC
1439950 CGGTCAA
1 CGGTCAA
1439957 CGGTCAA
1 CGGTCAA
1439964 CGGGTCAA
1 C-GGTCAA
1439972 CGGTCAA
1 CGGTCAA
1439979 CGGGTC--
1 C-GGTCAA
*
1439985 GGGTCAA
1 CGGTCAA
1439992 CGGGTCAA
1 C-GGTCAA
1440000 CGGTC
1 CGGTC
1440005 GGGTAAATGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 4 0.10
7 19 0.46
8 18 0.44
ACGTcount: A:0.22, C:0.27, G:0.36, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:1439971 original size:8 final size:8
Alignment explanation
Indices: 1439951--1440002 Score: 69
Period size: 8 Copynumber: 7.1 Consensus size: 8
1439941 GGTCAACTCC
1439951 GGTCAAC-
1 GGTCAACG
1439958 GGTCAACG
1 GGTCAACG
1439966 GGTCAAC-
1 GGTCAACG
1439973 GGTCAACG
1 GGTCAACG
1439981 GGT---CG
1 GGTCAACG
1439986 GGTCAACG
1 GGTCAACG
1439994 GGTCAACG
1 GGTCAACG
1440002 G
1 G
1440003 TCGGGTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.12
7 14 0.35
8 21 0.52
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.13
Consensus pattern (8 bp):
GGTCAACG
Found at i:1439971 original size:15 final size:15
Alignment explanation
Indices: 1439951--1440004 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
1439941 GGTCAACTCC
1439951 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1439966 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1439981 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1439994 GGTCAACGGTC
1 GGTCAACGGTC
1440005 GGGTAAATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.34
15 23 0.66
ACGTcount: A:0.22, C:0.26, G:0.37, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1439989 original size:20 final size:20
Alignment explanation
Indices: 1439964--1440008 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
1439954 CAACGGTCAA
1439964 CGGGTCAAC-GGTCAACGGGT
1 CGGGTCAACGGGTCAAC-GGT
1439984 CGGGTCAACGGGTCAACGGT
1 CGGGTCAACGGGTCAACGGT
1440004 CGGGT
1 CGGGT
1440009 AAATGGGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (20 bp):
CGGGTCAACGGGTCAACGGT
Found at i:1440016 original size:20 final size:21
Alignment explanation
Indices: 1439964--1440035 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 21
1439954 CAACGGTCAA
*
1439964 CGGGTCAAC-GGTCAACGGGT
1 CGGGTAAACGGGTCAACGGGT
*
1439984 CGGGTCAACGGGTCAAC-GGT
1 CGGGTAAACGGGTCAACGGGT
* *
1440004 CGGGTAAATGGGT---CGGTT
1 CGGGTAAACGGGTCAACGGGT
1440022 CGGGTAAACGGGTC
1 CGGGTAAACGGGTC
1440036 GGGTCGGGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
17 1 0.02
18 14 0.31
20 23 0.51
21 7 0.16
ACGTcount: A:0.19, C:0.21, G:0.42, T:0.18
Consensus pattern (21 bp):
CGGGTAAACGGGTCAACGGGT
Done.