Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 2 of 27
Found at i:151931 original size:55 final size:55
Alignment explanation
Indices: 151842--152425 Score: 737
Period size: 55 Copynumber: 10.6 Consensus size: 55
151832 TGTGTGGGCT
* * * * * * * * *
151842 TTAAAAGGGTACCACTGACTTGTGGGCTTAAAAAGGATGCCACGAAGTTTTGAAC
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* *
151897 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTTCCACGGAGTTGTGAAC
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
*
151952 TCTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTAGAC
1 T-TAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* * * * *
152007 TTAAAACGATGCCACAGAGTTGTGGAC-TTAAAACGATGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
152061 TTTAAAGGGTGCCACGGAGTTGTGGAC-TTAAAACGATGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
152115 TTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAATGGTACCACGGAGTTATGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* * * *
152170 TTAAAACGATGCCACGAAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
152225 TTTAAAAGGGTGCCACAGAGTTGTGGACTTT-AAAGGGTACCACAGAGTTGTGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
152280 TTAAAACGATGCCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
152335 TTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGTGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* * * *
152391 TTAAAAGGATGCCACTGAGTCGTAGACTTTAAAAG
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAG
152426 AAAATGCCAC
Statistics
Matches: 469, Mismatches: 52, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
53 2 0.00
54 147 0.31
55 212 0.45
56 108 0.23
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (55 bp):
TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
Found at i:153474 original size:1 final size:1
Alignment explanation
Indices: 153468--153511 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
153458 GGTGAAAAGG
** * *
153468 TTTTTTTTTGGTTTTTTTTTTGTTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
153512 AGGATTAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:153482 original size:11 final size:11
Alignment explanation
Indices: 153466--153507 Score: 61
Period size: 10 Copynumber: 4.0 Consensus size: 11
153456 AGGGTGAAAA
153466 GGTTTTTTTTT
1 GGTTTTTTTTT
153477 GGTTTTTTTTT
1 GGTTTTTTTTT
*
153488 TG-TTTTTTTT
1 GGTTTTTTTTT
153498 -GTTTTTTTTT
1 GGTTTTTTTTT
153508 TTTTAGGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 1 0.03
10 16 0.55
11 12 0.41
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
GGTTTTTTTTT
Found at i:153494 original size:21 final size:21
Alignment explanation
Indices: 153469--153509 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
153459 GTGAAAAGGT
153469 TTTTTTTTGGTTTTTTTTTTG
1 TTTTTTTTGGTTTTTTTTTTG
*
153490 TTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTGGTTTTTTTTTT
153510 TTAGGATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (21 bp):
TTTTTTTTGGTTTTTTTTTTG
Found at i:153495 original size:20 final size:20
Alignment explanation
Indices: 153470--153508 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
153460 TGAAAAGGTT
153470 TTTTTTTGGTTTTTTTTTTG
1 TTTTTTTGGTTTTTTTTTTG
*
153490 TTTTTTTTGTTTTTTTTTT
1 TTTTTTTGGTTTTTTTTTT
153509 TTTAGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (20 bp):
TTTTTTTGGTTTTTTTTTTG
Found at i:153508 original size:11 final size:11
Alignment explanation
Indices: 153467--153510 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
153457 GGGTGAAAAG
*
153467 GTTTTTTTTTG
1 GTTTTTTTTTT
153478 GTTTTTTTTTT
1 GTTTTTTTTTT
153489 GTTTTTTTTGTT
1 GTTTTTTTT-TT
153501 -TTTTTTTTTT
1 GTTTTTTTTTT
153511 TAGGATTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
10 2 0.06
11 27 0.87
12 2 0.06
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:153838 original size:24 final size:23
Alignment explanation
Indices: 153793--153838 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
153783 TGCTTTTGCA
*
153793 CTTTTGCTTTTCATTTTTTTGTG
1 CTTTTGCTTTGCATTTTTTTGTG
*
153816 CTTTTGCTTTGGACTTTTTTTGT
1 CTTTTGCTTTGCA-TTTTTTTGT
153839 CATTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.04, C:0.13, G:0.15, T:0.67
Consensus pattern (23 bp):
CTTTTGCTTTGCATTTTTTTGTG
Found at i:156801 original size:13 final size:13
Alignment explanation
Indices: 156783--156808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
156773 CAATTTTTTG
156783 TGTATCGATACAT
1 TGTATCGATACAT
156796 TGTATCGATACAT
1 TGTATCGATACAT
156809 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:157556 original size:21 final size:21
Alignment explanation
Indices: 157515--157558 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
157505 CTCCCCTTTA
* *
157515 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
157536 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
157557 TC
1 TC
157559 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:163318 original size:21 final size:21
Alignment explanation
Indices: 163289--163333 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
163279 AAGTTTTCAT
*
163289 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
163309 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
163331 TTT
1 TTT
163334 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:165569 original size:13 final size:13
Alignment explanation
Indices: 165551--165576 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
165541 CAATTTTTTG
165551 TGTATCGATACAT
1 TGTATCGATACAT
165564 TGTATCGATACAT
1 TGTATCGATACAT
165577 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:165688 original size:20 final size:20
Alignment explanation
Indices: 165636--165690 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
165626 CATCTTTTTC
*
165636 ATGTATCGATACATTGCAAT
1 ATGTATCGATACTTTGCAAT
165656 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-T
*
165676 GTGTATCGATACTTT
1 ATGTATCGATACTTT
165691 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAT
Found at i:170784 original size:20 final size:20
Alignment explanation
Indices: 170720--170794 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
170710 AAAAAGACAT
*
170720 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * * *
170740 AATATATCAATACATTTATA
1 AATGTATCGATACATTGAAA
* *
170760 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
170780 AATGTATCGATACAT
1 AATGTATCGATACAT
170795 CTGGGTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:172929 original size:15 final size:16
Alignment explanation
Indices: 172911--172949 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
172901 AACCACTTAG
172911 GAAGAAGCCACT-CAA
1 GAAGAAGCCACTCCAA
* *
172926 GAAGAAGCCAGTCCAG
1 GAAGAAGCCACTCCAA
172942 GAAGAAGC
1 GAAGAAGC
172950 ACTAACGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.44, C:0.23, G:0.28, T:0.05
Consensus pattern (16 bp):
GAAGAAGCCACTCCAA
Found at i:173411 original size:88 final size:86
Alignment explanation
Indices: 173293--173653 Score: 302
Period size: 88 Copynumber: 4.1 Consensus size: 86
173283 CTTGAAAATT
* * * *
173293 TTGACTAATGCATAATAATTTTTTTGAAACCCGAAAAATGTAACAGATGCATGGGTATC-GAATT
1 TTGACTAATGCATAATAAATTTTTTAAAACCCGAAAAATATGACAGATGCATGGGTATCAG-ATT
173357 CCTTTTGACACA-AATCCAAAAAAA
65 CCTTTTGACACATAA---AAAAAAA
* * * **
173381 TTGACTAATGCGTAATAAATTTCTTAAAACCC-AAAAGATATGACAAATATATGAGGTATCAGAT
1 TTGACTAATGCATAATAAATTTTTTAAAACCCGAAAA-ATATGACAGATGCATG-GGTATCAGAT
* *
173445 T-CTTTTTA-ACATGAAAAAAATAT
64 TCCTTTTGACACAT-AAAAAAA-AA
* * * * * *
173468 TTGACTAATGTATAATAAATTTTTTAAAACTCGAAAGATGTGATAGATGCATGGGATATTAGATT
1 TTGACTAATGCATAATAAATTTTTTAAAACCCGAAAAATATGACAGATGCATGGG-TATCAGATT
* * *
173533 CCTTCTT-ACACGATAGAAAATAT
65 CCTT-TTGACAC-ATAAAAAAAAA
* * * * *
173556 TTGACTAATACTTAATAAATTTTTTGAAGCCCGAAAGATATGACAGATGCATTGGGTATCAGATT
1 TTGACTAATGCATAATAAATTTTTTAAAACCCGAAAAATATGACAGATGCA-TGGGTATCAGATT
* * * *
173621 CCTTCTGACATAATAAAAAATAT
65 CCTTTTGACA-CATAAAAAAAAA
173644 TTGACTAATG
1 TTGACTAATG
173654 ACAGACAAAG
Statistics
Matches: 221, Mismatches: 37, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
86 7 0.03
87 56 0.25
88 131 0.59
89 24 0.11
90 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (86 bp):
TTGACTAATGCATAATAAATTTTTTAAAACCCGAAAAATATGACAGATGCATGGGTATCAGATTC
CTTTTGACACATAAAAAAAAA
Found at i:173595 original size:175 final size:175
Alignment explanation
Indices: 173287--173653 Score: 422
Period size: 175 Copynumber: 2.1 Consensus size: 175
173277 TTAGAACTTG
* *
173287 AAAAT-TTTGACTAATGCATAATAATTTTTTTGAAACCCGAAAAATGTAACAGATGCATGGGTAT
1 AAAATATTTGACTAATGCATAATAAATTTTTTAAAACCCGAAAAATGTAACAGATGCATGGGTAT
* * *
173351 CGAATTCCTTTTGACACAAATCCAAAAAAATTGACTAATGCGTAATAAATTTCTTAAAACCCAAA
66 AGAATTCCTTTTGACACAAATACAAAAAAATTGACTAATACGTAATAAATTTCTTAAAACCCAAA
* * *
173416 AGATATGACAAAT-ATATGAGGTATCAGATTCTTTTTAACATGA-AA
131 AGATATGACAAATCAT-TG-GGTATCAGATTCCTTCTAACATAATAA
* * * * *
173461 AAAATATTTGACTAATGTATAATAAATTTTTTAAAACTCGAAAGATGTGATAGATGCATGGGATA
1 AAAATATTTGACTAATGCATAATAAATTTTTTAAAACCCGAAAAATGTAACAGATGCATGGG-TA
* * * * * * * *
173526 TTAG-ATTCCTTCTT-ACAC-GATAGAAAATATTTGACTAATACTTAATAAATTTTTTGAAGCCC
65 -TAGAATTCCTT-TTGACACAAATACAAAAAAATTGACTAATACGTAATAAATTTCTTAAAACCC
* * *
173588 GAAAGATATGACAGATGCATTGGGTATCAGATTCCTTCTGACATAATAA
128 AAAAGATATGACAAAT-CATTGGGTATCAGATTCCTTCTAACATAATAA
173637 AAAATATTTGACTAATG
1 AAAATATTTGACTAATG
173654 ACAGACAAAG
Statistics
Matches: 162, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
174 5 0.03
175 117 0.72
176 34 0.21
177 6 0.04
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (175 bp):
AAAATATTTGACTAATGCATAATAAATTTTTTAAAACCCGAAAAATGTAACAGATGCATGGGTAT
AGAATTCCTTTTGACACAAATACAAAAAAATTGACTAATACGTAATAAATTTCTTAAAACCCAAA
AGATATGACAAATCATTGGGTATCAGATTCCTTCTAACATAATAA
Found at i:177059 original size:15 final size:14
Alignment explanation
Indices: 177039--177083 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
177029 GAAAGCGCGT
*
177039 AAAACAAAATAAAGA
1 AAAACAAAAGAAA-A
177054 AAAACAAAAGAAAA
1 AAAACAAAAGAAAA
177068 AAATACAAAA-AAAA
1 AAA-ACAAAAGAAAA
177082 AA
1 AA
177084 GCAACTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.84, C:0.07, G:0.04, T:0.04
Consensus pattern (14 bp):
AAAACAAAAGAAAA
Found at i:177564 original size:18 final size:19
Alignment explanation
Indices: 177541--177577 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
177531 AATATTTTAT
*
177541 TTTAAAATTATTA-AAAAA
1 TTTAAAAATATTATAAAAA
177559 TTTAAAAATATTATAAAAA
1 TTTAAAAATATTATAAAAA
177578 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTAAAAATATTATAAAAA
Found at i:177628 original size:20 final size:17
Alignment explanation
Indices: 177588--177631 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 17
177578 ATATTTTTTA
177588 AAATTAA-AAAATTAAT
1 AAATTAATAAAATTAAT
177604 AAATTAATAAAATTCAATTT
1 AAATTAATAAAATT-AA--T
177624 AAATTAAT
1 AAATTAAT
177632 TTCAATCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.29
17 6 0.25
18 2 0.08
20 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTAATAAAATTAAT
Found at i:180057 original size:2 final size:2
Alignment explanation
Indices: 180050--180079 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
180040 AATTTGCCTG
180050 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
180080 AAAGGAAGTT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:181861 original size:25 final size:25
Alignment explanation
Indices: 181814--181861 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
181804 CTTCAATCAC
** **
181814 CAAGAAATTAAAAAATATGTATATA
1 CAAGAAACAAAAAAATACATATATA
181839 CAAGAAACAAAAAAATACATATA
1 CAAGAAACAAAAAAATACATATA
181862 AAAAAAAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.21
Consensus pattern (25 bp):
CAAGAAACAAAAAAATACATATATA
Found at i:182711 original size:15 final size:15
Alignment explanation
Indices: 182691--182721 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
182681 AAAAACTTAG
*
182691 TATTTAATTTTTTAA
1 TATTTAATATTTTAA
182706 TATTTAATATTTTAA
1 TATTTAATATTTTAA
182721 T
1 T
182722 TTATCAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTAATATTTTAA
Found at i:183221 original size:24 final size:24
Alignment explanation
Indices: 183171--183221 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
183161 ATATTATTCA
* * *
183171 ATTTTTTGAAAAAATTTGATATCT
1 ATTTTTTGAAAAAATTTAAAATAT
183195 ATTTTTT-AAAAAATTTAAAAATAT
1 ATTTTTTGAAAAAATTT-AAAATAT
183219 ATT
1 ATT
183222 AAGTATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTTTTTGAAAAAATTTAAAATAT
Found at i:183997 original size:2 final size:2
Alignment explanation
Indices: 183990--184016 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
183980 CTTATCTACC
183990 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 T
184017 GAAACTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:184121 original size:20 final size:18
Alignment explanation
Indices: 184074--184152 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 18
184064 TGAATAATTT
184074 TTTATTAATTTAAATTAA
1 TTTATTAATTTAAATTAA
184092 TTTGATTTAATTTAAATTGATA
1 TTT-A-TTAATTTAAATT-A-A
*
184114 TTTATTAATTAAAAAATT-A
1 TTTATTAATT--TAAATTAA
184133 TTT-TT-ATTTAAATTTAA
1 TTTATTAATTTAAA-TTAA
184150 TTT
1 TTT
184153 TAAAATATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
15 3 0.06
16 2 0.04
17 7 0.14
18 5 0.10
19 5 0.10
20 18 0.35
21 2 0.04
22 9 0.18
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTATTAATTTAAATTAA
Found at i:187427 original size:2 final size:2
Alignment explanation
Indices: 187420--187445 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
187410 TGAGTTGCCC
187420 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
187446 CCTGTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:190604 original size:17 final size:17
Alignment explanation
Indices: 190582--190617 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
190572 TTTTTTATAA
*
190582 ATAAAAAATTATAAATT
1 ATAAAAAATTAAAAATT
*
190599 ATAAAATATTAAAAATT
1 ATAAAAAATTAAAAATT
190616 AT
1 AT
190618 TTATAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAAAATTAAAAATT
Found at i:193700 original size:100 final size:100
Alignment explanation
Indices: 193519--193774 Score: 334
Period size: 100 Copynumber: 2.6 Consensus size: 100
193509 AGTTACTTAG
* * * *
193519 AGTCAACAATTACGACCATCTCTTTCTATTGTCAAAGGTTAGTGAAGAATAGTCAACAATTACAA
1 AGTCAACAATTACGATCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACAA
* *
193584 CTAACTCTCTCTATTGTCAAAGGTTGACGAAGAAT
66 CTAACTCTCTCGATTGTCAAAGGTTGACAAAGAAT
* *
193619 AGTCAACAATTACAATCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTAC-G
1 AGTCAACAATTACGATCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACAA
* * * *
193683 GTCACCTTTCTCGATTGTCAAAGGTTGATAAAGAAT
66 CT-AACTCTCTCGATTGTCAAAGGTTGACAAAGAAT
* * * * * *
193719 AGTCAATAATTACGGTCACCTCTCTCGATTATTAAAAGTTGGTGAAGAATAGTCAA
1 AGTCAACAATTACGATCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAA
193775 TAATGGCAAC
Statistics
Matches: 136, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
99 1 0.01
100 135 0.99
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (100 bp):
AGTCAACAATTACGATCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACAA
CTAACTCTCTCGATTGTCAAAGGTTGACAAAGAAT
Found at i:193778 original size:50 final size:50
Alignment explanation
Indices: 193519--193774 Score: 298
Period size: 50 Copynumber: 5.1 Consensus size: 50
193509 AGTTACTTAG
** * * * *
193519 AGTCAACAATTACGACCATCTCTTTCTATTGTCAAAGGTTAGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
** * * **
193569 AGTCAACAATTAC-AACTAACTCTCTCTATTGTCAAAGGTTGACGAAGAAT
1 AGTCAACAATTACGGTC-ACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
** *
193619 AGTCAACAATTACAATCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
193669 AGTCAACAATTACGGTCACCTTTCTCGATTGTCAAAGGTTGATAAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * *
193719 AGTCAATAATTACGGTCACCTCTCTCGATTATTAAAAGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
193769 AGTCAA
1 AGTCAA
193775 TAATGGCAAC
Statistics
Matches: 181, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
49 2 0.01
50 177 0.98
51 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:198241 original size:50 final size:49
Alignment explanation
Indices: 198134--198332 Score: 194
Period size: 50 Copynumber: 4.1 Consensus size: 49
198124 AGTTACTTAG
* *
198134 AGTCAACAATTACGGCCACCTCTCTC----GTCAAAGGTTGAGGACGAAT
1 AGTCAACAATTAC-GACACCTCTCTCTATTGTCAAAGGTTGAGGAAGAAT
*
198180 AGTCAACAATTACGACGACCTCTCTTTATTGTCAAAGGTTG-GAGAAGAAT
1 AGTCAACAATTACGAC-ACCTCTCTCTATTGTCAAAGGTTGAG-GAAGAAT
* * * *
198230 AGTTAATAATTATGATCACCTCTCTCTATTGTCAAAGATTG-GTGAAGAAT
1 AGTCAACAATTACGA-CACCTCTCTCTATTGTCAAAGGTTGAG-GAAGAAT
* * * **
198280 AGTCAACAATTACGACCACATCTCTCGATTGTCAAATGTTGATAAAGAAT
1 AGTCAACAATTACGA-CACCTCTCTCTATTGTCAAAGGTTGAGGAAGAAT
198330 AGT
1 AGT
198333 TAATAATGAC
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
45 2 0.02
46 21 0.17
49 1 0.01
50 101 0.80
51 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (49 bp):
AGTCAACAATTACGACACCTCTCTCTATTGTCAAAGGTTGAGGAAGAAT
Found at i:199437 original size:24 final size:24
Alignment explanation
Indices: 199382--199437 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
199372 AATTTTTTTT
199382 TTAATATTTACATTTAATAATAATA
1 TTAA-ATTTACATTTAATAATAATA
* * *
199407 TTTAATTTATATTTAAATATTAATA
1 TTAAATTTACATTT-AATAATAATA
199432 -TAAATT
1 TTAAATT
199438 ATAAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAAATTTACATTTAATAATAATA
Found at i:199509 original size:17 final size:18
Alignment explanation
Indices: 199478--199511 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
199468 AAATTTTAAA
*
199478 AATATTATATTTATATCG
1 AATATTATATATATATCG
199496 AATA-TATATATATATC
1 AATATTATATATATATC
199512 CTATACTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (18 bp):
AATATTATATATATATCG
Found at i:200262 original size:2 final size:2
Alignment explanation
Indices: 200255--200284 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
200245 ATTTTTGTTA
200255 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
200285 TCCACAAAGT
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:202044 original size:2 final size:2
Alignment explanation
Indices: 202037--202069 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
202027 TGAATTTAAA
202037 AT AT AT 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 AT AT AT A
202070 AAGCTGTCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:203481 original size:2 final size:2
Alignment explanation
Indices: 203474--203514 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
203464 CAGCAAACTA
203474 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
203515 GTAAAATCCC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:205526 original size:3 final size:3
Alignment explanation
Indices: 205518--205551 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
205508 CTTCTGCTAC
205518 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
205552 TCGGTGCTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:205948 original size:15 final size:15
Alignment explanation
Indices: 205925--205954 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
205915 GAGTATCAAA
205925 TATAAAAATATATTT
1 TATAAAAATATATTT
*
205940 TATATAAATATATTT
1 TATAAAAATATATTT
205955 AATTTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAAAAATATATTT
Found at i:205996 original size:26 final size:26
Alignment explanation
Indices: 205967--206019 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
205957 TTTTTTTATG
205967 TTTTT-TATATA-ATTAAAAAATTATA
1 TTTTTATATATATATTAAAAAA-TATA
* *
205992 TTTTTATATTTATATTAAAATATATA
1 TTTTTATATATATATTAAAAAATATA
206018 TT
1 TT
206020 AAATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.21
26 11 0.46
27 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTTATATATATATTAAAAAATATA
Found at i:206872 original size:19 final size:21
Alignment explanation
Indices: 206848--206896 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
206838 CTTATTAAAA
206848 ATATTAAAAATT-TAT-TTTT
1 ATATTAAAAATTATATATTTT
* *
206867 ATATTAATATTTATATATTTT
1 ATATTAAAAATTATATATTTT
206888 ATAATTAAA
1 AT-ATTAAA
206897 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
20 3 0.12
21 6 0.25
22 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTAAAAATTATATATTTT
Found at i:207240 original size:21 final size:23
Alignment explanation
Indices: 207183--207270 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
207173 TAATAATTCA
* *
207183 TTTTTATA-TATATTTTGATAAG
1 TTTTTATATTATATTTTAATAAT
** *
207205 TTCGTATATTCATATCTTATTTATAAT
1 TTTTTATATT-ATA--TT-TTAATAAT
*
207232 TTTTTATATTATATTTTAATTAT
1 TTTTTATATTATATTTTAATAAT
207255 TTTTTATATTATATTT
1 TTTTTATATTATATTT
207271 GTATTTTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
22 6 0.11
23 23 0.43
24 5 0.09
26 5 0.09
27 14 0.26
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (23 bp):
TTTTTATATTATATTTTAATAAT
Found at i:207265 original size:12 final size:12
Alignment explanation
Indices: 207230--207266 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
207220 CTTATTTATA
207230 ATTTTTTATATT
1 ATTTTTTATATT
*
207242 ATATTTTA-ATT
1 ATTTTTTATATT
207253 ATTTTTTATATT
1 ATTTTTTATATT
207265 AT
1 AT
207267 ATTTGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTTTATATT
Found at i:207587 original size:22 final size:22
Alignment explanation
Indices: 207561--207609 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
207551 TATAATATCG
*
207561 TATTTTAATTATTTTTCTATTA
1 TATTTTAACTATTTTTCTATTA
* *
207583 TATTTTAACTATTTTTTTATTT
1 TATTTTAACTATTTTTCTATTA
207605 TATTT
1 TATTT
207610 ATGTTGTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (22 bp):
TATTTTAACTATTTTTCTATTA
Found at i:208081 original size:21 final size:19
Alignment explanation
Indices: 208035--208139 Score: 57
Period size: 20 Copynumber: 5.7 Consensus size: 19
208025 CATATTAATT
*
208035 TAATAATTTATGTTTTTATA
1 TAAT-ATTTATATTTTTATA
*
208055 TTATATTTATATATTTTATTA
1 TAATATTTATAT-TTTTA-TA
* *
208076 TAATA-TTATCGTATTTA-A
1 TAATATTTAT-ATTTTTATA
208094 -AATATTTTATATTTTTAT-
1 TAATA-TTTATATTTTTATA
208112 TAAT-TTTA-A--TTTA-A
1 TAATATTTATATTTTTATA
208126 TAATAATTTATATT
1 TAAT-ATTTATATT
208140 ATATAAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 27
0.66 0.07 0.27
Matches are distributed among these distances:
14 8 0.12
16 5 0.08
17 9 0.14
18 6 0.09
19 14 0.22
20 16 0.25
21 7 0.11
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (19 bp):
TAATATTTATATTTTTATA
Found at i:208117 original size:17 final size:17
Alignment explanation
Indices: 208097--208187 Score: 64
Period size: 17 Copynumber: 5.5 Consensus size: 17
208087 TATTTAAAAT
*
208097 ATTTTATATTTTTATTA
1 ATTTTATATTTATATTA
*
208114 ATTTTA-ATTTAATAATA
1 ATTTTATATTT-ATATTA
*
208131 A-TTTATA-TTATATAA
1 ATTTTATATTTATATTA
* ** *
208146 ATTTTAAAAATATATTT
1 ATTTTATATTTATATTA
* *
208163 ATATTATATTTTTA-TA
1 ATTTTATATTTATATTA
208179 ATTTTATAT
1 ATTTTATAT
208188 ATTTTATATT
Statistics
Matches: 55, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
15 5 0.09
16 24 0.44
17 26 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATATTTATATTA
Found at i:208182 original size:33 final size:36
Alignment explanation
Indices: 208100--208184 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 36
208090 TTAAAATATT
*
208100 TTATATTTTTATTAATTTTAATTTAATAATAATTTATA
1 TTATATTTTTA-TAATTTTAA-TAAATAATAATTTATA
208138 TTATA----TA-AATTTTAA-AAAT-AT-ATTTATA
1 TTATATTTTTATAATTTTAATAAATAATAATTTATA
208166 TTATATTTTTATAATTTTA
1 TTATATTTTTATAATTTTA
208185 TATATTTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
28 12 0.29
29 2 0.05
30 3 0.07
32 10 0.24
33 7 0.17
34 2 0.05
38 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (36 bp):
TTATATTTTTATAATTTTAATAAATAATAATTTATA
Found at i:208494 original size:32 final size:30
Alignment explanation
Indices: 208427--208531 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 30
208417 TGAGTCATGA
* * *
208427 AAAATTATT-AATTAATTAATATATTTATAT
1 AAAATTATTAAATT-TTTAATAAATTTACAT
208457 AAAAATTATTAAATTTGTTAATAAATTGTACAT
1 -AAAATTATTAAATTT-TTAATAAATT-TACAT
* *
208490 AAAATAATTAAATATTTTAATAATTTTTACAT
1 AAAATTATTAAAT-TTTTAATAA-ATTTACAT
*
208522 AAATTTATTA
1 AAAATTATTA
208532 GTTATTTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
31 9 0.15
32 45 0.73
33 8 0.13
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
AAAATTATTAAATTTTTAATAAATTTACAT
Found at i:208614 original size:14 final size:15
Alignment explanation
Indices: 208584--208625 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
208574 TTATTAAAAT
*
208584 TATTATTATATT-TA
1 TATTATTATATTAAA
*
208598 TATTTTTA-ATTAAA
1 TATTATTATATTAAA
208612 TATTATTATATTAA
1 TATTATTATATTAA
208626 TTTTTAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 3 0.13
14 15 0.65
15 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATTATATTAAA
Found at i:208639 original size:26 final size:28
Alignment explanation
Indices: 208584--208637 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
208574 TTATTAAAAT
*
208584 TATTATTATATTTATATTTTTAATTAAA
1 TATTATTATATTTATATTTTTAACTAAA
208612 TATTATTATA-TTA-ATTTTTAAACTAA
1 TATTATTATATTTATATTTTT-AACTAA
208638 TAAAAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
27 8 0.33
28 10 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TATTATTATATTTATATTTTTAACTAAA
Found at i:208821 original size:24 final size:22
Alignment explanation
Indices: 208769--208812 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
208759 TATTATTATT
208769 TTAAAATATTTAATTTAATTTAAC
1 TTAAAATATTT-ATTT-ATTTAAC
208793 TTAAAATATTTATTTATTTA
1 TTAAAATATTTATTTATTTA
208813 GATAGTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 4 0.20
24 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAAAATATTTATTTATTTAAC
Found at i:208872 original size:27 final size:26
Alignment explanation
Indices: 208825--208880 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
208815 TAGTAAATAA
*
208825 TTTATATTATTAATTACTTTAACTAT
1 TTTATATTATTAATTAATTTAACTAT
*
208851 TTTATATTAATTAATTAATTTAATTAT
1 TTTATATT-ATTAATTAATTTAACTAT
208878 TTT
1 TTT
208881 TTATAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATATTATTAATTAATTTAACTAT
Found at i:210548 original size:26 final size:26
Alignment explanation
Indices: 210504--210568 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
210494 CAAACTTTAA
*
210504 AAAAAT-ATTTAATATTTATATATAAAT
1 AAAAATAATTTAAT-TATAT-TATAAAT
* *
210531 AAAATATAATTTAATTATATTTTAATT
1 AAAA-ATAATTTAATTATATTATAAAT
210558 AAAAATAATTT
1 AAAAATAATTT
210569 TATATGTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 7 0.21
27 13 0.39
28 6 0.18
29 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AAAAATAATTTAATTATATTATAAAT
Found at i:210721 original size:23 final size:24
Alignment explanation
Indices: 210690--210761 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
210680 TAAATACATT
210690 TTATATCAAATCTTAAAAAAAA-TA
1 TTAT-TCAAATCTTAAAAAAAATTA
210714 TTATTCAAATCTTTAAAAAAAATTA
1 TTATTCAAATC-TTAAAAAAAATTA
* *
210739 TTTTTAAAAT-TT-AAAAAAATTA
1 TTATTCAAATCTTAAAAAAAATTA
210761 T
1 T
210762 AATATTTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
22 11 0.25
23 9 0.20
24 14 0.32
25 10 0.23
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (24 bp):
TTATTCAAATCTTAAAAAAAATTA
Found at i:210738 original size:22 final size:23
Alignment explanation
Indices: 210690--210757 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
210680 TAAATACATT
210690 TTATATCAAATCTTAAAAAAAATA
1 TTAT-TCAAATCTTAAAAAAAATA
210714 TTATTCAAATCTTTAAAAAAAATTA
1 TTATTCAAATC-TTAAAAAAAA-TA
* *
210739 TTTTTAAAAT-TTAAAAAAA
1 TTATTCAAATCTTAAAAAAA
210758 TTATAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 16 0.40
24 14 0.35
25 10 0.25
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
TTATTCAAATCTTAAAAAAAATA
Found at i:210758 original size:22 final size:23
Alignment explanation
Indices: 210697--210761 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 23
210687 ATTTTATATC
*
210697 AAATCTTAAAAAAAATATTATTCA
1 AAAT-TTAAAAAAATTATTATTCA
* *
210721 AATCTTTAAAAAAAATTATT-TTTA
1 AA-ATTT-AAAAAAATTATTATTCA
210745 AAATTTAAAAAAATTAT
1 AAATTTAAAAAAATTAT
210762 AATATTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 11 0.31
23 3 0.09
24 9 0.26
25 12 0.34
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTAAAAAAATTATTATTCA
Found at i:212273 original size:21 final size:18
Alignment explanation
Indices: 212249--212306 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 18
212239 TTTTCTTTTT
212249 TAATTTATCTTTCAAAAGAAA
1 TAATTTAT-TTT-AAAA-AAA
*
212270 TAATATATTTTAAAAAAA
1 TAATTTATTTTAAAAAAA
212288 TAGATTT-TTTTAATAAAAA
1 TA-ATTTATTTTAA-AAAAA
212307 GATAAGAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 11 0.33
19 12 0.36
20 3 0.09
21 7 0.21
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
TAATTTATTTTAAAAAAA
Found at i:213670 original size:16 final size:17
Alignment explanation
Indices: 213646--213678 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
213636 TTTTCATAGG
*
213646 TCATGTTAAA-TTATAT
1 TCATATTAAATTTATAT
213662 TCATATTAAATTTATAT
1 TCATATTAAATTTATAT
213679 AAAATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (17 bp):
TCATATTAAATTTATAT
Found at i:215033 original size:2 final size:2
Alignment explanation
Indices: 215026--215057 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
215016 AAATATGCAA
215026 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
215058 GAAGAAGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:215953 original size:26 final size:23
Alignment explanation
Indices: 215897--215953 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 23
215887 ATATTTATTT
215897 TTATAT-AATAAAAATTATATAA
1 TTATATAAATAAAAATTATATAA
*
215919 TATACATAAATATAAAATTAATATATA
1 T-TATATAAATA-AAAATT-ATATA-A
215946 TTATATAA
1 TTATATAA
215954 TTAAGAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 4 0.14
24 4 0.14
25 6 0.21
26 11 0.39
27 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTATATAAATAAAAATTATATAA
Found at i:217328 original size:7 final size:7
Alignment explanation
Indices: 217316--217352 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
217306 ATGAGCATAC
217316 ATTACGG
1 ATTACGG
217323 ATTACGG
1 ATTACGG
217330 ATTACGG
1 ATTACGG
217337 ATTACGG
1 ATTACGG
217344 ATTACGG
1 ATTACGG
217351 AT
1 AT
217353 GTAAATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (7 bp):
ATTACGG
Found at i:217916 original size:59 final size:58
Alignment explanation
Indices: 217792--217916 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 58
217782 TTTTTCTATA
*
217792 AATTATTATTATTTAAAATGATAAATAAATTTATATGTAAATATATTATTATCAATTTT
1 AATT-TTATTATTTAAAATGATAAATAAATTTATATGTAAATATATTATAATCAATTTT
* * * * *
217851 ATTTTTATTTATTTTAAGTGATAAATAAATTTATATTTAAATATATTATGAATTAA-TTT
1 AATTTTA-TTATTTAAAATGATAAATAAATTTATATGTAAATATATTAT-AATCAATTTT
217910 AATTTTA
1 AATTTTA
217917 AAAATTAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 3 0.05
59 50 0.88
60 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (58 bp):
AATTTTATTATTTAAAATGATAAATAAATTTATATGTAAATATATTATAATCAATTTT
Found at i:217943 original size:28 final size:28
Alignment explanation
Indices: 217902--217959 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
217892 TATATTATGA
217902 ATTAATTTAA-TTTTAAAAATTAATTATT
1 ATTAATTTAATTTTTAAAAATT-ATTATT
*
217930 ATTATATTT-ATTTTTTAAAATTATTATT
1 ATTA-ATTTAATTTTTAAAAATTATTATT
217958 AT
1 AT
217960 ATTTCATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTAATTTAATTTTTAAAAATTATTATT
Found at i:219130 original size:39 final size:39
Alignment explanation
Indices: 219085--219173 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 39
219075 TTTAAATTTT
219085 TATTTTATTATTTATTATATTATTAAA-AT-ATTAAAAAATA
1 TATTTTATTATTT-TTATA--ATTAAATATAATTAAAAAATA
*
219125 T-TTTTA-TA-TTTTATAATTAAATTTAATTAAAAAATA
1 TATTTTATTATTTTTATAATTAAATATAATTAAAAAATA
219161 TAATTTTATTATT
1 T-ATTTTATTATT
219174 AAATAATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
34 6 0.14
35 1 0.02
36 17 0.40
37 2 0.05
38 7 0.17
39 7 0.17
40 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (39 bp):
TATTTTATTATTTTTATAATTAAATATAATTAAAAAATA
Found at i:219171 original size:18 final size:19
Alignment explanation
Indices: 219144--219193 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
219134 TTTATAATTA
219144 AATTTAATTAAAAAAT-AT
1 AATTTAATTAAAAAATAAT
* **
219162 AATTTTATTATTAAATAAT
1 AATTTAATTAAAAAATAAT
219181 AATTTAAGTTAAA
1 AATTTAA-TTAAA
219194 CTATAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 13 0.54
19 8 0.33
20 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AATTTAATTAAAAAATAAT
Found at i:219193 original size:38 final size:36
Alignment explanation
Indices: 219114--219193 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
219104 TTATTAAAAT
**
219114 ATTAAAAAATATTTTTATATTTTATAATTAAATTTA
1 ATTAAAAAATATTTTTATATTAAATAATTAAATTTA
219150 ATTAAAAAATATAATTTTATTATTAAATAA-T-AATTTA
1 ATTAAAAAATAT--TTTTA-TATTAAATAATTAAATTTA
219187 AGTTAAA
1 A-TTAAA
219194 CTATAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
36 12 0.32
37 7 0.18
38 11 0.29
39 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTAAAAAATATTTTTATATTAAATAATTAAATTTA
Found at i:221500 original size:18 final size:19
Alignment explanation
Indices: 221451--221502 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
221441 TTTTTGGGCT
*
221451 TTTAATTTTTATAATCTAA
1 TTTAATTTTTAAAATCTAA
* *
221470 ATAAATCTTTTAAAAT-TAA
1 TTTAAT-TTTTAAAATCTAA
221489 TTTAATTTTTAAAA
1 TTTAATTTTTAAAA
221503 ACGCAAAGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.30
19 11 0.41
20 8 0.30
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAATTTTTAAAATCTAA
Found at i:221603 original size:24 final size:24
Alignment explanation
Indices: 221576--221649 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
221566 TTTATTGAAC
221576 TTTATATTATTTATTTTTATTTTT
1 TTTATATTATTTATTTTTATTTTT
* *
221600 TTTA-ATTTTTTAATTTTT-TAATTT
1 TTTATATTATTT-ATTTTTAT-TTTT
*
221624 TTT-TCTTATCTTATTTTTTATTTTT
1 TTTATATTAT-TTA-TTTTTATTTTT
221649 T
1 T
221650 AAAAAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
23 7 0.18
24 20 0.51
25 11 0.28
26 1 0.03
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATATTATTTATTTTTATTTTT
Found at i:221608 original size:8 final size:8
Alignment explanation
Indices: 221597--221626 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
221587 TATTTTTATT
221597 TTTTTTAA
1 TTTTTTAA
221605 TTTTTTAA
1 TTTTTTAA
221613 TTTTTTAA
1 TTTTTTAA
221621 TTTTTT
1 TTTTTT
221627 TCTTATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTAA
Found at i:221609 original size:16 final size:15
Alignment explanation
Indices: 221588--221651 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
221578 TATATTATTT
221588 ATTTTTATTTTTTTTA
1 ATTTTT-TTTTTTTTA
*
221604 ATTTTTTAATTTTTTA
1 ATTTTTT-TTTTTTTA
*
221620 ATTTTTTTCTTATCTT-
1 ATTTTTTT-TT-TTTTA
*
221636 ATTTTTTATTTTTTA
1 ATTTTTTTTTTTTTA
221651 A
1 A
221652 AAAAATTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
14 3 0.08
15 4 0.10
16 29 0.74
17 3 0.08
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTTTTTTTTTTTA
Found at i:223219 original size:3 final size:3
Alignment explanation
Indices: 223211--223235 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
223201 TTATACTTTT
223211 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
223236 CAAGGTACAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:224088 original size:19 final size:20
Alignment explanation
Indices: 224066--224118 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
224056 ATAATAAATA
*
224066 AAAAAATAATTAATGTATT-
1 AAAAAATAATTAATATATTG
* *
224085 AAAATATAATTTATATATTG
1 AAAAAATAATTAATATATTG
*
224105 ATAAAAT-ATTAATA
1 AAAAAATAATTAATA
224119 CATTATGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
AAAAAATAATTAATATATTG
Found at i:224264 original size:14 final size:14
Alignment explanation
Indices: 224245--224286 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
224235 TATTATAATT
224245 TTTAAAATACAAAA
1 TTTAAAATACAAAA
* *
224259 TTTAAAATACTAAT
1 TTTAAAATACAAAA
224273 TTTAATAATA-AAAA
1 TTTAA-AATACAAAA
224287 AAAAACTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTAAAATACAAAA
Found at i:224825 original size:14 final size:14
Alignment explanation
Indices: 224808--224859 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
224798 AAATTTAATT
*
224808 ATATAAATATATAA
1 ATATAAATATAAAA
*
224822 ATATGAATATAAAA
1 ATATAAATATAAAA
*
224836 ATA-AAATTTTAAAA
1 ATATAAA-TATAAAA
224850 ATATATAATA
1 ATATA-AATA
224860 ATTTCGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
13 2 0.07
14 24 0.80
15 2 0.07
16 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATATAAATATAAAA
Found at i:225776 original size:6 final size:6
Alignment explanation
Indices: 225765--225791 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
225755 TAATATAGAC
225765 ATTCCA ATTCCA ATTCCA ATTCCA ATT
1 ATTCCA ATTCCA ATTCCA ATTCCA ATT
225792 AAAGAGCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTCCA
Found at i:225940 original size:7 final size:7
Alignment explanation
Indices: 225928--225967 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
225918 ATAATTGACA
225928 TTTTATT
1 TTTTATT
225935 TTTTATT
1 TTTTATT
225942 TTTTA--
1 TTTTATT
*
225947 TTTT-TC
1 TTTTATT
225953 TTTTATT
1 TTTTATT
225960 TTTTATT
1 TTTTATT
225967 T
1 T
225968 AAAAGAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
5 4 0.14
6 4 0.14
7 21 0.72
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:226626 original size:20 final size:21
Alignment explanation
Indices: 226590--226628 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
226580 TATTTTTATT
226590 TAAAATTAATTATAAAATATA
1 TAAAATTAATTATAAAATATA
226611 TAAATATTAA-TA-AAAATA
1 TAAA-ATTAATTATAAAATA
226629 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAATTAATTATAAAATATA
Found at i:226639 original size:13 final size:13
Alignment explanation
Indices: 226621--226657 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
226611 TAAATATTAA
226621 TAAAAATAATTTT
1 TAAAAATAATTTT
226634 TAAAAAT-A-TTT
1 TAAAAATAATTTT
226645 TAAATAATAATTT
1 TAAA-AATAATTT
226658 AAGTTATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.33
12 4 0.19
13 8 0.38
14 2 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAAAATAATTTT
Found at i:226688 original size:6 final size:6
Alignment explanation
Indices: 226677--226702 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
226667 AATTAAATCA
226677 AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
226703 AATTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:229039 original size:20 final size:21
Alignment explanation
Indices: 229001--229039 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
228991 TAAATATAAA
229001 TCATAGTAAAATTTATTTACT
1 TCATAGTAAAATTTATTTACT
* *
229022 TCATA-TAATATTTTTTTA
1 TCATAGTAAAATTTATTTA
229040 ATTTTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (21 bp):
TCATAGTAAAATTTATTTACT
Found at i:229358 original size:19 final size:19
Alignment explanation
Indices: 229336--229376 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
229326 TCAAAACAAT
229336 AAAA-AAATTAATTTTTTGA
1 AAAATAAATTAATTTTTT-A
229355 AAAATAAATTAATTTTTTA
1 AAAATAAATTAATTTTTTA
229374 AAA
1 AAA
229377 TTATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATAAATTAATTTTTTA
Found at i:230295 original size:24 final size:23
Alignment explanation
Indices: 230268--230350 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 23
230258 AATTTTAAAC
*
230268 TTTAAAATAAAAAGTATTTAATAT
1 TTTAAAATAAAATGTATTT-ATAT
* **
230292 TTTAATATTTAATGTATTTCATAT
1 TTTAAAATAAAATGTATTT-ATAT
230316 TATT-AAATATAAATGT-TTTATAT
1 T-TTAAAATA-AAATGTATTTATAT
230339 TTTAATAATAAA
1 TTTAA-AATAAA
230351 TTATTAATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
22 2 0.04
23 8 0.17
24 30 0.64
25 7 0.15
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTAAAATAAAATGTATTTATAT
Found at i:230351 original size:22 final size:24
Alignment explanation
Indices: 230273--230355 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 24
230263 TAAACTTTAA
*
230273 AATAA-AAA-GTATTTAATATTTT
1 AATAATAAATGTATTTCATATTTT
* *
230295 AATATTTAATGTATTTCATATTATT
1 AATAATAAATGTATTTCATATT-TT
230320 AA-ATATAAATGT-TTT-ATATTTT
1 AATA-ATAAATGTATTTCATATTTT
230342 AATAATAAAT-TATT
1 AATAATAAATGTATT
230356 AATATTAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
21 1 0.02
22 16 0.32
23 8 0.16
24 15 0.30
25 10 0.20
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (24 bp):
AATAATAAATGTATTTCATATTTT
Found at i:232794 original size:32 final size:31
Alignment explanation
Indices: 232702--232798 Score: 88
Period size: 32 Copynumber: 2.9 Consensus size: 31
232692 CTCGAATTGT
* *
232702 TTATCTTT-AAGGCTAAGGTATAACCTTATAA
1 TTATCTTTCAAGGCTAAGATAGAACCTT-TAA
* *
232733 TCCTATCTTTTACAAAGACTAAAATAGAACCTTTACA
1 T--TATC-TTT-C-AAGGCTAAGATAGAACCTTTA-A
232770 TTATCTTTCAAGGCTAAGATAGAACCTTT
1 TTATCTTTCAAGGCTAAGATAGAACCTTT
232799 TAATCACTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
31 1 0.02
32 18 0.34
33 5 0.09
34 6 0.11
35 4 0.08
36 2 0.04
37 17 0.32
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (31 bp):
TTATCTTTCAAGGCTAAGATAGAACCTTTAA
Found at i:233287 original size:14 final size:14
Alignment explanation
Indices: 233232--233291 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
233222 ACACTGTATC
233232 GATACATGAATAGT
1 GATACATGAATAGT
*
233246 GATGAACAGTGATTTA-T
1 GAT--ACA-TGA-ATAGT
233263 CGATACATGAATAGT
1 -GATACATGAATAGT
*
233278 GATACGTGAATAGT
1 GATACATGAATAGT
233292 TATAAACAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
14 18 0.49
15 4 0.11
16 6 0.16
17 4 0.11
18 5 0.14
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (14 bp):
GATACATGAATAGT
Found at i:233352 original size:52 final size:52
Alignment explanation
Indices: 233205--233355 Score: 181
Period size: 46 Copynumber: 3.0 Consensus size: 52
233195 GGTGGACTCA
* *
233205 ATGTATCGATACTATTCACACTGTATCGATACATGAATAGTGATGAACAGTG
1 ATGTATCGATACTATTCGCAATGTATCGATACATGAATAGTGATGAACAGTG
* * * *
233257 ATTTATCGATAC-A-T-G-AA--TAGT-GATACGTGAATAGTTATAAACAGTG
1 ATGTATCGATACTATTCGCAATGTA-TCGATACATGAATAGTGATGAACAGTG
*
233303 ATGTATCGATACTATTCGCAATGTATCGATACATGAACAGTGATGAACAGTG
1 ATGTATCGATACTATTCGCAATGTATCGATACATGAATAGTGATGAACAGTG
233355 A
1 A
233356 AAATGAGATT
Statistics
Matches: 80, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
46 35 0.44
47 2 0.03
48 2 0.03
49 1 0.01
50 3 0.04
51 2 0.03
52 35 0.44
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACTATTCGCAATGTATCGATACATGAATAGTGATGAACAGTG
Found at i:233400 original size:13 final size:13
Alignment explanation
Indices: 233382--233406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
233372 CTGCCAGTTT
233382 ATGTATCGATACA
1 ATGTATCGATACA
233395 ATGTATCGATAC
1 ATGTATCGATAC
233407 TAAGCAAAAT
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):
ATGTATCGATACA
Found at i:233931 original size:21 final size:19
Alignment explanation
Indices: 233907--233961 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
233897 AATTTTATAA
*
233907 AATTTTATGTTAAATTTATTT
1 AATTTTATATT-AATTT-TTT
*
233928 AATTATATATTAATTTTTT
1 AATTTTATATTAATTTTTT
*
233947 AATTTAATA-TAATTT
1 AATTTTATATTAATTT
233962 AATGAACTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 5 0.17
21 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTTATATTAATTTTTT
Found at i:235327 original size:2 final size:2
Alignment explanation
Indices: 235322--235361 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
235312 GTTCCCCCCC
235322 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
235362 GAATCTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:240710 original size:31 final size:30
Alignment explanation
Indices: 240674--240831 Score: 99
Period size: 31 Copynumber: 5.0 Consensus size: 30
240664 TAATTGTTAC
240674 ATATTATATTTATATTATAATTATATTTAAA
1 ATATTAT-TTTATATTATAATTATATTTAAA
240705 ATATTATTTTTATATTATAATT-TATATT-AA
1 ATATTA-TTTTATATTATAATTATAT-TTAAA
* * * * *
240735 TTATT-TGTTATATTATTTATTTATTTTTATTA
1 ATATTATTTTATATTA--TAATTATATTTA-AA
* *
240767 ATATTATTTTTTA-TATAATATATTTTTTAATA
1 ATATTATTTTATATTATAAT-TA-TATTTAA-A
*
240799 ATATTATATTTATATGATATAAATATATATTAA
1 ATATTAT-TTTATAT--TATAATTATAT-TTAA
240832 TTAAATAATT
Statistics
Matches: 98, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
28 9 0.09
30 18 0.18
31 26 0.27
32 22 0.22
33 10 0.10
34 2 0.02
35 6 0.06
36 5 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
ATATTATTTTATATTATAATTATATTTAAA
Found at i:240732 original size:20 final size:22
Alignment explanation
Indices: 240674--240738 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 22
240664 TAATTGTTAC
240674 ATATTAT-ATTTATATTATAATT
1 ATATTATAATTTATATTAT-ATT
* *
240696 ATATT-TAA--AATATTATTTTT
1 ATATTATAATTTATATTA-TATT
240716 ATATTATAATTTATATTA-ATT
1 ATATTATAATTTATATTATATT
240737 AT
1 AT
240739 TTGTTATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
20 13 0.38
21 9 0.26
22 6 0.18
23 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTATAATTTATATTATATT
Found at i:240745 original size:16 final size:16
Alignment explanation
Indices: 240726--240756 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
240716 ATATTATAAT
240726 TTATATTAATTATTTG
1 TTATATTAATTATTTG
*
240742 TTATATTATTTATTT
1 TTATATTAATTATTT
240757 ATTTTTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTATATTAATTATTTG
Found at i:240749 original size:12 final size:12
Alignment explanation
Indices: 240729--240782 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
240719 TTATAATTTA
240729 TATTA-ATTATT
1 TATTATATTATT
*
240740 TGTTATATTATT
1 TATTATATTATT
240752 TATT-TATT-TT
1 TATTATATTATT
240762 TATTAATATTATT
1 TATT-ATATTATT
*
240775 TTTTATAT
1 TATTATAT
240783 AATATATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 6 0.17
11 8 0.22
12 17 0.47
13 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TATTATATTATT
Found at i:240770 original size:23 final size:23
Alignment explanation
Indices: 240708--240780 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
240698 ATTTAAAATA
* *
240708 TTATTTTTA-TATTATAATTTAT
1 TTATTTTTATTAATATTATTTAT
*
240730 ATTAATTATTTGTT-ATATTATTTAT
1 -TT-ATT-TTTATTAATATTATTTAT
240755 TTATTTTTATTAATATTATTT-T
1 TTATTTTTATTAATATTATTTAT
240777 TTAT
1 TTAT
240781 ATAATATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
22 10 0.24
23 14 0.33
24 5 0.12
25 12 0.29
26 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (23 bp):
TTATTTTTATTAATATTATTTAT
Found at i:240771 original size:16 final size:16
Alignment explanation
Indices: 240752--240809 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
240742 TTATATTATT
240752 TATTTATTTTTATTAA
1 TATTTATTTTTATTAA
240768 TA-TTATTTTTTATATAA
1 TATTTA-TTTTTAT-TAA
* *
240785 TATAT-TTTTTAATAA
1 TATTTATTTTTATTAA
240800 TATTATATTT
1 TATT-TATTT
240810 ATATGATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
15 9 0.26
16 16 0.47
17 8 0.24
18 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTATTTTTATTAA
Found at i:240773 original size:19 final size:18
Alignment explanation
Indices: 240728--240805 Score: 65
Period size: 20 Copynumber: 4.4 Consensus size: 18
240718 ATTATAATTT
*
240728 ATATTAATTATTTGTTATA
1 ATATTATTTATTT-TTATA
*
240747 TTATTTATTTATTTTTATTA
1 ATA-TTATTTATTTTTA-TA
*
240767 ATATTATTT-TTTATATA
1 ATATTATTTATTTTTATA
*
240784 ATA-TA-TT-TTTTAATA
1 ATATTATTTATTTTTATA
240799 ATATTAT
1 ATATTAT
240806 ATTTATATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
15 11 0.22
16 4 0.08
17 5 0.10
18 5 0.10
19 11 0.22
20 13 0.27
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (18 bp):
ATATTATTTATTTTTATA
Found at i:240963 original size:54 final size:54
Alignment explanation
Indices: 240899--241008 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
240889 GCTGCTCTAA
240899 ACTTTGTCCTGTCTGGTACTACCATACTGTAAAGCCAACTATGAAGCGGAGAAG
1 ACTTTGTCCTGTCTGGTACTACCATACTGTAAAGCCAACTATGAAGCGGAGAAG
240953 ACTTTGTCCTGTCTGGTACTACCATACTGTAAAGCCAACTATGAAGCGGAGAAG
1 ACTTTGTCCTGTCTGGTACTACCATACTGTAAAGCCAACTATGAAGCGGAGAAG
241007 AC
1 AC
241009 ACAAAACGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (54 bp):
ACTTTGTCCTGTCTGGTACTACCATACTGTAAAGCCAACTATGAAGCGGAGAAG
Found at i:244179 original size:6 final size:6
Alignment explanation
Indices: 244170--244208 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
244160 AATAATTAAA
*
244170 ATTTAT ATTTAT ATTTAA ATATT-T ATTTAT ATTTAT ATT
1 ATTTAT ATTTAT ATTTAT AT-TTAT ATTTAT ATTTAT ATT
244209 ATACATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 2 0.07
6 25 0.86
7 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:246301 original size:23 final size:23
Alignment explanation
Indices: 246275--246325 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
246265 ACAAAATATT
246275 ATATGATATGA-TATTAACGTATA
1 ATATGATATGAGTATTAACGTA-A
* *
246298 ATATGTTATGAGTTATTAATGTAA
1 ATATGATATGAG-TATTAACGTAA
246322 ATAT
1 ATAT
246326 ATTTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.42
24 5 0.21
25 9 0.38
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (23 bp):
ATATGATATGAGTATTAACGTAA
Found at i:255625 original size:14 final size:14
Alignment explanation
Indices: 255623--255678 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
255613 TATTTAATAA
255623 AATATAAATATATTT
1 AATA-AAATATATTT
255638 AATAAAATATA-TT
1 AATAAAATATATTT
* *
255651 --TAAAATACATCT
1 AATAAAATATATTT
255663 AATAAAATATATTT
1 AATAAAATATATTT
255677 AA
1 AA
255679 AACTGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
11 8 0.24
12 1 0.03
13 2 0.06
14 19 0.56
15 4 0.12
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAAAATATATTT
Found at i:255633 original size:20 final size:20
Alignment explanation
Indices: 255608--255648 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
255598 TTAATATTTA
255608 AAATATATTTAATAAAATAT
1 AAATATATTTAATAAAATAT
255628 AAATATATTTAATAAAATAT
1 AAATATATTTAATAAAATAT
255648 A
1 A
255649 TTTAAAATAC
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATATATTTAATAAAATAT
Found at i:255656 original size:25 final size:25
Alignment explanation
Indices: 255601--255680 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 25
255591 AATCGAATTA
255601 ATATTTAAAATATATTTAAT-AAA-
1 ATATTTAAAATATATTTAATAAAAT
255624 ATA--T-AAATATATTTAATAAAAT
1 ATATTTAAAATATATTTAATAAAAT
* *
255646 ATATTTAAAATACATCTAATAAAAT
1 ATATTTAAAATATATTTAATAAAAT
255671 ATATTTAAAA
1 ATATTTAAAA
255681 CTGAAAAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
20 13 0.26
21 4 0.08
22 3 0.06
23 3 0.06
24 1 0.02
25 26 0.52
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATTTAAAATATATTTAATAAAAT
Found at i:258674 original size:25 final size:24
Alignment explanation
Indices: 258646--258697 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
258636 AAAATTATTT
*
258646 ATAATT-TTTATTAAATATAATAAAA
1 ATAATTATTTAAT-AATATAA-AAAA
*
258671 ATAATTATTTAATATTATAAAAAA
1 ATAATTATTTAATAATATAAAAAA
258695 ATA
1 ATA
258698 CCTTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 12 0.50
26 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAATTATTTAATAATATAAAAAA
Found at i:259189 original size:12 final size:13
Alignment explanation
Indices: 259157--259198 Score: 59
Period size: 12 Copynumber: 3.2 Consensus size: 13
259147 ATTAAAGATT
*
259157 ATATAAAAAAATCA
1 ATATAAAAATAT-A
259171 ATATAAAAATATA
1 ATATAAAAATATA
259184 AT-TAAAAATATA
1 ATATAAAAATATA
259196 ATA
1 ATA
259199 AGACATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.46
13 3 0.12
14 11 0.42
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
ATATAAAAATATA
Found at i:259796 original size:15 final size:15
Alignment explanation
Indices: 259772--259805 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
259762 AATAATATAG
*
259772 ATAATGATATACAAT
1 ATAATAATATACAAT
*
259787 ATAATAATATAGAAT
1 ATAATAATATACAAT
259802 ATAA
1 ATAA
259806 GTGTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (15 bp):
ATAATAATATACAAT
Found at i:260210 original size:10 final size:10
Alignment explanation
Indices: 260195--260252 Score: 56
Period size: 10 Copynumber: 6.4 Consensus size: 10
260185 ATGTTTAAGA
260195 TATATATATT
1 TATATATATT
*
260205 TATATAAATT
1 TATATATATT
260215 T-TAT-TA--
1 TATATATATT
260221 TATATAT-TT
1 TATATATATT
260230 TA-ATATATT
1 TATATATATT
*
260239 TATATATTTT
1 TATATATATT
260249 TATA
1 TATA
260253 ACTTTTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
6 1 0.03
7 3 0.08
8 6 0.15
9 9 0.23
10 20 0.51
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATATATT
Found at i:260223 original size:14 final size:14
Alignment explanation
Indices: 260204--260237 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
260194 ATATATATAT
260204 TTATATAAATTTTA
1 TTATATAAATTTTA
*
260218 TTATATATATTTTA
1 TTATATAAATTTTA
*
260232 ATATAT
1 TTATAT
260238 TTATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:261380 original size:17 final size:16
Alignment explanation
Indices: 261346--261399 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
261336 AAAATTATTT
261346 ACTTATTTTTTAAATTTTA
1 ACTTATTTTTT---TTTTA
261365 ACTTATTTTTTCTTTTA
1 ACTTATTTTTT-TTTTA
*
261382 ACATATTTATTTTTTTA
1 ACTTATTT-TTTTTTTA
261399 A
1 A
261400 AGAAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 18 0.56
18 3 0.09
19 11 0.34
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (16 bp):
ACTTATTTTTTTTTTA
Found at i:263621 original size:86 final size:85
Alignment explanation
Indices: 263452--263618 Score: 277
Period size: 86 Copynumber: 2.0 Consensus size: 85
263442 AAAACAATTT
*
263452 TATATTCATTAAAAAAAGAAAGGAAGAAAATTATGGAATTGCAAGGGAGAAAAAAAATAAAGTAA
1 TATATTCATAAAAAAAAGAAAGGAAGAAAATTATGGAATTGCAA-GGAGAAAAAAAATAAAGTAA
263517 AAGTTTAATTTCCTTTTTTTC
65 AAGTTTAATTTCCTTTTTTTC
* *
263538 TATATTCATAAAAAAAAGAAAGGAAGAAAATTATGGAATTGCAA-GTG-AAAATAATAAAGTAAA
1 TATATTCATAAAAAAAAGAAAGGAAGAAAATTATGGAATTGCAAGGAGAAAAAAAATAAAGTAAA
263601 AGTTTAA-TTCCTTTTTTT
66 AGTTTAATTTCCTTTTTTT
263619 TTTCCTTGTA
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
82 11 0.14
83 22 0.28
84 2 0.03
86 43 0.55
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.31
Consensus pattern (85 bp):
TATATTCATAAAAAAAAGAAAGGAAGAAAATTATGGAATTGCAAGGAGAAAAAAAATAAAGTAAA
AGTTTAATTTCCTTTTTTTC
Found at i:264571 original size:2 final size:2
Alignment explanation
Indices: 264564--264592 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
264554 TTTTATTATT
264564 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 T
264593 TTTGAATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:280186 original size:16 final size:16
Alignment explanation
Indices: 280162--280214 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
280152 AAATTTTAGA
* *
280162 TTAATTTTAGATTATT
1 TTAAGTTTAAATTATT
280178 TTAAGTTTAAATTATT
1 TTAAGTTTAAATTATT
*
280194 TT-AGATTTAAGTTACTT
1 TTAAG-TTTAAATTA-TT
280211 TTAA
1 TTAA
280215 TTAAAATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 2 0.06
16 24 0.77
17 4 0.13
18 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (16 bp):
TTAAGTTTAAATTATT
Found at i:280278 original size:15 final size:15
Alignment explanation
Indices: 280229--280283 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
280219 AATTTCTTCG
*
280229 AATTTAGAATATTTTA
1 AATTT-GAATAATTTA
* *
280245 AATTCGAATCATCTTA
1 AATTTGAATAAT-TTA
280261 AATTTGAATAATTTA
1 AATTTGAATAATTTA
280276 AATTTGAA
1 AATTTGAA
280284 ACTCGAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 16 0.48
16 17 0.52
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (15 bp):
AATTTGAATAATTTA
Found at i:284148 original size:18 final size:18
Alignment explanation
Indices: 284125--284162 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
284115 TATATATGTT
284125 GTATTATTGAGGCTTTTC
1 GTATTATTGAGGCTTTTC
284143 GTATTATTGAGGCTTTTC
1 GTATTATTGAGGCTTTTC
284161 GT
1 GT
284163 CTATTAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.24, T:0.50
Consensus pattern (18 bp):
GTATTATTGAGGCTTTTC
Found at i:285956 original size:20 final size:21
Alignment explanation
Indices: 285904--285956 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
285894 TTATTTATAA
*
285904 ATTAATAAA-AAATATTATTT
1 ATTAATAAATATATATTATTT
** *
285924 ATTAATATTTATATATTTTTT
1 ATTAATAAATATATATTATTT
285945 A-TAATAAATATA
1 ATTAATAAATATA
285957 AATAAAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTAATAAATATATATTATTT
Found at i:286511 original size:27 final size:27
Alignment explanation
Indices: 286479--286552 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
286469 ATTAATATTT
286479 TTATATATTATAAATATATTTAAAATA
1 TTATATATTATAAATATATTTAAAATA
*
286506 TTATATATTTATATAA-AT-TTTAATATA
1 TTATATA-TTATA-AATATATTTAAAATA
* *
286533 TTA-ATTTTAT-ATTATATTTA
1 TTATATATTATAAATATATTTA
286553 TATAACGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 1 0.03
24 2 0.05
25 8 0.20
26 2 0.05
27 18 0.45
28 7 0.17
29 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTATATATTATAAATATATTTAAAATA
Found at i:286522 original size:20 final size:20
Alignment explanation
Indices: 286483--286522 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
286473 ATATTTTTAT
*
286483 ATATTATAAATATATTTAAA
1 ATATTATAAATATATATAAA
* *
286503 ATATTATATATTTATATAAA
1 ATATTATAAATATATATAAA
286523 TTTTAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTATAAATATATATAAA
Found at i:286861 original size:11 final size:11
Alignment explanation
Indices: 286831--286861 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
286821 TTCTTCTTCT
286831 TTTTTTTTTCA
1 TTTTTTTTTCA
*
286842 ATTTTTTTTCA
1 TTTTTTTTTCA
286853 TTTTTTTTT
1 TTTTTTTTT
286862 TTTTGGTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:289896 original size:20 final size:22
Alignment explanation
Indices: 289857--289897 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
289847 TTAATTAAGG
289857 TAATATATTAAATAAATTTTTT
1 TAATATATTAAATAAATTTTTT
289879 TAATA-ATTAAAT-AATTTTT
1 TAATATATTAAATAAATTTTT
289898 AAATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATATTAAATAAATTTTTT
Found at i:289902 original size:19 final size:21
Alignment explanation
Indices: 289858--289904 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
289848 TAATTAAGGT
*
289858 AATATATTAAATAAATTTTTTT
1 AATA-ATTAAATAAATTTTTTA
289880 AATAATTAAAT-AA-TTTTTA
1 AATAATTAAATAAATTTTTTA
289899 AATAAT
1 AATAAT
289905 ATTTATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 2 0.08
21 7 0.29
22 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATAATTAAATAAATTTTTTA
Found at i:289904 original size:22 final size:22
Alignment explanation
Indices: 289857--289907 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
289847 TTAATTAAGG
*
289857 TAATATATTAAATAAATTTTTT
1 TAATATATTAAATAAATTTTTA
289879 TAATA-ATTAAAT-AATTTTTA
1 TAATATATTAAATAAATTTTTA
289899 -AATAATATT
1 TAAT-ATATT
289908 TATAAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 8 0.31
21 10 0.38
22 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATATTAAATAAATTTTTA
Found at i:290187 original size:4 final size:4
Alignment explanation
Indices: 290178--290202 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
290168 GTAAGAATAC
290178 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
290203 TCCTCTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:292267 original size:18 final size:18
Alignment explanation
Indices: 292246--292294 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 18
292236 ATATATTAAA
292246 ATATTATAAATTATTTTT
1 ATATTATAAATTATTTTT
* *
292264 ATATTA-ATATT-TATTT
1 ATATTATAAATTATTTTT
*
292280 ATTTTAT-AATTATTT
1 ATATTATAAATTATTT
292295 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
16 12 0.50
17 6 0.25
18 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTATAAATTATTTTT
Done.