Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold121
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: 1076282
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 28062 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:971906 original size:10 final size:11
Alignment explanation
Indices: 971883--971911 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
971873 CTATTGAAAT
971883 TTATCTTGCAA
1 TTATCTTGCAA
971894 TTATCTT-CAA
1 TTATCTTGCAA
971904 TTATCTTG
1 TTATCTTG
971912 AAAATAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (11 bp):
TTATCTTGCAA
Found at i:974950 original size:20 final size:21
Alignment explanation
Indices: 974922--974973 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
974912 TTGCAAGCAC
* *
974922 GTATTGATACATTAATTTA-T
1 GTATCGATACATTAACTTATT
974942 GTATCGATACATTAACTTATT
1 GTATCGATACATTAACTTATT
974963 GTATCGATACA
1 GTATCGATACA
974974 AATTGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (21 bp):
GTATCGATACATTAACTTATT
Found at i:980064 original size:40 final size:39
Alignment explanation
Indices: 980016--980093 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
980006 AGTAAAAAGA
* *
980016 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCAATACATT
* * *
980055 CATACATGTATCGGTATATTGAAAAATGTATCAATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCAATACAT
980094 CTGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCAATACATT
Found at i:980083 original size:20 final size:20
Alignment explanation
Indices: 980019--980093 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
980009 AAAAAGACAT
*
980019 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * *
980039 AATATATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* * *
980059 CATGTATCGGTATATTGAAA
1 AATGTATCGATACATTGAAA
*
980079 AATGTATCAATACAT
1 AATGTATCGATACAT
980094 CTGGGTAAAA
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:980704 original size:32 final size:32
Alignment explanation
Indices: 980656--980717 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
980646 AAAAAAATGG
* *
980656 TGCCACTAACTTGTGTGGGCTTTGAAAAGAGT
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAGT
980688 TGCCACCAACTCGTGTGGGCTTTGAAAAGA
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGA
980718 ATCAAGCAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (32 bp):
TGCCACCAACTCGTGTGGGCTTTGAAAAGAGT
Found at i:981867 original size:28 final size:28
Alignment explanation
Indices: 981759--982402 Score: 880
Period size: 28 Copynumber: 22.6 Consensus size: 28
981749 AAAACCATTA
* *
981759 ACTTATGGGCTTTGAAATGAGTTGCCACCG
1 ACTTGTGGGCTTTGAAA-GAG-TGCCACTG
* *
981789 ACTTGTGTGGGTTATGAAAGGAGTGCCACTA
1 ACTTGTG-GGCTT-TGAAA-GAGTGCCACTG
981820 ACTTGTGTGGGCTTTGAAAG-GATGCCACTG
1 AC-T-TGTGGGCTTTGAAAGAG-TGCCACTG
*
981850 ACTTGTGGGCTTTAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
* *
981878 ACTCGTGGGC-TTGAAAG-GTGCCACTA
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
*
981904 ACTTGTGGGCTTTGAAAGAGTGCCACTA
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
*
981932 ACTTGTGGGCTTTGAAAAGAGTGCCACTT
1 ACTTGTGGGCTTTG-AAAGAGTGCCACTG
*
981961 AATTGTGGGCTTTGAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTG-AAAGAGTGCCACTG
*
981990 ACTTGTGGGCTTTGAAAAAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
*
982018 ACTTGTGGGCTTTGAAAAAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
* *
982046 ACTTGTAGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
982074 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTG-AAAGAGTGCCACTG
* * *
982103 ATTTGTGGGCTTTGAAAGGGTGCCATTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
* *
982131 ACTTATGGGCTTTGAAAAGAGTGCCACTA
1 ACTTGTGGGCTTTG-AAAGAGTGCCACTG
* * *
982160 AATTGTGGGCTTTGAAAGGGTGTCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
982188 ACTTGTGGGCTTTGGAAAGAGTGCCACTG
1 ACTTGTGGGCTTT-GAAAGAGTGCCACTG
*
982217 AATTGTGGGCTTTGAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
982245 ACTTGTGGGCTTTGAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
* *
982273 ATTTGTGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
982301 ACTTGTGGGCTTTGAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
*
982329 ACTTGTGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTG
**
982357 ACTCATGGGCTTTGAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTG-AAAGAGTGCCACTG
*
982386 ACTCGTGGGCTTTGAAA
1 ACTTGTGGGCTTTGAAA
982403 AGGATGAACA
Statistics
Matches: 552, Mismatches: 49, Indels: 28
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.03
27 13 0.02
28 316 0.57
29 156 0.28
30 16 0.03
31 17 0.03
32 13 0.02
33 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (28 bp):
ACTTGTGGGCTTTGAAAGAGTGCCACTG
Found at i:981975 original size:57 final size:56
Alignment explanation
Indices: 981759--982402 Score: 880
Period size: 57 Copynumber: 11.3 Consensus size: 56
981749 AAAACCATTA
* * * *
981759 ACTTATGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGTTATGAAAGGAGTGCCACTA
1 ACTTGTGGGCTTTGAAA-GAG-TGCCACTGACTTGTG-GGCTT-TGAAA-GAGTGCCACTG
*
981820 ACTTGTGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTAAAAGAGTGCCACTG
1 AC-T-TGTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
* * *
981878 ACTCGTGGGC-TTGAAAG-GTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTA
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
* *
981932 ACTTGTGGGCTTTGAAAAGAGTGCCACTTAATTGTGGGCTTTGAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTG
* *
981990 ACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
* *
982046 ACTTGTAGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTG
* * * * *
982103 ATTTGTGGGCTTTGAAAGGGTGCCATTGACTTATGGGCTTTGAAAAGAGTGCCACTA
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTG
* * *
982160 AATTGTGGGCTTTGAAAGGGTGTCACTGACTTGTGGGCTTTGGAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTT-GAAAGAGTGCCACTG
*
982217 AATTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
* *
982273 ATTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
* **
982329 ACTTGTGGGCTTTGAAAGGGTGCCACTGACTCATGGGCTTTGAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTG
*
982386 ACTCGTGGGCTTTGAAA
1 ACTTGTGGGCTTTGAAA
982403 AGGATGAACA
Statistics
Matches: 534, Mismatches: 40, Indels: 22
0.90 0.07 0.04
Matches are distributed among these distances:
54 42 0.08
55 11 0.02
56 170 0.32
57 231 0.43
58 40 0.07
59 4 0.01
60 4 0.01
61 17 0.03
62 2 0.00
63 13 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (56 bp):
ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
Found at i:983638 original size:13 final size:12
Alignment explanation
Indices: 983620--983678 Score: 82
Period size: 13 Copynumber: 4.8 Consensus size: 12
983610 ACCCTTTTCT
983620 TTTTTTTTTTTG
1 TTTTTTTTTTTG
* *
983632 CTATTTTTTCTTG
1 -TTTTTTTTTTTG
983645 TTTTTTTTTTTG
1 TTTTTTTTTTTG
983657 TTTTTTTGTTTTG
1 TTTTTTT-TTTTG
983670 TTTTTTTTT
1 TTTTTTTTT
983679 GTAAAAGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
12 19 0.46
13 22 0.54
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:983648 original size:25 final size:25
Alignment explanation
Indices: 983620--983678 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
983610 ACCCTTTTCT
983620 TTTTTTTTTTTGCTATTTTT-TCTTG
1 TTTTTTTTTTTG-TATTTTTGTCTTG
* *
983645 TTTTTTTTTTTGTTTTTTTGTTTTG
1 TTTTTTTTTTTGTATTTTTGTCTTG
983670 TTTTTTTTT
1 TTTTTTTTT
983679 GTAAAAGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 6 0.19
25 25 0.81
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.86
Consensus pattern (25 bp):
TTTTTTTTTTTGTATTTTTGTCTTG
Found at i:983678 original size:23 final size:24
Alignment explanation
Indices: 983620--983681 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
983610 ACCCTTTTCT
983620 TTTTTTTTTTTGCTATTTTTTCTTG
1 TTTTTTTTTTTG-TATTTTTTCTTG
*
983645 TTTTTTTTTTTGT-TTTTTTGTT-
1 TTTTTTTTTTTGTATTTTTTCTTG
983667 TTGTTTTTTTTTGTA
1 TT-TTTTTTTTTGTA
983682 AAAGACACCC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
22 2 0.06
23 19 0.56
24 1 0.03
25 12 0.35
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.84
Consensus pattern (24 bp):
TTTTTTTTTTTGTATTTTTTCTTG
Found at i:997709 original size:20 final size:20
Alignment explanation
Indices: 997635--997706 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
997625 AAAAAGACAT
* *
997635 AATGTATCAATACATTGAAG
1 AATGTATCGATACATTGAAA
* * *
997655 AATATATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
997675 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
997695 AATGTATCGATA
1 AATGTATCGATA
997707 TATCTAGGTA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:998103 original size:2 final size:2
Alignment explanation
Indices: 998096--998126 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
998086 ATTGAATGAT
*
998096 TA TA TA TA AA 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 T
998127 TTAGTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:998953 original size:2 final size:2
Alignment explanation
Indices: 998946--998975 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
998936 ACCTTAATTT
998946 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
998976 GAAAGATCCT
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):
TA
Found at i:999199 original size:3 final size:3
Alignment explanation
Indices: 999191--999220 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
999181 ATTAACGTTT
999191 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
999221 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:999690 original size:7 final size:7
Alignment explanation
Indices: 999680--999710 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
999670 ATATTTAATA
999680 AATTTAT
1 AATTTAT
999687 AATTTAT
1 AATTTAT
999694 AATTTAT
1 AATTTAT
999701 AATTTAT
1 AATTTAT
999708 AAT
1 AAT
999711 ATTTTAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTAT
Found at i:1002325 original size:18 final size:18
Alignment explanation
Indices: 1002302--1002347 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1002292 TAGGTCATAC
*
1002302 ATATATATATGTATGTAT
1 ATATATATATATATGTAT
1002320 ATATATATATATATGTAT
1 ATATATATATATATGTAT
* *
1002338 GTATTTATAT
1 ATATATATAT
1002348 CCAATATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (18 bp):
ATATATATATATATGTAT
Found at i:1002330 original size:22 final size:22
Alignment explanation
Indices: 1002302--1002347 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1002292 TAGGTCATAC
1002302 ATATATATATGTATGTATATAT
1 ATATATATATGTATGTATATAT
*
1002324 ATATATATATGTATGTATTTAT
1 ATATATATATGTATGTATATAT
1002346 AT
1 AT
1002348 CCAATATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
ATATATATATGTATGTATATAT
Found at i:1002521 original size:7 final size:7
Alignment explanation
Indices: 1002505--1002539 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
1002495 AGAGAGATTA
*
1002505 TAAATAT
1 TAAATTT
1002512 TAAATTT
1 TAAATTT
1002519 TAAATTT
1 TAAATTT
1002526 TAAATTT
1 TAAATTT
1002533 TAAATTT
1 TAAATTT
1002540 ATTAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TAAATTT
Found at i:1002645 original size:37 final size:37
Alignment explanation
Indices: 1002592--1002664 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
1002582 ATTAAGTATG
*
1002592 TTATTTTAGTTCCAAAGAGAT-AGGAACGGTAGTTCCC
1 TTATTCTAGTTCCAAAGAG-TGAGGAACGGTAGTTCCC
* *
1002629 TTATTCTAGTTTCAAAGAGTGAGGAATGGTAGTTCC
1 TTATTCTAGTTCCAAAGAGTGAGGAACGGTAGTTCC
1002665 ATTAGCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (37 bp):
TTATTCTAGTTCCAAAGAGTGAGGAACGGTAGTTCCC
Found at i:1003365 original size:23 final size:22
Alignment explanation
Indices: 1003337--1003379 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1003327 TAAAACTCCA
1003337 TCAATTTCAATAAAAACCAAAAC
1 TCAATTT-AATAAAAACCAAAAC
* *
1003360 TCAATTTAATTAAACCCAAA
1 TCAATTTAATAAAAACCAAA
1003380 TGGAAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (22 bp):
TCAATTTAATAAAAACCAAAAC
Found at i:1009388 original size:52 final size:52
Alignment explanation
Indices: 1009310--1009459 Score: 223
Period size: 52 Copynumber: 2.9 Consensus size: 52
1009300 CGAAATATGA
1009310 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
* * *
1009362 AAATTTGCCTGTATGTATCGATACATT-ATAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGA-ATAGTGTATCGATACATCTGGGC
**
1009414 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTGAAT-AGTGTATCGATACAT
1009460 TTGAGTAATG
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
Found at i:1009536 original size:33 final size:33
Alignment explanation
Indices: 1009499--1009565 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1009489 AGTAGCTTAA
1009499 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1009532 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1009565 A
1 A
1009566 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1009539 original size:13 final size:13
Alignment explanation
Indices: 1009521--1009545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1009511 CAAAAAAATA
1009521 TGTATCGATACAT
1 TGTATCGATACAT
1009534 TGTATCGATACA
1 TGTATCGATACA
1009546 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1010510 original size:52 final size:55
Alignment explanation
Indices: 1010381--1010531 Score: 191
Period size: 55 Copynumber: 2.8 Consensus size: 55
1010371 AAGTGATAAA
* * * * * *
1010381 GATGTCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAGAG
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAGAG
* * * *
1010436 GATGTCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-GAATG-G
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAGAG
1010489 G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1010532 GTAATGAGGA
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
52 39 0.46
53 2 0.02
54 4 0.05
55 40 0.47
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (55 bp):
GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAGAG
Found at i:1010785 original size:344 final size:344
Alignment explanation
Indices: 1010145--1010877 Score: 1306
Period size: 344 Copynumber: 2.1 Consensus size: 344
1010135 GTCTTGCAAT
* * * * * *
1010145 GTGCCACTATGCAGATTCAAGGCCTG-TCACACTGGACTTAAAGGTGATGAGGATGAAGAGTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCT-ATATTGGACTTAAAGGTAATGAGGATGAAGAGTGAT
*
1010209 AAAAGGACCAATACATTGATTCTCGGCCAACGATATTGGGTTTAGAGATGAGAAAAGGGATAAAG
65 AAAAGGACCAATACATTGATTCACGGCCAACGATATTGGGTTTAGAGATGAGAAAAGGGATAAAG
1010274 GAGCCAATATGCGGCTAGCGATATTAGGCTCGAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
130 GAGCCAATATGCGGCTAGCGATATTAGGCTCGAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
* *
1010339 AGCGACATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGTCAATATGTTGATTCACGG
195 AGCGACATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGA
*
1010404 CCAACGATATTGGGCTTAAAGATGAGAAAGAGGATGTCAATATGCTGATTCAAGGCCAGCTACAT
260 CCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATATGCTGATTCAAGGCCAGCTACAT
* **
1010469 TGAACTTAAAGATGGAATGG
325 TGAACTTAAAGATGAAAAAG
*
1010489 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTAATGAGGATGAAGAGTGATG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTAATGAGGATGAAGAGTGATA
*
1010554 AAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTTAGAGATGAGAAAAGGGATAAAGG
66 AAAGGACCAATACATTGATTCACGGCCAACGATATTGGGTTTAGAGATGAGAAAAGGGATAAAGG
1010619 AGCCAATATGCGGCTAGCGATATTAGGCTCGAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCA
131 AGCCAATATGCGGCTAGCGATATTAGGCTCGAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCA
1010684 GCGACATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGAC
196 GCGACATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGAC
*
1010749 CAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATT
261 CAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATATGCTGATTCAAGGCCAGCTACATT
1010814 GAACTTAAAGATGAAAAAG
326 GAACTTAAAGATGAAAAAG
1010833 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
1010878 GCCAATGTGC
Statistics
Matches: 372, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
344 371 1.00
345 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.23
Consensus pattern (344 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTAATGAGGATGAAGAGTGATA
AAAGGACCAATACATTGATTCACGGCCAACGATATTGGGTTTAGAGATGAGAAAAGGGATAAAGG
AGCCAATATGCGGCTAGCGATATTAGGCTCGAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGAC
CAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATATGCTGATTCAAGGCCAGCTACATT
GAACTTAAAGATGAAAAAG
Found at i:1010890 original size:43 final size:44
Alignment explanation
Indices: 1010828--1011017 Score: 229
Period size: 43 Copynumber: 4.1 Consensus size: 44
1010818 TTAAAGATGA
1010828 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
1010872 -AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
1010915 AAAGATGAAGGTGTCAATATGCTGATTTAAGGCCAGCGATATTGGACTT
1 --A-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
1010964 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT
1 -AA---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1011012 AAAAGG
1 AAAAGG
1011018 AGACGCCACC
Statistics
Matches: 124, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
43 40 0.32
44 4 0.03
47 4 0.03
48 40 0.32
49 36 0.29
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (44 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:1010903 original size:95 final size:93
Alignment explanation
Indices: 1010775--1011006 Score: 313
Period size: 95 Copynumber: 2.4 Consensus size: 93
1010765 AAAGATGAGA
*
1010775 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAAAAGGTGCCAA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG---AAGGTGCCAA
*
1010840 TATGCTGATTCAAGGCCAGCTATATTGGACTT
62 TATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1010872 -AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGAAGGTGTCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATG
*
1010936 CTGATTTAAGGCCAGCGATATTGGACTT
66 CTGATTCAAGGCCAGCGATATTGGACTT
* *
1010964 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 -AA---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
1011007 GGCTTAAAAG
Statistics
Matches: 121, Mismatches: 9, Indels: 10
0.86 0.06 0.07
Matches are distributed among these distances:
92 39 0.32
94 1 0.01
95 42 0.35
96 5 0.04
97 34 0.28
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (93 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATG
CTGATTCAAGGCCAGCGATATTGGACTT
Found at i:1011124 original size:30 final size:30
Alignment explanation
Indices: 1011075--1011348 Score: 186
Period size: 30 Copynumber: 9.0 Consensus size: 30
1011065 TATGCTTTTG
*
1011075 AAGGTTGCTACTGACTTGTGGGCTTTTGAAA
1 AAGG-TGCCACTGACTTGTGGGCTTTTGAAA
* **
1011106 AAGGTGCCACTAACTTGTGGGCTTAAAAAGAAA
1 AAGGTGCCACTGACTTGTGGGCTT---TTGAAA
* * * *
1011139 AAGAGTGCTA-TAGAGTTGTGAGCTTATAAAAGAAA
1 AAG-GTGCCACT-GACTTGTGGGCTT-T---TGAAA
* * * *
1011174 AAGAGTGCCACGGAGTTGTGGAC-TTTGGAA
1 AAG-GTGCCACTGACTTGTGGGCTTTTGAAA
* * *
1011204 AAGATGCCACCGACTTGTGGGC-TTCGAAA
1 AAGGTGCCACTGACTTGTGGGCTTTTGAAA
*
1011233 AAGGGTGCCACTGATTTGTGGGC-TTTG---
1 AA-GGTGCCACTGACTTGTGGGCTTTTGAAA
* *
1011260 AAGGTTGCCACTGACTTGTAGGCTTTGGAAA
1 AAGG-TGCCACTGACTTGTGGGCTTTTGAAA
**
1011291 AAAATGCCACTGACTTGTGGGC-TTTGAAA
1 AAGGTGCCACTGACTTGTGGGCTTTTGAAA
*
1011320 AAGATGCCACTGACTTGTGGGCTTTTGAA
1 AAGGTGCCACTGACTTGTGGGCTTTTGAA
1011349 GGGTGAGGAA
Statistics
Matches: 194, Mismatches: 33, Indels: 33
0.75 0.13 0.13
Matches are distributed among these distances:
26 2 0.01
27 18 0.09
28 3 0.02
29 49 0.25
30 67 0.35
31 6 0.03
32 1 0.01
33 9 0.05
34 16 0.08
35 23 0.12
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (30 bp):
AAGGTGCCACTGACTTGTGGGCTTTTGAAA
Found at i:1011190 original size:35 final size:34
Alignment explanation
Indices: 1011102--1011193 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 34
1011092 GTGGGCTTTT
* *
1011102 GAAAAAG-GTGCCACTA-ACTTGTGGGCTTAAAAA
1 GAAAAAGAGTGCCAC-AGAGTTGTGAGCTTAAAAA
* *
1011135 GAAAAAGAGTGCTATAGAGTTGTGAGCTTATAAAA
1 GAAAAAGAGTGCCACAGAGTTGTGAGCTTA-AAAA
*
1011170 GAAAAAGAGTGCCACGGAGTTGTG
1 GAAAAAGAGTGCCACAGAGTTGTG
1011194 GACTTTGGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
33 8 0.16
34 16 0.33
35 25 0.51
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (34 bp):
GAAAAAGAGTGCCACAGAGTTGTGAGCTTAAAAA
Found at i:1011221 original size:29 final size:29
Alignment explanation
Indices: 1011172--1011344 Score: 188
Period size: 29 Copynumber: 5.9 Consensus size: 29
1011162 TTATAAAAGA
* * *
1011172 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* * *
1011202 AAAAGATGCCACCGACTTGTGGGCTTCGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
1011231 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
1011260 -AAGGTTGCCACTGACTTGTAGGCTTTGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
1011288 AAAAAAATGCCACTGACTTGTGGGCTTTGA
1 -AAAAGATGCCACTGACTTGTGGGCTTTGG
1011318 AAAAGATGCCACTGACTTGTGGGCTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
1011345 TGAAGGGTGA
Statistics
Matches: 119, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
27 20 0.17
28 3 0.03
29 48 0.40
30 48 0.40
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.27
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:1012807 original size:14 final size:13
Alignment explanation
Indices: 1012784--1012819 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1012774 ATCCGGACCC
1012784 TTTTTT-TTTGTTT
1 TTTTTTGTTTG-TT
1012797 TTTTTTGTTTGTT
1 TTTTTTGTTTGTT
1012810 TTTTTTGTTT
1 TTTTTTGTTT
1012820 TGCTCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (13 bp):
TTTTTTGTTTGTT
Found at i:1012821 original size:14 final size:13
Alignment explanation
Indices: 1012784--1012835 Score: 68
Period size: 14 Copynumber: 3.8 Consensus size: 13
1012774 ATCCGGACCC
1012784 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
1012797 TTTTTTGTTTGTTT
1 TTTTTT-TTTGTTT
* *
1012811 TTTTTGTTTTGCTC
1 TTTTT-TTTTGTTT
1012825 TTTTTTTTTGT
1 TTTTTTTTTGT
1012836 GAAGGACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 11 0.32
14 22 0.65
15 1 0.03
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:1026718 original size:52 final size:51
Alignment explanation
Indices: 1026640--1026789 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
1026630 CGAAATATGA
1026640 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
1026692 AAATTTGCCTGCATGTATCGATACATTTTATAATATATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
1026744 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACAT
1026790 TTGAGTAATG
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1026869 original size:13 final size:13
Alignment explanation
Indices: 1026851--1026875 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1026841 TAAAAAAATA
1026851 TGTATCGATACAT
1 TGTATCGATACAT
1026864 TGTATCGATACA
1 TGTATCGATACA
1026876 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1027470 original size:6 final size:6
Alignment explanation
Indices: 1027459--1027513 Score: 69
Period size: 6 Copynumber: 9.3 Consensus size: 6
1027449 CTCAAACATT
* *
1027459 TTTTTC TTTTTC TTTTTC --CTTC TTTTTC TTCTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1027505 TTTCTTC TT
1 TTT-TTC TT
1027514 CACCCCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
4 3 0.07
6 34 0.81
7 5 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:1027508 original size:22 final size:22
Alignment explanation
Indices: 1027457--1027514 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
1027447 CACTCAAACA
*
1027457 TTTTTTTCTTTTTCTTTTTCCT
1 TTTTTTTCTTCTTCTTTTTCCT
*
1027479 TCTTTTTCTTCTTCTTTTT-CT
1 TTTTTTTCTTCTTCTTTTTCCT
1027500 TTTTCTTTCTTCTTC
1 TTTT-TTTCTTCTTC
1027515 ACCCCAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTCTTCTTCTTTTTCCT
Found at i:1028924 original size:61 final size:61
Alignment explanation
Indices: 1028859--1029031 Score: 165
Period size: 61 Copynumber: 2.8 Consensus size: 61
1028849 CAATGTGTTA
* * *
1028859 ATTCAAGGTCAACGACATTAGACTTAAAGATGCA-AAGAATGATAAAAGTG-TCGATATGCTG
1 ATTCAAGGTCAACGATATTAGATTTAAAGATG-AGAAGAATGATAAAAGTGCT-AATATGCTG
* * * * *
1028920 ATTCATGG-CAATGATA-TCGAGTTTGAAAGATGAGAAAAATGATAAATGTGCTAATATGCTG
1 ATTCAAGGTCAACGATATTAGA-TTT-AAAGATGAGAAGAATGATAAAAGTGCTAATATGCTG
* * * * *
1028981 ATTCAAGGTCAACGATATTGGATTTAAAAATGATAAGAATGAGAAGAGTGC
1 ATTCAAGGTCAACGATATTAGATTTAAAGATGAGAAGAATGATAAAAGTGC
1029032 CAATCTGTCA
Statistics
Matches: 89, Mismatches: 17, Indels: 12
0.75 0.14 0.10
Matches are distributed among these distances:
59 3 0.03
60 9 0.10
61 63 0.71
62 11 0.12
63 3 0.03
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.27
Consensus pattern (61 bp):
ATTCAAGGTCAACGATATTAGATTTAAAGATGAGAAGAATGATAAAAGTGCTAATATGCTG
Found at i:1029223 original size:31 final size:31
Alignment explanation
Indices: 1029177--1029270 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 31
1029167 CATTAGGTTT
*
1029177 AGAAGGGTTGCCACTACTTGTGTGGGCTTTAG
1 AGAA-GGTTGCCACTACTTATGTGGGCTTTAG
* *
1029209 AGAAGGTTGTCACTAACTTATATGGGCTTTAG
1 AGAAGGTTGCCACT-ACTTATGTGGGCTTTAG
* * *
1029241 A-AAGGTTACCACCATCTTTTGTGGGCTTTA
1 AGAAGGTTGCCACTA-CTTATGTGGGCTTTA
1029271 AAAAGAGATG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.02
31 31 0.60
32 20 0.38
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (31 bp):
AGAAGGTTGCCACTACTTATGTGGGCTTTAG
Found at i:1029422 original size:32 final size:32
Alignment explanation
Indices: 1029339--1029537 Score: 108
Period size: 32 Copynumber: 6.4 Consensus size: 32
1029329 GATTTTGAAG
*
1029339 AGGGTTGCCATCGACTTGTGTAGGCTTTGAAAA
1 AGGGTTGCCACCGACTTGTGTAGGCTTT-AAAA
* * * * *
1029372 AAGGATACCACCAACTTGTGTAGGCTTTAAAG
1 AGGGTTGCCACCGACTTGTGTAGGCTTTAAAA
* * * * * *
1029404 GGGGTTGCCACCGGCTTGTATGGGCTTTATAG
1 AGGGTTGCCACCGACTTGTGTAGGCTTTAAAA
** **
1029436 AGGG-CACCACTTACTTGTG--GGCTTTTAAAA
1 AGGGTTGCCACCGACTTGTGTAGGC-TTTAAAA
* * **
1029466 A--GATGCCACTGACTCATG-A-GCTTTAGAAA
1 AGGGTTGCCACCGACTTGTGTAGGCTTTA-AAA
* *
1029495 A-GGTTACCACCGACTTGTGTGGGCTTTAAAA
1 AGGGTTGCCACCGACTTGTGTAGGCTTTAAAA
*
1029526 AGAGTTGCCACC
1 AGGGTTGCCACC
1029538 ATTTTATGTG
Statistics
Matches: 121, Mismatches: 37, Indels: 17
0.69 0.21 0.10
Matches are distributed among these distances:
28 5 0.04
29 19 0.16
30 18 0.15
31 13 0.11
32 43 0.36
33 23 0.19
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (32 bp):
AGGGTTGCCACCGACTTGTGTAGGCTTTAAAA
Found at i:1029581 original size:31 final size:32
Alignment explanation
Indices: 1029485--1029591 Score: 94
Period size: 32 Copynumber: 3.4 Consensus size: 32
1029475 TGACTCATGA
1029485 GCTTTAGAAAA-GGTTACCACC-GACTTGTGTGG
1 GCTTTA-AAAAGGGTTACCACCAG-CTTGTGTGG
* * ** *
1029517 GCTTTAAAAAGAGTTGCCACCATTTTATGTGG
1 GCTTTAAAAAGGGTTACCACCAGCTTGTGTGG
* *
1029549 GCTTT-AAGAGGGTTACCACCAGCTTGTATGG
1 GCTTTAAAAAGGGTTACCACCAGCTTGTGTGG
* *
1029580 GCATTGAAAAGG
1 GCTTTAAAAAGG
1029592 TGCCATTGAT
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
31 27 0.47
32 31 0.53
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (32 bp):
GCTTTAAAAAGGGTTACCACCAGCTTGTGTGG
Found at i:1029636 original size:28 final size:28
Alignment explanation
Indices: 1029577--1030116 Score: 467
Period size: 28 Copynumber: 19.1 Consensus size: 28
1029567 CCAGCTTGTA
* * *
1029577 TGGGCATTGAAAAGG-TGCCATTGATTTG
1 TGGGCTTTG-AAAGGATGCCACTGACTTG
* *
1029605 TGGGCTTTGAAAGGGTGTCACTGACTCT-
1 TGGGCTTTGAAAGGATGCCACTGACT-TG
* * *
1029633 TGGGCTTTTAAAATGATGCC-CATGACTCG
1 TGGGC-TTTGAAAGGATGCCAC-TGACTTG
* * **
1029662 TGGGCTTTGAAAAGATGCCACTAACTCA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * **
1029690 TGGGCTTTTGAAAGAATGCTACTGACTCA
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
* * * * *
1029719 TAGGCTTTAAAAGGTTACCACTGACTCG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
1029747 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
1029775 TGGGCTTTTGAAAGGATGCCACTGACTTG
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
* *
1029804 TGGGCTTTGAAAGGGTGCCACTGACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
1029832 TGTGCTTTAAAAGGATGCCACTGAATTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
*
1029860 TGGGCTTTTGAAAGGATGCCACTAACTTG
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
* *
1029889 TGGGTTTTTGAAAGGATGCCATTGACTTG
1 TGGG-CTTTGAAAGGATGCCACTGACTTG
* **
1029918 TGGGCTTTGAAAGGAT-CCTCTGACTCA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * * * *
1029945 TGAGCTTTGGAAGGTTGCCCCTTACTCG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
1029973 TGGGCTTTGAAAGGGTGCCACTAACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
1030001 TGGGCTTTGAAAGGGTACCGCTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * ** *
1030029 TGAGCTTTTGAAAGGGTATCATTGACTTG
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
* * * *
1030058 TGTGCTTTGAAAGGGTGCCCCTAACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
1030086 TGGGCTTTGGAAGGGTGCCACTGATTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
1030114 TGG
1 TGG
1030117 CCACTGACTC
Statistics
Matches: 420, Mismatches: 80, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
27 25 0.06
28 249 0.59
29 146 0.35
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.31
Consensus pattern (28 bp):
TGGGCTTTGAAAGGATGCCACTGACTTG
Found at i:1029672 original size:85 final size:86
Alignment explanation
Indices: 1029577--1030116 Score: 438
Period size: 85 Copynumber: 6.4 Consensus size: 86
1029567 CCAGCTTGTA
* * * * *
1029577 TGGGCATTGAAAAGG-TGCCATTGATTTGTGGGC-TTTGAAAGGGTGTCACTGACTCT-TGGGCT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACT-TGTGGGC-
*
1029639 TTTAAAATGATGCC-CATGACTCG
64 TTTAAAAGGATGCCAC-TGACTCG
* ** * * ** *
1029662 TGGGCTTTGAAAA-GATGCCACTAACTCATGGGCTTTTGAAAGAATGCTACTGACTCATAGGCTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTT
* *
1029726 TAAAAGGTTACCACTGACTCG
66 TAAAAGGATGCCACTGACTCG
1029747 TGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTT
* * **
1029811 TGAAAGGGTGCCACTGACTTA
66 TAAAAGGATGCCACTGACTCG
* * * *
1029832 TGTGCTTT-AAAAGGATGCCACTGAATTGTGGGCTTTTGAAAGGATGCCACTAACTTGTGGGTTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGG-CT
* * *
1029896 TTGAAAGGATGCCATTGACTTG
65 TTAAAAGGATGCCACTGACTCG
* ** * * * * * *
1029918 TGGGCTTTG-AAAGGAT-CCTCTGACTCATGAGC-TTTGGAAGGTTGCCCCTTACTCGTGGGCTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTT
* * * **
1029980 TGAAAGGGTGCCACTAACTTA
66 TAAAAGGATGCCACTGACTCG
* * * * * ** * *
1030001 TGGGCTTTG-AAAGGGTACCGCTGACTTGTGAGCTTTTGAAAGGGTATCATTGACTTGTGTGCTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTT
* * * * *
1030065 TGAAAGGGTGCCCCTAACTTG
66 TAAAAGGATGCCACTGACTCG
* * *
1030086 TGGGCTTTG-GAAGGGTGCCACTGATTTGTGG
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGG
1030117 CCACTGACTC
Statistics
Matches: 374, Mismatches: 71, Indels: 20
0.80 0.15 0.04
Matches are distributed among these distances:
83 34 0.09
84 39 0.10
85 245 0.66
86 56 0.15
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.31
Consensus pattern (86 bp):
TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTT
TAAAAGGATGCCACTGACTCG
Found at i:1029673 original size:57 final size:56
Alignment explanation
Indices: 1029604--1030109 Score: 323
Period size: 57 Copynumber: 8.9 Consensus size: 56
1029594 CCATTGATTT
* * *
1029604 GTGGGCTTTGAAAGGGTGTCACTGACTCTTGGGCTTTTAAAATGATGCC-CATGACTC
1 GTGGGCTTTGAAAGGATGCCACTGACTCTTGGGCTTTTGAAA-GATGCCAC-TGACTC
* * * *
1029661 GTGGGCTTTGAAAAGATGCCACTAACTCATGGGCTTTTGAAAGAATGCTACTGACTC
1 GTGGGCTTTGAAAGGATGCCACTGACTCTTGGGCTTTTGAAAG-ATGCCACTGACTC
* * * * * * *
1029718 ATAGGCTTTAAAAGGTTACCACTGACTCGTGGGC-TTTGAAAGGATGCCACTGACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTCTTGGGCTTTTGAAA-GATGCCACTGACTC
* *
1029774 GTGGGCTTTTGAAAGGATGCCACTGACT-TGTGGGC-TTTGAAAGGGTGCCACTGACTT
1 GTGGGC-TTTGAAAGGATGCCACTGACTCT-TGGGCTTTTGAAA-GATGCCACTGACTC
* * * * * *
1029831 ATGTGCTTTAAAAGGATGCCACTGAAT-TGTGGGCTTTTGAAAGGATGCCACTAACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTCT-TGGGCTTTTGAAA-GATGCCACTGACTC
* * *
1029888 GTGGGTTTTTGAAAGGATGCCATTGACT-TGTGGGC-TTTGAAAGGAT-CCTCTGACTC
1 GTGGG-CTTTGAAAGGATGCCACTGACTCT-TGGGCTTTTGAAA-GATGCCACTGACTC
* * * * * * * * * *
1029944 ATGAGCTTTGGAAGGTTGCCCCTTACTCGTGGGC-TTTGAAAGGGTGCCACTAACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTCTTGGGCTTTTGAAA-GATGCCACTGACTC
* * * * * * ** * *
1030000 ATGGGCTTTGAAAGGGTACCGCTGACT-TGTGAGCTTTTGAAAGGGTATCATTGACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTCT-TGGGCTTTTGAAA-GATGCCACTGACTC
* * * * * * *
1030057 GTGTGCTTTGAAAGGGTGCCCCTAACT-TGTGGGCTTTGGAAGGGTGCCACTGA
1 GTGGGCTTTGAAAGGATGCCACTGACTCT-TGGGCTTTTGAAAGATGCCACTGA
1030110 TTTGTGGCCA
Statistics
Matches: 363, Mismatches: 75, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
55 31 0.09
56 99 0.27
57 207 0.57
58 26 0.07
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (56 bp):
GTGGGCTTTGAAAGGATGCCACTGACTCTTGGGCTTTTGAAAGATGCCACTGACTC
Found at i:1030168 original size:28 final size:29
Alignment explanation
Indices: 1030137--1030213 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
1030127 GTGGGCTTTG
*
1030137 AAAGGGTGCCACTGACTTAT-AGGATTTA
1 AAAGGGTGCCACTGACTTATAAGCATTTA
* * *
1030165 AAAGGGTGCCACTAACTTATAAGCTTTTG
1 AAAGGGTGCCACTGACTTATAAGCATTTA
* *
1030194 AAAGGATGCCACTGATTTAT
1 AAAGGGTGCCACTGACTTAT
1030214 GGGCTTCTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (29 bp):
AAAGGGTGCCACTGACTTATAAGCATTTA
Found at i:1030346 original size:28 final size:28
Alignment explanation
Indices: 1030116--1030419 Score: 178
Period size: 28 Copynumber: 10.5 Consensus size: 28
1030106 CTGATTTGTG
* *
1030116 GCCACTGACTCGTGGGCTTTGAAAGGGT
1 GCCACTGACTTGTGGGCTTTAAAAGGGT
* * *
1030144 GCCACTGACTTATAGGATTTAAAAGGGT
1 GCCACTGACTTGTGGGCTTTAAAAGGGT
* * ** * *
1030172 GCCACTAACTTATAAGCTTTTGAAAGGAT
1 GCCACTGACTTGTGGGC-TTTAAAAGGGT
* * *
1030201 GCCACTGATTTATGGGCTTCTGAAAA-GAT
1 GCCACTGACTTGTGGGCTT-T-AAAAGGGT
* * * * *
1030230 GTCATTGACTCGTGAGCTTTAGAAAAGGTT
1 GCCACTGACTTGTGGGCTTT--AAAAGGGT
* *
1030260 GCTACTGACTTGTGTGGGCTTTGAGAAGGGTT
1 GCCACTGAC-T-TGTGGGCTTT-AAAAGGG-T
* * *
1030292 GCCACTTATTTGTATGGGCTTTGAAAGGGT
1 GCCACTGACTTG--TGGGCTTTAAAAGGGT
* * * * *
1030322 GTCACTGATTTTTGAGCTTTAAAAGGAT
1 GCCACTGACTTGTGGGCTTTAAAAGGGT
* *
1030350 GCCACTAACTCGTGGGCTTTAAAAGGGT
1 GCCACTGACTTGTGGGCTTTAAAAGGGT
* **
1030378 GCCATTGACTTGTGGGCTTTAAAAATAGT
1 GCCACTGACTTGTGGGCTTT-AAAAGGGT
*
1030407 GCCACTAACTTGT
1 GCCACTGACTTGT
1030420 ACGCTTTGAA
Statistics
Matches: 211, Mismatches: 54, Indels: 21
0.74 0.19 0.07
Matches are distributed among these distances:
28 91 0.43
29 61 0.29
30 23 0.11
31 13 0.06
32 23 0.11
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (28 bp):
GCCACTGACTTGTGGGCTTTAAAAGGGT
Found at i:1030425 original size:29 final size:29
Alignment explanation
Indices: 1030337--1030433 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 29
1030327 TGATTTTTGA
* *
1030337 GCTTTAAAAGGA-TGCCACTAACTCGTGG
1 GCTTTAAAAAGAGTGCCACTAACTTGTGG
* * *
1030365 GCTTT-AAAAGGGTGCCATTGACTTGTGG
1 GCTTTAAAAAGAGTGCCACTAACTTGTGG
* **
1030393 GCTTTAAAAATAGTGCCACTAACTTGTAC
1 GCTTTAAAAAGAGTGCCACTAACTTGTGG
1030422 GCTTTGAAAAAG
1 GCTTT-AAAAAG
1030434 GAAAAAGATT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
27 4 0.07
28 23 0.43
29 22 0.41
30 5 0.09
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (29 bp):
GCTTTAAAAAGAGTGCCACTAACTTGTGG
Found at i:1031606 original size:11 final size:11
Alignment explanation
Indices: 1031563--1031603 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
1031553 GCCTTTGCAC
1031563 TTTTT-TTTTG
1 TTTTTCTTTTG
1031573 TTTTTCTTTTG
1 TTTTTCTTTTG
* *
1031584 CTTTTCATTT-
1 TTTTTCTTTTG
1031594 TTTTTCTTTT
1 TTTTTCTTTT
1031604 TTTGAAGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.02, C:0.10, G:0.05, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTG
Found at i:1035170 original size:13 final size:13
Alignment explanation
Indices: 1035152--1035201 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
1035142 TTCAATGATT
1035152 TGTATCGATACAA
1 TGTATCGATACAA
1035165 TGTATCGATACATAA
1 TGTATCGATAC--AA
1035180 GTTGTATCGATACAA
1 --TGTATCGATACAA
*
1035195 TGCATCG
1 TGTATCG
1035202 CTACGAAGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 17 0.53
15 4 0.12
17 11 0.34
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1035264 original size:13 final size:13
Alignment explanation
Indices: 1035246--1035270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1035236 ATTACCCAAA
1035246 TGTATCGATACAT
1 TGTATCGATACAT
1035259 TGTATCGATACA
1 TGTATCGATACA
1035271 CAGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1035335 original size:52 final size:52
Alignment explanation
Indices: 1035279--1035407 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1035269 CACAGATCTT
1035279 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTACCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTACCGATACACTATGAAA
* *
1035331 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTACCGATACACTATGAAA
1035383 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1035408 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTACCGATACACTATGAAA
Found at i:1037543 original size:24 final size:26
Alignment explanation
Indices: 1037516--1037566 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1037506 TCAAAAATTT
*
1037516 ATTCAT-C-GGGGATACTCCAACCCC
1 ATTCATCCAGGGGACACTCCAACCCC
1037540 ATTCATCCGAGGGGACACTCCAACCCC
1 ATTCATCC-AGGGGACACTCCAACCCC
1037567 TTTTTCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 1 0.04
27 16 0.70
ACGTcount: A:0.25, C:0.39, G:0.18, T:0.18
Consensus pattern (26 bp):
ATTCATCCAGGGGACACTCCAACCCC
Found at i:1041446 original size:17 final size:17
Alignment explanation
Indices: 1041424--1041457 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1041414 TCAAATTCTA
*
1041424 GTATGCTCTTCCTTTTC
1 GTATGCGCTTCCTTTTC
*
1041441 GTATGCGCTTCTTTTTC
1 GTATGCGCTTCCTTTTC
1041458 ATCGTTGAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.15, T:0.53
Consensus pattern (17 bp):
GTATGCGCTTCCTTTTC
Found at i:1043067 original size:28 final size:29
Alignment explanation
Indices: 1043013--1043068 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
1043003 TGGAATATAT
1043013 ATATATATTATTTCTATTGGTAAGCTTGA
1 ATATATATTATTTCTATTGGTAAGCTTGA
* * *
1043042 ATATATTTTTTTTC-ATTGGTATGCTTG
1 ATATATATTATTTCTATTGGTAAGCTTG
1043069 GTTGGAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (29 bp):
ATATATATTATTTCTATTGGTAAGCTTGA
Found at i:1043351 original size:16 final size:17
Alignment explanation
Indices: 1043319--1043353 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1043309 AAATGATAAT
1043319 TTTTCATATTTTATTTC
1 TTTTCATATTTTATTTC
*
1043336 TTTTCAT-TTTTTTTTC
1 TTTTCATATTTTATTTC
1043352 TT
1 TT
1043354 ACCAATCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCATATTTTATTTC
Found at i:1044066 original size:22 final size:23
Alignment explanation
Indices: 1044041--1044084 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1044031 CCATCAAACA
*
1044041 AAATTTTAAATTTAA-TTATTTC
1 AAATGTTAAATTTAATTTATTTC
**
1044063 AAATGTTAGGTTTAATTTATTT
1 AAATGTTAAATTTAATTTATTT
1044085 TTATCATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (23 bp):
AAATGTTAAATTTAATTTATTTC
Found at i:1047669 original size:11 final size:11
Alignment explanation
Indices: 1047653--1047677 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1047643 CTCCAAAGTC
1047653 TTTTTTATTTT
1 TTTTTTATTTT
1047664 TTTTTTATTTT
1 TTTTTTATTTT
1047675 TTT
1 TTT
1047678 ATTTTTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:1048603 original size:19 final size:18
Alignment explanation
Indices: 1048576--1048614 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1048566 AAAAAAAACT
*
1048576 AAAAAATAATAATAATTA
1 AAAAAATAAAAATAATTA
*
1048594 AAAAATATAAAAATATTTA
1 AAAAA-ATAAAAATAATTA
1048613 AA
1 AA
1048615 GTTAAGGTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATAAAAATAATTA
Found at i:1050936 original size:2 final size:2
Alignment explanation
Indices: 1050929--1050960 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1050919 ATATAACGTG
1050929 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
1050961 TAAGAAAAGT
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:1051262 original size:21 final size:21
Alignment explanation
Indices: 1051239--1051279 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
1051229 AAAATTAAAA
1051239 TTTTAATATT-TATATTTTTTAT
1 TTTTAA-ATTATA-ATTTTTTAT
1051261 TTTTAAATTATAATTTTTT
1 TTTTAAATTATAATTTTTT
1051280 TATGTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTAAATTATAATTTTTTAT
Found at i:1051385 original size:2 final size:2
Alignment explanation
Indices: 1051380--1051411 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1051370 TATATATATT
*
1051380 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1051412 ATTTTAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1052745 original size:16 final size:16
Alignment explanation
Indices: 1052724--1052755 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1052714 GTTTTCTTAA
*
1052724 TAAAAATATTAAAAAT
1 TAAAAATAATAAAAAT
1052740 TAAAAATAATAAAAAT
1 TAAAAATAATAAAAAT
1052756 ATTTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAATAATAAAAAT
Found at i:1052910 original size:23 final size:23
Alignment explanation
Indices: 1052857--1052906 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
1052847 AGATTCAGCC
1052857 AAAAATATTATAATAGATAATAT
1 AAAAATATTATAATAGATAATAT
* *
1052880 AAACATATT-T-ATATATAATAT
1 AAAAATATTATAATAGATAATAT
1052901 CAAAAA
1 -AAAAA
1052907 ATATCACTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 10 0.43
22 5 0.22
23 8 0.35
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAAATATTATAATAGATAATAT
Found at i:1053503 original size:29 final size:30
Alignment explanation
Indices: 1053459--1053523 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
1053449 TATTATACTC
1053459 AAATAAATTTTAAATTTTAAATTTA-TATT
1 AAATAAATTTTAAATTTTAAATTTATTATT
* *
1053488 AAATAAATCTTT-AATTTTTAATTTATTCTT
1 AAATAAAT-TTTAAATTTTAAATTTATTATT
1053518 AAATAA
1 AAATAA
1053524 GCGTTAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
AAATAAATTTTAAATTTTAAATTTATTATT
Found at i:1053530 original size:29 final size:29
Alignment explanation
Indices: 1053471--1053531 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1053461 ATAAATTTTA
* *
1053471 AATTTTAAATTTATATTAAATAAATCTTT
1 AATTTTAAATTTATATTAAATAAAGCGTT
* *
1053500 AATTTTTAATTTATTCTTAAAT-AAGCGTT
1 AATTTTAAATTTA-TATTAAATAAAGCGTT
1053529 AAT
1 AAT
1053532 ATTTGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (29 bp):
AATTTTAAATTTATATTAAATAAAGCGTT
Found at i:1055410 original size:13 final size:13
Alignment explanation
Indices: 1055388--1055450 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
1055378 TAATAATTTT
*
1055388 AAATACAATATAA
1 AAATATAATATAA
*
1055401 AAATATAATATAT
1 AAATATAATATAA
* *
1055414 TAATA-AATAT-T
1 AAATATAATATAA
1055425 AAA-ATAATATAA
1 AAATATAATATAA
*
1055437 TAAATATGATATAA
1 -AAATATAATATAA
1055451 TTTATTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
10 1 0.03
11 8 0.20
12 5 0.12
13 18 0.45
14 8 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:1055427 original size:37 final size:36
Alignment explanation
Indices: 1055377--1055449 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
1055367 TATTTTAAAT
*
1055377 TTAATAATTTTAAATACAATATAA-AAATATAATATA
1 TTAATAATATTAAA-ACAATATAATAAATATAATATA
* *
1055413 TTAATAAATATTAAAATAATATAATAAATATGATATA
1 TTAAT-AATATTAAAACAATATAATAAATATAATATA
1055450 ATTTATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (36 bp):
TTAATAATATTAAAACAATATAATAAATATAATATA
Found at i:1055437 original size:20 final size:20
Alignment explanation
Indices: 1055394--1055443 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1055384 TTTTAAATAC
*
1055394 AATATAA-AAATA-TAATAT
1 AATATAATAAATATTAAAAT
1055412 -AT-TAATAAATATTAAAAT
1 AATATAATAAATATTAAAAT
1055430 AATATAATAAATAT
1 AATATAATAAATAT
1055444 GATATAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 3 0.11
17 7 0.26
18 5 0.19
19 2 0.07
20 10 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATAATAAATATTAAAAT
Found at i:1055541 original size:17 final size:17
Alignment explanation
Indices: 1055490--1055542 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
1055480 TTAATAAATG
* *
1055490 TATTATATTTGTATTTT
1 TATTATATTTATATTTA
* *
1055507 TAATATATATAATAATTTA
1 TATTATAT-TTAT-ATTTA
1055526 TATTATATTTATATTTA
1 TATTATATTTATATTTA
1055543 CATAATTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 12 0.43
18 5 0.18
19 11 0.39
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATATTTATATTTA
Found at i:1055814 original size:12 final size:13
Alignment explanation
Indices: 1055797--1055867 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 13
1055787 ATGTAACGGT
*
1055797 AATTATAA-AATA
1 AATTATAATAAAA
1055809 AATTATAATAAAA
1 AATTATAATAAAA
*
1055822 AATTATCATTAAAA
1 AATTAT-AATAAAA
*
1055836 ACATTA-AATTAAA
1 A-ATTATAATAAAA
*
1055849 AATATATATATAAAT
1 AAT-TATA-ATAAAA
1055864 AATT
1 AATT
1055868 TAAAATTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
12 10 0.21
13 17 0.36
14 9 0.19
15 11 0.23
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTATAATAAAA
Found at i:1055836 original size:14 final size:13
Alignment explanation
Indices: 1055808--1055850 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1055798 ATTATAAAAT
*
1055808 AAATTATAATAAA
1 AAATTATATTAAA
1055821 AAATTATCATTAAA
1 AAATTAT-ATTAAA
*
1055835 AACATTAAATTAAA
1 AA-ATTATATTAAA
1055849 AA
1 AA
1055851 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 7 0.27
14 15 0.58
15 4 0.15
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATTATATTAAA
Found at i:1055862 original size:28 final size:30
Alignment explanation
Indices: 1055800--1055862 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
1055790 TAACGGTAAT
1055800 TATAAAATAAATTATAATAAAAAATTATCA
1 TATAAAATAAATTATAATAAAAAATTATCA
* *
1055830 T-TAAAA-ACATTA-AATTAAAAATATAT-A
1 TATAAAATAAATTATAATAAAAAAT-TATCA
1055857 TATAAA
1 TATAAA
1055863 TAATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 11 0.38
28 12 0.41
29 5 0.17
30 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (30 bp):
TATAAAATAAATTATAATAAAAAATTATCA
Found at i:1056440 original size:30 final size:30
Alignment explanation
Indices: 1056377--1056486 Score: 109
Period size: 29 Copynumber: 3.7 Consensus size: 30
1056367 GTTTAAAAGG
* **
1056377 AAAAAAATATATTTA-TCTTAAAAT-TTTA
1 AAAAAAATATATTTATTTTTTTAATATTTA
1056405 TAAAAAAATATATTTATTTTTTTAATATTTA
1 -AAAAAAATATATTTATTTTTTTAATATTTA
* * *
1056436 AAAAATATTTATTT-TTTTTTTAAAATTTA
1 AAAAAAATATATTTATTTTTTTAATATTTA
* *
1056465 ATTAAAAATATATTTATCTTTT
1 A-AAAAAATATATTTATTTTTT
1056487 AAGTTATTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
29 30 0.45
30 28 0.42
31 9 0.13
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
AAAAAAATATATTTATTTTTTTAATATTTA
Found at i:1056502 original size:14 final size:15
Alignment explanation
Indices: 1056478--1056506 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1056468 AAAAATATAT
1056478 TTATCTTTTAAGTTA
1 TTATCTTTTAAGTTA
1056493 TTAT-TTTTAAGTTA
1 TTATCTTTTAAGTTA
1056507 ATTTTAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (15 bp):
TTATCTTTTAAGTTA
Found at i:1056647 original size:16 final size:16
Alignment explanation
Indices: 1056628--1056659 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1056618 AATTATTTTT
1056628 AATTATTATTAAATTA
1 AATTATTATTAAATTA
1056644 AATTATTATTAAATTA
1 AATTATTATTAAATTA
1056660 TATTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:1056887 original size:25 final size:25
Alignment explanation
Indices: 1056859--1056918 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
1056849 AATTTTTACA
1056859 TAAAAATAATATA-ATATATT-AATAT
1 TAAAAATAATATATATA-ATTGAAT-T
**
1056884 TAAATTTAATATATATAATTGAATT
1 TAAAAATAATATATATAATTGAATT
*
1056909 TAAAGATAAT
1 TAAAAATAAT
1056919 TTCAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
TAAAAATAATATATATAATTGAATT
Found at i:1059108 original size:62 final size:62
Alignment explanation
Indices: 1059035--1059175 Score: 246
Period size: 62 Copynumber: 2.3 Consensus size: 62
1059025 ATAAAAATAT
* *
1059035 TGGGGCTAAATTAAAAAGTTTCCTTTTTAAAAGTTTTAATTCACGGGAGTCCATGAATTTAC
1 TGGGGCCAAATTAAAAAGTTTCCTTTTTAAAAGTTTTAATTCACGGGAGTCCATGAATTTAA
**
1059097 TGGGGCCAAATTAAAATTTTTCCTTTTTAAAAGTTTTAATTCACGGGAGTCCATGAATTTAA
1 TGGGGCCAAATTAAAAAGTTTCCTTTTTAAAAGTTTTAATTCACGGGAGTCCATGAATTTAA
1059159 TGGGGCCAAATTAAAAA
1 TGGGGCCAAATTAAAAA
1059176 TTTTATTTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 74 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (62 bp):
TGGGGCCAAATTAAAAAGTTTCCTTTTTAAAAGTTTTAATTCACGGGAGTCCATGAATTTAA
Found at i:1059438 original size:8 final size:8
Alignment explanation
Indices: 1059404--1059440 Score: 51
Period size: 7 Copynumber: 4.8 Consensus size: 8
1059394 AAGAAGTTAT
1059404 ATTTAATAA
1 ATTT-ATAA
1059413 ATTTA-AA
1 ATTTATAA
1059420 ATTTA-AA
1 ATTTATAA
1059427 ATTTATAA
1 ATTTATAA
1059435 ATTTAT
1 ATTTAT
1059441 TTTTATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.52
8 9 0.33
9 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
ATTTATAA
Found at i:1060693 original size:20 final size:20
Alignment explanation
Indices: 1060655--1060694 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1060645 AACATCTTTC
*
1060655 AAATATAAAAATAACAAACT
1 AAATATAAAAATAAAAAACT
1060675 AAATATAAAAA-AATAAAACT
1 AAATATAAAAATAA-AAAACT
1060695 TGTAATAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATATAAAAATAAAAAACT
Found at i:1061757 original size:28 final size:29
Alignment explanation
Indices: 1061708--1061767 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
1061698 TTTTATGTAA
1061708 ATTTTAATATATTTATATATTAA-TATTAT
1 ATTTTAATATATTTATATATTAAGT-TTAT
*
1061737 ATTTTAAT-TATTTTTATATTAAGTTTAT
1 ATTTTAATATATTTATATATTAAGTTTAT
1061765 ATT
1 ATT
1061768 GTATAATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
ATTTTAATATATTTATATATTAAGTTTAT
Found at i:1061780 original size:30 final size:28
Alignment explanation
Indices: 1061708--1061780 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 28
1061698 TTTTATGTAA
1061708 ATTTTAAT-ATATTTATATATTAATATTAT
1 ATTTTAATCAT-TTT-TATATTAATATTAT
*
1061737 ATTTTAATTATTTTTATATTAAGT-TTAT
1 ATTTTAATCATTTTTATATTAA-TATTAT
1061765 ATTGTATAATCATTTT
1 ATT-T-TAATCATTTT
1061781 ACGTTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 15 0.38
29 13 0.33
30 11 0.28
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (28 bp):
ATTTTAATCATTTTTATATTAATATTAT
Found at i:1061955 original size:33 final size:32
Alignment explanation
Indices: 1061895--1061961 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1061885 AAAATATTAC
*
1061895 ATATAAATTTTAAAAAATTAATAATTTATTTT
1 ATATAAATTTTAAAAAATTAATAATTTATATT
* * * *
1061927 ATATAAATTTTTATAACTTTATATATTTATATT
1 ATATAAATTTTAAAAAATTAATA-ATTTATATT
1061960 AT
1 AT
1061962 TTTTATGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (32 bp):
ATATAAATTTTAAAAAATTAATAATTTATATT
Found at i:1062197 original size:2 final size:2
Alignment explanation
Indices: 1062185--1062216 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1062175 GATTTTATGT
*
1062185 TA TA CA 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
1062217 CAGGGAGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1062305 original size:20 final size:20
Alignment explanation
Indices: 1062243--1062311 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 20
1062233 TTCGTAATTC
* *
1062243 AATAAT-ATTAAAATTTTAA
1 AATAATAATTTAATTTTTAA
*
1062262 ATATAATAGTTTAATTTTT--
1 A-ATAATAATTTAATTTTTAA
*
1062281 -TTAATAATTTAATTTTTAA
1 AATAATAATTTAATTTTTAA
1062300 AATAATTAATTT
1 AATAA-TAATTT
1062312 TTTAAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 15 0.39
19 1 0.03
20 8 0.21
21 14 0.37
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (20 bp):
AATAATAATTTAATTTTTAA
Found at i:1062308 original size:16 final size:17
Alignment explanation
Indices: 1062266--1062318 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
1062256 TTTTAAATAT
* *
1062266 AATAGTTTAATTTTTTT
1 AATAATTTAATTTTTTA
*
1062283 AATAATTTAATTTTTAA
1 AATAATTTAATTTTTTA
1062300 AATAA-TTAATTTTTTA
1 AATAATTTAATTTTTTA
1062316 AAT
1 AAT
1062319 TTAATATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
AATAATTTAATTTTTTA
Found at i:1062366 original size:27 final size:28
Alignment explanation
Indices: 1062299--1062376 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 28
1062289 TTAATTTTTA
1062299 AAATAATTAATTTTTTAAATTT-AATAT
1 AAATAATTAATTTTTTAAATTTAAATAT
* *
1062326 -GAT-ATTAAAATTTTTAAATTTAAATAT
1 AAATAATT-AATTTTTTAAATTTAAATAT
*
1062353 AAATAATT-ATTTTTTCACATTTAA
1 AAATAATTAATTTTTT-AAATTTAA
1062377 TATTTTATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 3 0.07
26 15 0.37
27 11 0.27
28 9 0.22
29 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (28 bp):
AAATAATTAATTTTTTAAATTTAAATAT
Found at i:1063633 original size:16 final size:16
Alignment explanation
Indices: 1063604--1063655 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1063594 ATATTTTAAA
*
1063604 TTTTATATAATAAATAT
1 TTTTA-ATATTAAATAT
1063621 TTTTAATATTAAA-AT
1 TTTTAATATTAAATAT
* *
1063636 TTATAAATATAAAATAT
1 TT-TTAATATTAAATAT
1063653 TTT
1 TTT
1063656 ATTTATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 4 0.13
16 17 0.57
17 9 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAATATTAAATAT
Found at i:1063690 original size:22 final size:20
Alignment explanation
Indices: 1063639--1063710 Score: 58
Period size: 22 Copynumber: 3.5 Consensus size: 20
1063629 TTAAAATTTA
**
1063639 TAAATATAAAATATTTTATT
1 TAAATATAAAATATAATATT
1063659 TATAATTATAAAATAATAAATATT
1 TA-AA-TATAAAAT-AT-AATATT
*
1063683 TAAATATATATATATAATA--
1 TAAATATA-AAATATAATATT
1063702 TAAATATAA
1 TAAATATAA
1063711 TTTTTAACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.02
19 8 0.18
20 2 0.05
21 6 0.14
22 14 0.32
23 7 0.16
24 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATATAAAATATAATATT
Found at i:1063877 original size:6 final size:6
Alignment explanation
Indices: 1063841--1063952 Score: 58
Period size: 6 Copynumber: 18.5 Consensus size: 6
1063831 TGATGTGTTT
* * *
1063841 TATTTA TTTTTA TAATTA T-TTTA TA-TTA TATTTA TATTT- T-TTTT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
* *
1063885 TA-TTA TATTAAAAA TATTATA TATTTA TATGTA T-TTGATA TATTTATA
1 TATTTA TATT---TA TATT-TA TATTTA TATTTA TATT--TA TA-TT-TA
1063933 TATTTA TATTTA TA-TTA TAT
1 TATTTA TATTTA TATTTA TAT
1063953 AAGTATTTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
4 3 0.04
5 21 0.25
6 37 0.44
7 11 0.13
8 5 0.06
9 7 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:1063889 original size:21 final size:22
Alignment explanation
Indices: 1063838--1063893 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
1063828 TTGTGATGTG
*
1063838 TTTTATTTATTTTTATAATTATT
1 TTTTA-TTATATTTATAATTATT
* *
1063861 TTATATTATATTTAT-ATTTTT
1 TTTTATTATATTTATAATTATT
1063882 TTTTATTATATT
1 TTTTATTATATT
1063894 AAAAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 16 0.55
22 9 0.31
23 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTATATTTATAATTATT
Found at i:1063952 original size:27 final size:25
Alignment explanation
Indices: 1063856--1063980 Score: 86
Period size: 27 Copynumber: 5.0 Consensus size: 25
1063846 ATTTTTATAA
1063856 TTAT-TTTATATTATATT-TATATT
1 TTATATTTATATTATATTATATATT
*
1063879 TT-T-TTT-TATTATATTAAAAATATT
1 TTATATTTATATTATATT--ATATATT
*
1063903 ATATATTTATATGTAT-TTGATATATT
1 TTATATTTATAT-TATATT-ATATATT
*
1063929 TATATATTTATATTTATATTATATAAGTA
1 T-TATATTTATA-TTATATTATAT-A-TT
*
1063958 TT-T-TTTATAATATATTATATATT
1 TTATATTTATATTATATTATATATT
1063981 AATTATTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
21 9 0.11
22 4 0.05
23 3 0.04
24 7 0.09
25 11 0.13
26 15 0.18
27 23 0.28
28 8 0.10
29 2 0.02
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATATTTATATTATATTATATATT
Found at i:1063994 original size:28 final size:31
Alignment explanation
Indices: 1063937--1063994 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 31
1063927 TTTATATATT
1063937 TATATTTATATTATATAAGTATTTTTTATAA
1 TATATTTATATTATATAAGTATTTTTTATAA
*
1063968 TATA-TTATA-TAT-TAATTATTTTTTATA
1 TATATTTATATTATATAAGTATTTTTTATA
1063995 TTTATATCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 14 0.54
29 3 0.12
30 5 0.19
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (31 bp):
TATATTTATATTATATAAGTATTTTTTATAA
Found at i:1063995 original size:25 final size:26
Alignment explanation
Indices: 1063935--1064001 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
1063925 TATTTATATA
1063935 TTTATATTTATATTATATAAGTATTTT
1 TTTATATTTATA-TATATAAGTATTTT
*
1063962 TTATAATATATTATATAT-TAATTA-TTT
1 TT-T-ATAT-TTATATATATAAGTATTTT
1063989 TTTATATTTATAT
1 TTTATATTTATAT
1064002 CGTATTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
24 6 0.17
25 4 0.11
26 1 0.03
27 7 0.19
28 6 0.17
29 7 0.19
30 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (26 bp):
TTTATATTTATATATATAAGTATTTT
Found at i:1064009 original size:27 final size:25
Alignment explanation
Indices: 1063935--1064001 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 25
1063925 TATTTATATA
1063935 TTTATATTTATATTATATAAGTATTT
1 TTTATATTTATATTAT-TAAGTATTT
* *
1063961 TTTATAATATATTATATATTAATTATTT
1 TTTAT-ATTTA-TAT-TATTAAGTATTT
1063989 TTTATATTTATAT
1 TTTATATTTATAT
1064002 CGTATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 8 0.23
27 8 0.23
28 16 0.46
29 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (25 bp):
TTTATATTTATATTATTAAGTATTT
Found at i:1064402 original size:20 final size:20
Alignment explanation
Indices: 1064374--1064448 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1064364 TTTTACCTTG
1064374 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1064394 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1064414 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1064434 ATGTATCGATACATT
1 ATGTATCGATACATT
1064449 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1064441 original size:40 final size:39
Alignment explanation
Indices: 1064374--1064451 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1064364 TTTTACCTTG
* *
1064374 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1064414 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1064452 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1065396 original size:22 final size:22
Alignment explanation
Indices: 1065362--1065415 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1065352 AGCCTTTGAC
1065362 CATGCA-TTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1065383 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1065405 CATGCATTTTT
1 CATGCATTTTT
1065416 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.19
22 26 0.81
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:1071869 original size:12 final size:12
Alignment explanation
Indices: 1071852--1071881 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1071842 ACCCAATCCT
1071852 AAAAAAAACAAA
1 AAAAAAAACAAA
*
1071864 AAAAAAACCAAA
1 AAAAAAAACAAA
1071876 AAAAAA
1 AAAAAA
1071882 CCTTTTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:1071883 original size:11 final size:11
Alignment explanation
Indices: 1071852--1071883 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1071842 ACCCAATCCT
*
1071852 AAAAAAAACAA
1 AAAAAAAACCA
1071863 AAAAAAAACCA
1 AAAAAAAACCA
1071874 AAAAAAAACC
1 AAAAAAAACC
1071884 TTTTCACCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACCA
Found at i:1072987 original size:28 final size:27
Alignment explanation
Indices: 1072908--1073578 Score: 1009
Period size: 27 Copynumber: 24.5 Consensus size: 27
1072898 TAAAGCCCAT
1072908 AACTCCGTGGCACCCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
*
1072935 AACTCCGTGGCACCCTTGTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
1072962 AACTCCGTGGCATCCCTTTTAAGTCCAC
1 AACTCCGTGGCA-CCCTTTTAAGTCCAC
* *
1072990 AACTTCGTGGCATCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTT-AAGTCCAC
* **
1073018 AACTCTGTGGCATTCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
1073045 AACTCCGTGGCACCCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
*
1073072 AACTCCGTGGCATCCCTTTTAAGACCAC
1 AACTCCGTGGCA-CCCTTTTAAGTCCAC
1073100 AACTCCGTGGCACCCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
*
1073127 AACTCCGTGGCACCCTTTTAAGTCCAT
1 AACTCCGTGGCACCCTTTTAAGTCCAC
*
1073154 AACTCCGTGGCATCTCTTTTAAGTCCAC
1 AACTCCGTGGCA-CCCTTTTAAGTCCAC
*
1073182 AACTCTGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTT-AAGTCCAC
*
1073210 AACTCCGTGGCACCCTTTTTAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
*
1073237 AACTCCATGGCACCCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
*
1073264 AACTTCGTGGCACCCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
1073291 AACTCCGTGGCACCCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
1073318 AACTCCGTGGCACCCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
*
1073345 AACTTCGTGGCACCCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
*
1073372 AACTCTGTGGCACCCTTTTAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
* *
1073399 AACTCCGTGGCATCCTTTTAAGACCAC
1 AACTCCGTGGCACCCTTTTAAGTCCAC
* *
1073426 AACTCTGTGGCACCCTTTTAAGTCCAT
1 AACTCCGTGGCACCCTTTTAAGTCCAC
* *
1073453 AACTCCGTGGCATCTCTTTTGAGTCCAC
1 AACTCCGTGGCA-CCCTTTTAAGTCCAC
* * *
1073481 AACTCTGTGGCAACCTTTTAAAATCCAC
1 AACTCCGTGGCACCCTTTT-AAGTCCAC
*
1073509 AACTCCGTGGCACCCTTTTAAAATCCAC
1 AACTCCGTGGCACCCTTTT-AAGTCCAC
* *
1073537 AACTCCGTGGCACTCTTTTAAAATCCAC
1 AACTCCGTGGCACCCTTTT-AAGTCCAC
*
1073565 AACTCTGTGGCACC
1 AACTCCGTGGCACC
1073579 AATTTCAAAG
Statistics
Matches: 589, Mismatches: 48, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
27 370 0.63
28 219 0.37
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.28
Consensus pattern (27 bp):
AACTCCGTGGCACCCTTTTAAGTCCAC
Found at i:1073039 original size:110 final size:108
Alignment explanation
Indices: 1072908--1073578 Score: 1009
Period size: 110 Copynumber: 6.1 Consensus size: 108
1072898 TAAAGCCCAT
*
1072908 AACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTGTAAGTCCACAACTCCGTGGC
1 AACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGC
* *
1072973 ATCCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAAGTCCAC
66 A-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCAC
* **
1073018 AACTCTGTGGCATTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGC
1 AACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGC
*
1073083 ATCCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCAC
66 A-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC
* * *
1073127 AACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGG
1 AACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGG
*
1073192 CACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCAC
65 CACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC
* *
1073237 AACTCCATGGCACCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCCGTGGC
1 AACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGC
1073302 ACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC
66 ACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC
* *
1073345 AACTTCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGC
1 AACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGC
* * * *
1073410 ATCCTTTTAAGACCACAACTCTGTGGCACCCTTTTAAGTCCAT
66 ACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC
* * * * *
1073453 AACTCCGTGGCATCTCTTTTGAGTCCACAACTCTGTGGCAACCTTTTAAAATCCACAACTCCGTG
1 AACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTG
* * *
1073518 GCACCCTTTTAAAATCCACAACTCCGTGGCACTCTTTTAAAATCCAC
64 GCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCAC
*
1073565 AACTCTGTGGCACC
1 AACTCCGTGGCACC
1073579 AATTTCAAAG
Statistics
Matches: 512, Mismatches: 43, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
108 145 0.28
109 113 0.22
110 213 0.42
111 24 0.05
112 17 0.03
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.28
Consensus pattern (108 bp):
AACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGC
ACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC
Found at i:1073697 original size:28 final size:28
Alignment explanation
Indices: 1072895--1074666 Score: 1339
Period size: 28 Copynumber: 62.5 Consensus size: 28
1072885 AGTGTGACCT
* * *
1072895 CTTT-AAAGCCCATAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1072922 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1072949 CTTGT--AAGTCCACAACTCCGTGGCATCC
1 CTT-TCAAAGCCCACAAGTCAGTGGCA-CC
* * * *
1072977 CTTT-TAAGTCCACAACTTC-GTGGCATC
1 CTTTCAAAGCCCACAA-GTCAGTGGCACC
* * * * **
1073004 CTTTTAAAGTCCACAACTCTGTGGCATT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1073032 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1073059 CTTT-TAAGTCCACAACTCCGTGGCATCC
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * * *
1073087 CTTT-TAAGACCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1073114 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * * * *
1073141 CTTT-TAAGTCCATAACTCCGTGGCATCT
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * * *
1073169 CTTT-TAAGTCCACAACTCTGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1073196 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
** * *
1073224 CTTT-TTAGTCCACAACTCCA-TGGCACC
1 CTTTCAAAGCCCACAAGT-CAGTGGCACC
* * *
1073251 CTTT-TAAGTCCACAACTTC-GTGGCACC
1 CTTTCAAAGCCCACAA-GTCAGTGGCACC
* * * *
1073278 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1073305 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1073332 CTTT-TAAGTCCACAACTTC-GTGGCACC
1 CTTTCAAAGCCCACAA-GTCAGTGGCACC
* * * *
1073359 CTTT-TAAGTCCACAACTCTGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * * *
1073386 CTTT-TAAGTCCACAACTCCGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1073413 CTTT-TAAGACCACAACTCTGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * * * *
1073440 CTTT-TAAGTCCATAACTCCGTGGCATCT
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CC
** * * * *
1073468 CTTT-TGAGTCCACAACTCTGTGGCAAC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* ** * *
1073495 CTTTTAAAATCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* ** * * *
1073523 CTTTTAAAATCCACAACTCCGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* ** * *
1073551 CTTTTAAAATCCACAACTCTGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1073579 AATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 -CTTTCAAAG-CC-CACAAGTCAGTGGC-ACC
*
1073611 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACC
*
1073643 CATTTCAAAGCCCACACAAGTCGGTGGCACC
1 C-TTTCAAAG-CC-CACAAGTCAGTGGCACC
1073674 CTTTCAAAGCCCACAAGTCAGTGGCACCC
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * *
1073703 CTTTCAAAGCTCACGCAAGTTAGTGACACC
1 CTTTCAAAGC-C-CACAAGTCAGTGGCACC
* *
1073733 CTTTTAAAGCCCACAAGTTAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
*
1073762 TTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1073790 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1073818 TTTTTCAAAGCCCACGCAAGTCAGTGGCACC
1 -CTTTCAAAGCCCA--CAAGTCAGTGGCACC
**
1073849 CTTTTGAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * * *
1073877 ATTGCGAAGCCCACAATTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1073905 GTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1073933 CTTTTAAAGCCCACACAAGTCAGTGACACTC
1 CTTTCAAAG-CC-CACAAGTCAGTGGCAC-C
*
1073964 CTTTCAAAGCTCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
1073993 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * *
1074022 TTTTCAAAGCCCACAAATCAGTGGCACTT
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1074051 TTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1074079 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1074107 CTTTCAGAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1074135 CTTTCGAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * * * * * *
1074163 ATTGCGAAGCCTATAATTTAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1074191 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1074219 CTTTTAAAGCCCACACAAGTCAGTGGCACTC
1 CTTTCAAAG-CC-CACAAGTCAGTGGCAC-C
* * *
1074250 CTTTTAAAGCTCACGCAAGTCAGTGGTACC
1 CTTTCAAAGC-C-CACAAGTCAGTGGCACC
* * *
1074280 TTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1074308 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1074336 CTTTCAAAGCCCACGAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1074364 CTTTCAAAGCACACACAAGTCAGTGGCACTC
1 CTTTCAAAGC-C-CACAAGTCAGTGGCAC-C
1074395 CTTTCAAAGCCCACGCAAGTCAGTGGCACC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACC
* * *
1074425 TTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1074453 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1074481 TTTTC-AAGCCCACGAGTCAGTGGTACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1074508 TTTTCAAAGCCCACGAGTCAGTGGCA-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1074535 CTTTCAAAGCCCACAAGTGAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1074563 CTTTCAAAGCCCACGAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1074591 CTTTCAAAGCCCACGCAAGTCAGTTGCACC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACC
* **
1074621 CTTTTAAAGCCCACGCAAGTCAGTAACACTC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCAC-C
*
1074652 TTTTCAAAGCCCACA
1 CTTTCAAAGCCCACA
1074667 TGTGTCAGTG
Statistics
Matches: 1537, Mismatches: 162, Indels: 90
0.86 0.09 0.05
Matches are distributed among these distances:
26 4 0.00
27 416 0.27
28 637 0.41
29 166 0.11
30 139 0.09
31 114 0.07
32 61 0.04
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.24
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:1074331 original size:145 final size:143
Alignment explanation
Indices: 1073581--1074717 Score: 1207
Period size: 145 Copynumber: 7.8 Consensus size: 143
1073571 GTGGCACCAA
* * *
1073581 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCAT
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-T
* *
1073646 TTCAAAGCCCACACAAGTCGGTGGCACCCTTTCAAAGCC-CACAAGTCAGTGGCACCCCTTTCAA
58 TTCAAAGCCCACACAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCA-CCTTTTCAA
* * * *
1073710 AGCTCACGCAAGTTAGTGACACCC
122 AGCCCACG--AGTCAGTGGCACTC
* *
1073734 TTTTAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * * *
1073799 -CC-CACAAGTTAGTGGCACCTTTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTT-GAAGCCC
65 CCCACACAAGTCAGTGGCACC-CTTTCAAAG-CCACACAAGTCAGTGGCA-CCTTTTCAAAGCCC
*
1073861 ACAAGTCAGTGGCAC-C
127 ACGAGTCAGTGGCACTC
* * * * *
1073877 ATTGCGAAGCCCACAATTCAGTGGCACTGTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAG
1 -TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * *
1073942 CCCACACAAGTCAGTGACACTCCTTTCAAAG-CTCACAAGTCAGTGGCACTCCTTTCAAAGCCCA
65 CCCACACAAGTCAGTGGCAC-CCTTTCAAAGCCACACAAGTCAGTGGCAC-CTTTTCAAAGCCCA
*
1074006 CAAGTCAGTGGCACTC
128 CGAGTCAGTGGCACTC
* * *
1074022 TTTTCAAAGCCCACAAATCAGTGGCACTTTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAA
1 -TTTCAAAGCCCACAAGTCAGTGGCAC-TCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
* * * * *
1074087 G-CC-CACAAGTTAGTGGCACCCTTTCAGAGCC-CACAAGTTAGTGGCACCCTTTCGAAGCCCAC
64 GCCCACACAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCACCTTTTCAAAGCCCAC
*
1074149 AAGTCAGTGGCAC-C
129 GAGTCAGTGGCACTC
* * * * * * *
1074163 ATTGCGAAGCCTATAATTTAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAG
1 -TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * *
1074228 CCCACACAAGTCAGTGGCACTCCTTTTAAAGCTCACGCAAGTCAGTGGTACCTTTTCAAAGCCCA
65 CCCACACAAGTCAGTGGCAC-CCTTTCAAAGC-CACACAAGTCAGTGGCACCTTTTCAAAGCCCA
1074293 CGAGTCAGTGGCACTC
128 CGAGTCAGTGGCACTC
* *
1074309 TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTTAGTGGCACCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* *
1074373 CACACACAAGTCAGTGGCACTCCTTTCAAAGCCCACGCAAGTCAGTGGCACCTTTTCAAAGCCCA
65 CCCACACAAGTCAGTGGCAC-CCTTTCAAAG-CCACACAAGTCAGTGGCACCTTTTCAAAGCCCA
1074438 CGAGTCAGTGGCACTC
128 CGAGTCAGTGGCACTC
* * *
1074454 TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTC-AAGCCCACGAGTCAGTGGTACCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* *
1074517 -CC-CACGAGTCAGTGGCA-CCTTTCAAAGCC-CACAAGTGAGTGGCA-CTCTTTCAAAGCCCAC
65 CCCACACAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCACCT-TTTCAAAGCCCAC
1074577 GAGTCAGTGGCA-TCC
129 GAGTCAGTGGCACT-C
* * * ** *
1074592 TTTCAAAGCCCACGCAAGTCAGTTGCACCCTTTTAAAGCCCACGCAAGTCAGTAACACTCTTTTC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTCAAAGCCCA--CAAGTCAGTGGCAC-CCTTTC
*** ** *
1074657 AAAGCCCACATGTGTCAGTGGCAACTTTTTTCAAAGCCTACACAAG-CTAGTGGCACATTTT
61 AAAGCCCACACAAGTCAGTGGC-AC-CCTTTCAAAGCC-ACACAAGTC-AGTGGCACCTTTT
1074718 TTTAAAAAAA
Statistics
Matches: 852, Mismatches: 92, Indels: 82
0.83 0.09 0.08
Matches are distributed among these distances:
137 3 0.00
138 51 0.06
139 2 0.00
140 61 0.07
141 31 0.04
142 57 0.07
143 99 0.12
144 126 0.15
145 256 0.30
146 67 0.08
147 25 0.03
148 13 0.02
149 12 0.01
150 11 0.01
151 28 0.03
152 3 0.00
153 7 0.01
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (143 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
CCACACAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACGA
GTCAGTGGCACTC
Found at i:1075301 original size:20 final size:20
Alignment explanation
Indices: 1075273--1075347 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1075263 TTTTACCTTG
1075273 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1075293 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
1075313 ATGCATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1075333 ATGTATCGATACATT
1 ATGTATCGATACATT
1075348 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Done.