Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008739.1 Hibiscus syriacus cultivar Beakdansim tig00111817_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 827959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:1089 original size:20 final size:20
Alignment explanation
Indices: 1066--1104 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1056 CTTTAGGTAA
1066 AGTTTCAAAACTCTTGAAAT
1 AGTTTCAAAACTCTTGAAAT
* *
1086 AGTTTCGAAGCTCTTGAAA
1 AGTTTCAAAACTCTTGAAA
1105 AGTATCGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
AGTTTCAAAACTCTTGAAAT
Found at i:5295 original size:34 final size:32
Alignment explanation
Indices: 5235--5304 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
5225 CCTTACAAAC
*
5235 TCCCTAGTTTTTCCGGGATAAACTAGAACATT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
* * *
5267 TCCCTAGCTTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
5301 TCCC
1 TCCC
5305 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:5783 original size:19 final size:21
Alignment explanation
Indices: 5759--5814 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
5749 ATCTGTACCC
5759 GGGGAATC-GATACCCCT-GG
1 GGGGAATCTGATACCCCTGGG
* *
5778 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCTGATACCCCTGGG
5799 GGGGAATCTG-TACCCC
1 GGGGAATCTGATACCCC
5815 CTGGACAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.25
20 12 0.38
21 12 0.38
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGAATCTGATACCCCTGGG
Found at i:5802 original size:21 final size:21
Alignment explanation
Indices: 5759--5818 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
5749 ATCTGTACCC
5759 GGGGAATC-GATA-CCCCT-GG
1 GGGGAATCTG-TACCCCCTGGG
*
5778 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
5799 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
5819 ACAATCTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.25
20 6 0.17
21 21 0.58
ACGTcount: A:0.15, C:0.28, G:0.37, T:0.20
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:8855 original size:34 final size:32
Alignment explanation
Indices: 8792--8861 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
8782 CCTTACAAAC
*
8792 TCCCTAGTTTTTCCGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
* * *
8824 TCCCTAGCTTTTACACGGGATTAGCTCGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
8858 TCCC
1 TCCC
8862 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:9169 original size:21 final size:21
Alignment explanation
Indices: 9143--9184 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9133 CCAGAATGGG
*
9143 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
9164 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
9185 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:9319 original size:15 final size:15
Alignment explanation
Indices: 9299--9355 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
9289 ACCATGCAGG
9299 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
9314 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
9330 TGGGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
9348 GGGGAATC
1 GGGGAATC
9356 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:9338 original size:19 final size:19
Alignment explanation
Indices: 9297--9406 Score: 96
Period size: 20 Copynumber: 6.1 Consensus size: 19
9287 AAACCATGCA
9297 GGGGGGAATCTGTA-CCC-
1 GGGGGGAATCTGTACCCCT
9314 --GGGGAATC-GATACCCCT
1 GGGGGGAATCTG-TACCCCT
*
9331 GGGGGGAATCTGT-TCCC-
1 GGGGGGAATCTGTACCCCT
9348 --GGGGAATC-GATACCCCCT
1 GGGGGGAATCTG-TA-CCCCT
*
9366 GGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCTG-TACCCCT
9386 GGGGGGAATCTGTACCCCT
1 GGGGGGAATCTGTACCCCT
9405 GG
1 GG
9407 ACAATTTGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
14 2 0.03
15 19 0.25
16 3 0.04
17 3 0.04
18 3 0.04
19 17 0.23
20 26 0.35
21 2 0.03
ACGTcount: A:0.16, C:0.27, G:0.36, T:0.20
Consensus pattern (19 bp):
GGGGGGAATCTGTACCCCT
Found at i:9365 original size:35 final size:34
Alignment explanation
Indices: 9297--9382 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 34
9287 AAACCATGCA
*
9297 GGGGGGAATCTGTACCCGGGGAATCGATACCCCT
1 GGGGGGAATCTGTTCCCGGGGAATCGATACCCCT
9331 GGGGGGAATCTGTTCCCGGGGAATCGATACCCCCT
1 GGGGGGAATCTGTTCCCGGGGAATCGATA-CCCCT
9366 GGGGGGAATCTGTTCCC
1 GGGGGGAATCTGTTCCC
9383 CCTGGGGGGA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 28 0.56
35 22 0.44
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.20
Consensus pattern (34 bp):
GGGGGGAATCTGTTCCCGGGGAATCGATACCCCT
Found at i:14866 original size:4 final size:4
Alignment explanation
Indices: 14857--14883 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
14847 AAGCTTGGAG
14857 ATGA ATGA ATGA ATGA ATGA ATGA ATG
1 ATGA ATGA ATGA ATGA ATGA ATGA ATG
14884 CTTGCATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
ATGA
Found at i:15399 original size:18 final size:18
Alignment explanation
Indices: 15377--15421 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
15367 TTCAAACTGT
15377 AATTTAATTATTGATTTTG
1 AATTTAATT-TTGATTTTG
*
15396 ATTTTGAA-TTTGATTTTG
1 AATTT-AATTTTGATTTTG
15414 AATTTAAT
1 AATTTAAT
15422 CACTTAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 5 0.23
20 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (18 bp):
AATTTAATTTTGATTTTG
Found at i:15402 original size:12 final size:12
Alignment explanation
Indices: 15377--15418 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
15367 TTCAAACTGT
*
15377 AATTTAATTATTG
1 AATTTGATT-TTG
*
15390 ATTTTGATTTTG
1 AATTTGATTTTG
15402 AATTTGATTTTG
1 AATTTGATTTTG
15414 AATTT
1 AATTT
15419 AATCACTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (12 bp):
AATTTGATTTTG
Found at i:24515 original size:23 final size:23
Alignment explanation
Indices: 24489--24533 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24479 CACCACAGCT
*
24489 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
24512 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
24534 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:24782 original size:149 final size:149
Alignment explanation
Indices: 24512--24816 Score: 583
Period size: 149 Copynumber: 2.0 Consensus size: 149
24502 CGAAGTGCCC
* *
24512 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
24577 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACCCATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
24642 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
24661 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
24726 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
24791 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
24810 CGTAGAC
1 CGTAGAC
24817 CCTCGACTCT
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCTAAGAACCG
Found at i:25327 original size:5 final size:5
Alignment explanation
Indices: 25317--25345 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
25307 TTCATATAAC
25317 TCATT TCATT TCATT TCATT TCATT TCAT
1 TCATT TCATT TCATT TCATT TCATT TCAT
25346 ATCTATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (5 bp):
TCATT
Found at i:26315 original size:21 final size:21
Alignment explanation
Indices: 26291--26335 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
26281 TCTTGTTCGT
*
26291 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
26312 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
26333 TTG
1 TTG
26336 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:29616 original size:23 final size:23
Alignment explanation
Indices: 29590--29634 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29580 CACCACAGCT
*
29590 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
29613 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
29635 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:29883 original size:149 final size:149
Alignment explanation
Indices: 29613--29917 Score: 583
Period size: 149 Copynumber: 2.0 Consensus size: 149
29603 CGAAGTGCCC
* *
29613 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
29678 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACCCATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
29743 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
29762 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
29827 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
29892 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
29911 CGTAGAC
1 CGTAGAC
29918 CCTCGACTCT
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCTAAGAACCG
Found at i:30358 original size:2 final size:2
Alignment explanation
Indices: 30351--30390 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
30341 TCTCTTAGAC
30351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30391 TCACATGTTC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31151 original size:23 final size:23
Alignment explanation
Indices: 31125--31169 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31115 CACCACAGCT
*
31125 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
31148 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
31170 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:31418 original size:149 final size:149
Alignment explanation
Indices: 31148--31453 Score: 567
Period size: 149 Copynumber: 2.1 Consensus size: 149
31138 CGAAGTGCCC
* *
31148 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
31213 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACCCATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
31278 CATATGTCCCTAAGAACCG
131 CATATATCCCTAAGAACCG
*
31297 CGTAGACTTGCATCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
31362 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
31427 CATATATCCCTAAGAACCG
131 CATATATCCCTAAGAACCG
31446 CGTAGACT
1 CGTAGACT
31454 CTCGACTCTT
Statistics
Matches: 152, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATATCCCTAAGAACCG
Found at i:31895 original size:2 final size:2
Alignment explanation
Indices: 31888--31915 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31878 TCTCTTAGAC
31888 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
31916 CACATGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32966 original size:21 final size:20
Alignment explanation
Indices: 32936--32979 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
32926 TCTTGTTCGT
* *
32936 TTGAAGGGTATCGGTTCCCC
1 TTGAAGGGTACCGATTCCCC
32956 TTGAATGGGTACCGATTCCCC
1 TTGAA-GGGTACCGATTCCCC
32977 TTG
1 TTG
32980 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:37386 original size:21 final size:21
Alignment explanation
Indices: 37318--37398 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
37308 TTGGTGCAGA
*
37318 GGGAATCGA-TCCCCTCCAT-G
1 GGGAACCGATTCCCC-CCATAG
**
37338 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCCCAT--AG
37362 GGGAACCGATTCCCCCCATAG
1 GGGAACCGATTCCCCCCATAG
* *
37383 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
37399 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 26 0.53
22 5 0.10
23 17 0.35
24 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCATAG
Found at i:40093 original size:14 final size:16
Alignment explanation
Indices: 40076--40108 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
40066 AAAATAAATA
40076 TTAAAAT-AAT-TTAT
1 TTAAAATAAATATTAT
40090 TTAAAATAAATATTAT
1 TTAAAATAAATATTAT
40106 TTA
1 TTA
40109 TTATATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATAAATATTAT
Found at i:40103 original size:13 final size:13
Alignment explanation
Indices: 40066--40103 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
40056 TCGATATTGA
40066 AAAATAAATA-TT
1 AAAATAAATATTT
*
40078 AAAATAATTTATTT
1 AAAATAA-ATATTT
40092 AAAATAAATATT
1 AAAATAAATATT
40104 ATTTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 6 0.27
14 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:41191 original size:16 final size:16
Alignment explanation
Indices: 41170--41224 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
41160 ACCGTTGGCT
41170 GAGGCGGTTGGAGGCA
1 GAGGCGGTTGGAGGCA
*
41186 GAGGCGGCTGGAGGCA
1 GAGGCGGTTGGAGGCA
41202 GAGGCGGTTGGAGGCA
1 GAGGCGGTTGGAGGCA
41218 GAGGCGG
1 GAGGCGG
41225 CTAGGGTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.18, C:0.15, G:0.58, T:0.09
Consensus pattern (16 bp):
GAGGCGGTTGGAGGCA
Found at i:41349 original size:3 final size:3
Alignment explanation
Indices: 41341--41450 Score: 114
Period size: 3 Copynumber: 37.0 Consensus size: 3
41331 TATATATATT
* * * * *
41341 TAA TAA TAA TAA TAA TAG TAA TAT TTA TAA TAA TAA TAA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
41389 TAG TAA TAA TAA TAA TAA TAA T-A TTA TAG TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
41436 TTA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA
41451 ATCAATATGG
Statistics
Matches: 85, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
2 2 0.02
3 83 0.98
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:42415 original size:113 final size:113
Alignment explanation
Indices: 41795--42401 Score: 918
Period size: 113 Copynumber: 5.4 Consensus size: 113
41785 AACAAGTTCT
* * *
41795 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAAT
* * * * * *
41860 T-TGAGCAAAA-ATCTGAACAAATTCGTCTCATTATGAACTTCTTCATCA
66 TCAG-GCAAAAGGT-TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
* **** * * *
41908 TTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGAT-GAA
* * *
41973 TTGA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCC
65 TTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
* * *
42021 TTCTTCAGATGAGTTCATT-TCATTATGAACTTTTTCTGGAAAGGCTGATCCATCAATTGATGAA
1 TTCTTCAGATGAGTTC-TTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAA
42085 TTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTAT-C
65 TTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-TCC
42134 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAAT
42199 TCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
66 TCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
42247 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAAT
*
42312 TCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTGTTCTTCC
66 TCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
42360 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
42402 TGTCAATCTA
Statistics
Matches: 454, Mismatches: 32, Indels: 16
0.90 0.06 0.03
Matches are distributed among these distances:
112 8 0.02
113 439 0.97
114 7 0.02
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAAT
TCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
Found at i:43363 original size:83 final size:83
Alignment explanation
Indices: 43219--43738 Score: 853
Period size: 83 Copynumber: 6.3 Consensus size: 83
43209 CTTATTTCTA
* *
43219 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACAAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
43284 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
43302 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
*
43367 GAATACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * * *
43385 CTATGAGCATATTTATTTTCCAACTTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
43450 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
43468 CTATGAGCATATTCATCTTCCAACTTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
43533 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
43551 CTATGAGCATATTCAT-TTCCCAACTTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTT-CCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAA
43615 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* * *
43634 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACCCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
43699 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
43717 CTATGAGCAAATTCATCTTCCA
1 CTATGAGCAAATTCATCTTCCA
43739 TTTAATGTTT
Statistics
Matches: 416, Mismatches: 19, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
82 2 0.00
83 412 0.99
84 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:44901 original size:1 final size:1
Alignment explanation
Indices: 44897--44945 Score: 62
Period size: 1 Copynumber: 49.0 Consensus size: 1
44887 TCTTTTTCTC
* * * *
44897 TTTTTTTTTTTTCTCTTTTTTTTTTTTTTTTCTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
44946 CTTCAAGCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:44909 original size:15 final size:15
Alignment explanation
Indices: 44879--44945 Score: 84
Period size: 15 Copynumber: 4.4 Consensus size: 15
44869 CCCCCCCCCC
44879 CTTTTTCTTCTTTTTCT
1 CTTTTT-TT-TTTTTCT
44896 CTTTTTTTTTTTTCT
1 CTTTTTTTTTTTTCT
44911 CTTTTTTTTTTTT-T
1 CTTTTTTTTTTTTCT
*
44925 -TTTCTTTTTTTTTTT
1 CTTT-TTTTTTTTTCT
44940 CTTTTT
1 CTTTTT
44946 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.06
14 10 0.21
15 23 0.49
16 5 0.11
17 6 0.13
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
CTTTTTTTTTTTTCT
Found at i:44918 original size:18 final size:17
Alignment explanation
Indices: 44889--44948 Score: 93
Period size: 17 Copynumber: 3.5 Consensus size: 17
44879 CTTTTTCTTC
*
44889 TTTTTCTCTTTTTTTTT
1 TTTTTCTTTTTTTTTTT
*
44906 TTTCTCTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTT
44923 TTTTTCTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTT
44940 CTTTTTCTT
1 -TTTTTCTT
44949 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 31 0.79
18 8 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTT
Found at i:44919 original size:19 final size:18
Alignment explanation
Indices: 44897--44948 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
44887 TCTTTTTCTC
44897 TTTTTTTTTTTTCTCTTTT
1 TTTTTTTTTTTTCT-TTTT
44916 TTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTCTTTTT
*
44934 TTTTTTCTTTTTCTT
1 TTTTTTTTTTTTCTT
44949 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 18 0.56
19 14 0.44
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (18 bp):
TTTTTTTTTTTTCTTTTT
Found at i:56315 original size:13 final size:13
Alignment explanation
Indices: 56278--56317 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
56268 TCGTTATTGA
56278 AAAATAAATA-TT
1 AAAATAAATATTT
*
56290 AAAATAATTTATTT
1 AAAATAA-ATATTT
56304 AAAATAAATATTT
1 AAAATAAATATTT
56317 A
1 A
56318 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:57542 original size:16 final size:16
Alignment explanation
Indices: 57521--57577 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
57511 ACCGTTGGCT
*
57521 GAGGCGGTTGGAGGCA
1 GAGGCGGCTGGAGGCA
57537 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
*
57553 GAGGCGACTGGAGGCA
1 GAGGCGGCTGGAGGCA
57569 GAGGCGGCT
1 GAGGCGGCT
57578 AGGGTTAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.19, C:0.18, G:0.54, T:0.09
Consensus pattern (16 bp):
GAGGCGGCTGGAGGCA
Found at i:57698 original size:3 final size:3
Alignment explanation
Indices: 57690--57809 Score: 123
Period size: 3 Copynumber: 40.0 Consensus size: 3
57680 TATATATATT
* * * *
57690 TAA TAA TAA TAA TAA TAT TTA TAA TAA TAT TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
57738 TAT TTA TAG TAA TAA TAA TAA TAA TAA TAT TTA TAG TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
57786 TAA TAA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
57810 ATCAATATGG
Statistics
Matches: 91, Mismatches: 26, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:57988 original size:15 final size:17
Alignment explanation
Indices: 57963--57998 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
57953 AAAGGGGGAG
57963 AAGGTGTGTGTTTTTAA
1 AAGGTGTGTGTTTTTAA
57980 AAGGTGTGTGTTTTTAA
1 AAGGTGTGTGTTTTTAA
57997 AA
1 AA
57999 TGATAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (17 bp):
AAGGTGTGTGTTTTTAA
Found at i:60507 original size:42 final size:42
Alignment explanation
Indices: 60451--60561 Score: 213
Period size: 42 Copynumber: 2.6 Consensus size: 42
60441 TGATCTAAGG
*
60451 TGATGTTGATCCAACTCCTTATGTGATGGACTAGCGAAATGA
1 TGATGCTGATCCAACTCCTTATGTGATGGACTAGCGAAATGA
60493 TGATGCTGATCCAACTCCTTATGTGATGGACTAGCGAAATGA
1 TGATGCTGATCCAACTCCTTATGTGATGGACTAGCGAAATGA
60535 TGATGCTGATCCAACTCCTTATGTGAT
1 TGATGCTGATCCAACTCCTTATGTGAT
60562 AGAAGAGCAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (42 bp):
TGATGCTGATCCAACTCCTTATGTGATGGACTAGCGAAATGA
Found at i:60889 original size:138 final size:138
Alignment explanation
Indices: 60617--60969 Score: 548
Period size: 138 Copynumber: 2.5 Consensus size: 138
60607 ACAATCTAAC
* * *
60617 GTTCTTCTCATTATGAACTTCTTCTCCCTTATCAGATGAGTTATTCTCATTACGAACTCTCCACT
1 GTTCTTCTCATTATGAACTTCTTCTCCCTCATC-GATGAGTTCTTCTCATTATGAACTCTCCACT
* * *
60682 GGAAAGGTTGATCCCTCGAGTGATGCGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTAAG
65 GGAAATGTTGATCCCTCGAGTGAGGCATTGCTGATTCAACTCCATATGTGATGAATCGAGCTAAG
60747 GTTGAACAA
130 GTTGAACAA
* * *
60756 GTTCTACTCATTATGAACTT-TTTTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATT
1 GTTCTTCTCATTATGAACTTCTTCTCCCTCATC-GATGAGTTCTTCTCATTATGAACTCTCCACT
* *
60820 GGAAATGTTGATCCCT-GAAGTGAGGTATTGTTGATTCAACTCCATATGTGATGAATCGAGCTAA
65 GGAAATGTTGATCCCTCG-AGTGAGGCATTGCTGATTCAACTCCATATGTGATGAATCGAGCTAA
*
60884 GGTTGAATAA
129 GGTTGAACAA
60894 GTTCTTCTCATTATGAACTTCTTCTCCCTCATCGACTGAGTTCTTCTCATTATGAACTCTCCACT
1 GTTCTTCTCATTATGAACTTCTTCTCCCTCATCGA-TGAGTTCTTCTCATTATGAACTCTCCACT
60959 GGAAATGTTGA
65 GGAAATGTTGA
60970 CTGGCTCATT
Statistics
Matches: 195, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
137 1 0.01
138 125 0.64
139 69 0.35
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (138 bp):
GTTCTTCTCATTATGAACTTCTTCTCCCTCATCGATGAGTTCTTCTCATTATGAACTCTCCACTG
GAAATGTTGATCCCTCGAGTGAGGCATTGCTGATTCAACTCCATATGTGATGAATCGAGCTAAGG
TTGAACAA
Found at i:61851 original size:58 final size:55
Alignment explanation
Indices: 61710--61918 Score: 169
Period size: 58 Copynumber: 3.7 Consensus size: 55
61700 ATTTACAGTT
* *
61710 ATCAAGAAACCCCT-AAAATTAGGCTTAGCTTCTTTCAAAAATTCATTT--A-A-AAAC
1 ATCAAGAAACCCCTGAAAATTAGGCTTAG-TT-TCT-AAAAATT-ATTTGCAGATAATC
* ** * * * *
61764 ATCAAGAAACCCTTGAAAATCGGGTTTAGTTTCTAAAAATCTTTCGTTTTCAG-TTATC
1 ATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTAAAAA---TT-ATTTGCAGATAATC
* *
61822 ATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCCTTTAAAAATTATTTGGAGATAATC
1 ATCAAGAAACCCCTGAAAATTAGGCTTAGTTT-C--TAAAAATTATTTGCAGATAATC
*
61880 ATCAAGAAACCCCTGGAAATTAGGCTTAGTTTCTAAAAA
1 ATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTAAAAA
61919 CTCGTTTGAA
Statistics
Matches: 124, Mismatches: 19, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
52 5 0.04
53 2 0.02
54 15 0.12
55 23 0.19
57 7 0.06
58 65 0.52
59 1 0.01
61 6 0.05
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (55 bp):
ATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTAAAAATTATTTGCAGATAATC
Found at i:61912 original size:116 final size:112
Alignment explanation
Indices: 61710--61918 Score: 287
Period size: 116 Copynumber: 1.8 Consensus size: 112
61700 ATTTACAGTT
61710 ATCAAGAAACCCCTAAAATTAGGCTTAGCTTCTTTCAAAAATTCATTTAAAAACATCAAGAAACC
1 ATCAAGAAACCCCTAAAATTAGGCTTAGCTTCTTTCAAAAATTCATTTAAAAACATCAAGAAACC
* * *
61775 CTTGAAAATCGGGTTTAGTTTCTAAAAATCTTTCGTTTTCAGTTATC
66 CCTGAAAATCAGGCTTAGTTTCTAAAAATCTTTCGTTTTCAGTTATC
* *
61822 ATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCCTTT-AAAAATT-ATTTGGAGATAATCATCAA
1 ATCAAGAAACCCCT-AAAATTAGGCTTAGCTT-CTTTCAAAAATTCATTT--A-A-AAACATCAA
* *
61885 GAAACCCCTGGAAATTAGGCTTAGTTTCTAAAAA
60 GAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAA
61919 CTCGTTTGAA
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
112 18 0.21
113 23 0.27
114 5 0.06
115 1 0.01
116 37 0.44
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (112 bp):
ATCAAGAAACCCCTAAAATTAGGCTTAGCTTCTTTCAAAAATTCATTTAAAAACATCAAGAAACC
CCTGAAAATCAGGCTTAGTTTCTAAAAATCTTTCGTTTTCAGTTATC
Found at i:62010 original size:20 final size:21
Alignment explanation
Indices: 61982--62053 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 21
61972 TATCTTGCTC
*
61982 GAAAAACTTA-TAGATGGCCT
1 GAAAGACTTACTAGATGGCCT
*
62002 GAAAGACTTACTCATCAT-G-CT
1 GAAAGACTTACT-A-GATGGCCT
62023 CGAAAGACTTACT-GATGGCCT
1 -GAAAGACTTACTAGATGGCCT
*
62044 GAATGACTTA
1 GAAAGACTTA
62054 TGCTGATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 2 0.05
20 19 0.45
21 5 0.12
22 14 0.33
23 2 0.05
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (21 bp):
GAAAGACTTACTAGATGGCCT
Found at i:62033 original size:42 final size:40
Alignment explanation
Indices: 61947--62054 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 40
61937 GCCTGAAGGT
* * *
61947 CTTATGGATGGCC-CAAAGTACTTATTATCTTGCTCGAAAAA
1 CTTAT-GATGGCCTGAAAG-ACTTATCATCATGCTCGAAAAA
*
61988 CTTATAGATGGCCTGAAAGACTTACTCATCATGCTCGAAAGA
1 CTTAT-GATGGCCTGAAAGACTTA-TCATCATGCTCGAAAAA
*
62030 CTTACTGATGGCCTGAATGACTTAT
1 CTTA-TGATGGCCTGAAAGACTTAT
62055 GCTGATTTGA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
41 18 0.31
42 39 0.67
43 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (40 bp):
CTTATGATGGCCTGAAAGACTTATCATCATGCTCGAAAAA
Found at i:62302 original size:22 final size:22
Alignment explanation
Indices: 62277--62389 Score: 94
Period size: 22 Copynumber: 5.3 Consensus size: 22
62267 TGGCCCAAAG
62277 GACTTACACATCATGCTCGAAA
1 GACTTACACATCATGCTCGAAA
* * *
62299 GACTT--AC-TGATGGCCCGAAT
1 GACTTACACATCAT-GCTCGAAA
62319 GACTTACACATCATGCTCGAAA
1 GACTTACACATCATGCTCGAAA
* * *
62341 GACTT--AC-TGATGGTCCGAAT
1 GACTTACACATCATGCT-CGAAA
*
62361 GACTTACACATCATGCTTGAAA
1 GACTTACACATCATGCTCGAAA
*
62383 GGCTTAC
1 GACTTAC
62390 TCATTAAGAA
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.12
20 24 0.35
22 29 0.42
23 8 0.12
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (22 bp):
GACTTACACATCATGCTCGAAA
Found at i:62312 original size:42 final size:42
Alignment explanation
Indices: 62265--62390 Score: 207
Period size: 42 Copynumber: 3.0 Consensus size: 42
62255 ATGTCTTATG
* *
62265 GATGGCCCAAAGGACTTACACATCATGCTCGAAAGACTTACT
1 GATGGCCCGAATGACTTACACATCATGCTCGAAAGACTTACT
62307 GATGGCCCGAATGACTTACACATCATGCTCGAAAGACTTACT
1 GATGGCCCGAATGACTTACACATCATGCTCGAAAGACTTACT
* * *
62349 GATGGTCCGAATGACTTACACATCATGCTTGAAAGGCTTACT
1 GATGGCCCGAATGACTTACACATCATGCTCGAAAGACTTACT
62391 CATTAAGAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (42 bp):
GATGGCCCGAATGACTTACACATCATGCTCGAAAGACTTACT
Found at i:62322 original size:20 final size:20
Alignment explanation
Indices: 62294--62367 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
62284 ACATCATGCT
62294 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* * *
62314 CGAATGACTTACACATCAT-GCT
1 CGAAAGACTT--AC-TGATGGCC
*
62336 CGAAAGACTTACTGATGGTC
1 CGAAAGACTTACTGATGGCC
*
62356 CGAATGACTTAC
1 CGAAAGACTTAC
62368 ACATCATGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 3 0.07
20 23 0.55
22 13 0.31
23 3 0.07
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:62551 original size:53 final size:53
Alignment explanation
Indices: 62487--62685 Score: 260
Period size: 52 Copynumber: 3.8 Consensus size: 53
62477 ATTAAAAATC
**
62487 AACATCAAGAAACCCCTAAAAAATTATACTTAGTTTC-TAAAAATTCATTTGAA
1 AACATCAAGAAACCCCT-AAAAATTAGGCTTAGTTTCTTAAAAATTCATTTGAA
* * **
62540 AACATCAAGAAATCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTTGAA
1 AACATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTAAAAATTCATTTGAA
* * **
62593 AACATTAAGAAACCTCT-AAAATTAGGCTTAGTTTCTTTCAAATTCATTTGAA
1 AACATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTAAAAATTCATTTGAA
* *
62645 AACATCGAGAAACCCCTGAAAATTAGGCTTAGTTTC-TAAAA
1 AACATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTAAAA
62686 TCTTTTGTTT
Statistics
Matches: 128, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
52 66 0.52
53 62 0.48
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.32
Consensus pattern (53 bp):
AACATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTAAAAATTCATTTGAA
Found at i:62614 original size:52 final size:52
Alignment explanation
Indices: 62487--62681 Score: 250
Period size: 53 Copynumber: 3.7 Consensus size: 52
62477 ATTAAAAATC
** **
62487 AACATCAAGAAACCCCTAAAAAATTATACTTAGTTTC-TAAAAATTCATTTGAA
1 AACATCAAGAAA-CCCT-AAAAATTAGGCTTAGTTTCTTTCAAATTCATTTGAA
* *
62540 AACATCAAGAAATCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTTGAA
1 AACATCAAGAAA-CCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCATTTGAA
*
62593 AACATTAAGAAACCTCT-AAAATTAGGCTTAGTTTCTTTCAAATTCATTTGAA
1 AACATCAAGAAACC-CTAAAAATTAGGCTTAGTTTCTTTCAAATTCATTTGAA
* *
62645 AACATCGAGAAACCCCTGAAAATTAGGCTTAGTTTCT
1 AACATCAAGAAA-CCCTAAAAATTAGGCTTAGTTTCT
62682 AAAATCTTTT
Statistics
Matches: 127, Mismatches: 11, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
52 63 0.50
53 64 0.50
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (52 bp):
AACATCAAGAAACCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCATTTGAA
Found at i:62667 original size:105 final size:105
Alignment explanation
Indices: 62487--62681 Score: 275
Period size: 105 Copynumber: 1.8 Consensus size: 105
62477 ATTAAAAATC
*
62487 AACATCAAGAAACCCCTAAAAAATTATACTTAGTTTCTAAAAATTCATTTGAAAACATCAAGAAA
1 AACATCAAGAAACCCCT-AAAAATTAGACTTAGTTTCTAAAAATTCATTTGAAAACATCAAGAAA
*
62552 TCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTTGAA
65 CCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTTGAA
* * * ** *
62593 AACATTAAGAAACCTCT-AAAATTAGGCTTAGTTTCTTTCAAATTCATTTGAAAACATCGAGAAA
1 AACATCAAGAAACCCCTAAAAATTAGACTTAGTTTC-TAAAAATTCATTTGAAAACATCAAGAAA
* *
62657 CCCCTGAAAATTAGGCTTAGTTTCT
65 CCCCTAAAAATTAGGCTTAATTTCT
62682 AAAATCTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
104 16 0.21
105 47 0.60
106 15 0.19
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (105 bp):
AACATCAAGAAACCCCTAAAAATTAGACTTAGTTTCTAAAAATTCATTTGAAAACATCAAGAAAC
CCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTTGAA
Found at i:62864 original size:36 final size:40
Alignment explanation
Indices: 62768--62907 Score: 114
Period size: 40 Copynumber: 3.6 Consensus size: 40
62758 ATAAATTTTG
* *
62768 GTTTTAAGAAAAAACAATCTTAAGTGAAATGAATATTCTT
1 GTTTTAAGAAAAAATAATCTCAAGTGAAATGAATATTCTT
* * * *
62808 GTTTCAGGTAAAAACT-ATCTCAAGTGAGATG-A-A-TCTT
1 GTTTTAAG-AAAAAATAATCTCAAGTGAAATGAATATTCTT
* *
62845 GTTTTAAG-AAAAATAATCTCTAGTGAAACGAA-ATTTCTT
1 GTTTTAAGAAAAAATAATCTCAAGTGAAATGAATA-TTCTT
* *
62884 GTTTTGAGTAAAAAAT-GTCTCAAG
1 GTTTTAAG-AAAAAATAATCTCAAG
62908 CGAGACAAAG
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
35 5 0.06
36 12 0.15
37 12 0.15
38 1 0.01
39 12 0.15
40 25 0.32
41 11 0.14
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (40 bp):
GTTTTAAGAAAAAATAATCTCAAGTGAAATGAATATTCTT
Found at i:62895 original size:76 final size:77
Alignment explanation
Indices: 62750--62912 Score: 181
Period size: 76 Copynumber: 2.1 Consensus size: 77
62740 GAAAGAACCC
* * * *
62750 CAAGCGATATAAATTTTGGTTTTAAGAAAAAACAATCTTAAGTGAAATGAATATTCTTGTTTCAG
1 CAAGCGAGATGAATCTT-GTTTTAAGAAAAAACAATCTTAAGTGAAACGAATATTCTTGTTTCAG
*
62815 GTAAAAACTATCT
65 GTAAAAAATATCT
* * *
62828 CAAGTGAGATGAATCTTGTTTTAAG-AAAAATAATCTCT-AGTGAAACGAA-ATTTCTTGTTT-T
1 CAAGCGAGATGAATCTTGTTTTAAGAAAAAACAATCT-TAAGTGAAACGAATA-TTCTTGTTTCA
*
62889 GAGTAAAAAATGTCT
64 G-GTAAAAAATATCT
62904 CAAGCGAGA
1 CAAGCGAGA
62913 CAAAGTATGT
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
75 2 0.03
76 48 0.67
77 9 0.12
78 13 0.18
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (77 bp):
CAAGCGAGATGAATCTTGTTTTAAGAAAAAACAATCTTAAGTGAAACGAATATTCTTGTTTCAGG
TAAAAAATATCT
Found at i:63351 original size:65 final size:67
Alignment explanation
Indices: 63281--63406 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 67
63271 TCAAGTGAGA
* *
63281 TGAAATTTAT-TTTAAAATAAAAATGTCTCAAGTGAGACAAAATTTATTTTTA-AGAAAAATAAC
1 TGAAATTTATGTTTAAAAGAAAAATGTCTCAAGTGAGACAAAATTTATTTTAAGAGAAAAATAAC
63344 TT
66 TT
* ** * * *
63346 TGAAATTTGTGTTTCGAAGGAAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAA
1 TGAAATTTATGTTTAAAAGAAAAATGTCTCAAGTGAGACAAAATTTATTTTAAGAGAAAAA
63407 ATGTCTCAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 9 0.18
66 35 0.69
67 7 0.14
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (67 bp):
TGAAATTTATGTTTAAAAGAAAAATGTCTCAAGTGAGACAAAATTTATTTTAAGAGAAAAATAAC
TT
Found at i:63442 original size:103 final size:103
Alignment explanation
Indices: 63164--63443 Score: 336
Period size: 103 Copynumber: 2.7 Consensus size: 103
63154 ATTTTAGGGG
* * * * * *
63164 AATGTCTCAAGTGAAACGATGA-TTGTTTT--GAGAGAAATTGTCTCAAGCGAGACAAAATTTGG
1 AATGTCTCAAGTGAGACGA-AATTTGTTTTAAGAGAAAAAATGTCTCAAGTGAGACAAAATTTGT
*
63226 TTCAAGTAAAAGAACTTTGAAATTTGTGTTCCGAAGAAA
65 TTCAAGAAAAAGAACTTTGAAATTTGTGTTCCGAAGAAA
* * * *
63265 AATATCTCAAGTGAGATGAAATTTATTTTAA-A-ATAAAAATGTCTCAAGTGAGACAAAATTTAT
1 AATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGA-AAAAATGTCTCAAGTGAGACAAAATTT-G
* * * *
63328 TTTTAAGAAAAATAACTTTGAAATTTGTGTTTCGAAGGAA
64 TTTCAAGAAAAAGAACTTTGAAATTTGTGTTCCGAAGAAA
*
63368 AATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAAATGTCTCAAGTGAGATAAAATTTGTT
1 AATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAAATGTCTCAAGTGAGACAAAATTTGTT
*
63433 TCGAAAAAAAA
66 TC-AAGAAAAA
63444 CACCCAACTA
Statistics
Matches: 149, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
100 1 0.01
101 23 0.15
102 25 0.17
103 65 0.44
104 34 0.23
105 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (103 bp):
AATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAAATGTCTCAAGTGAGACAAAATTTGTT
TCAAGAAAAAGAACTTTGAAATTTGTGTTCCGAAGAAA
Found at i:64628 original size:10 final size:10
Alignment explanation
Indices: 64609--64696 Score: 65
Period size: 10 Copynumber: 8.5 Consensus size: 10
64599 ATTGTCATCA
64609 TTTTTCTTTG
1 TTTTTCTTTG
*
64619 TTTCTCTTTG
1 TTTTTCTTTG
64629 CTTTTTTCTTTG
1 --TTTTTCTTTG
64641 TTTTTCTTTG
1 TTTTTCTTTG
*
64651 CTCTTT-TTT-
1 -TTTTTCTTTG
*
64660 TTTTGCTTT-
1 TTTTTCTTTG
*
64669 TTCTTCTTTG
1 TTTTTCTTTG
64679 CTATTTTTCTTTG
1 ---TTTTTCTTTG
64692 TTTTT
1 TTTTT
64697 ATCCTCGCCT
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
8 3 0.05
9 10 0.16
10 27 0.44
11 4 0.06
12 9 0.15
13 9 0.15
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTCTTTG
Found at i:64636 original size:22 final size:22
Alignment explanation
Indices: 64609--64694 Score: 91
Period size: 22 Copynumber: 3.6 Consensus size: 22
64599 ATTGTCATCA
64609 TTTTTCTTTGTTTCTCTTTGCT
1 TTTTTCTTTGTTTCTCTTTGCT
*
64631 TTTTTCTTTGTTTTTCTTTGCTCT
1 TTTTTCTTTGTTTCTCTTTG--CT
*
64655 TTTTTTTTTGCTTTTTCTTCTTTGCT
1 TTTTTCTTTG---TTTC-TCTTTGCT
64681 ATTTTTCTTTGTTT
1 -TTTTTCTTTGTTT
64695 TTATCCTCGC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
22 19 0.36
24 14 0.26
26 2 0.04
27 12 0.23
28 6 0.11
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (22 bp):
TTTTTCTTTGTTTCTCTTTGCT
Found at i:64664 original size:14 final size:13
Alignment explanation
Indices: 64623--64696 Score: 77
Period size: 14 Copynumber: 5.9 Consensus size: 13
64613 TCTTTGTTTC
64623 TCTTTGC-TTTTT
1 TCTTTGCTTTTTT
64635 TCTTTG---TTTT
1 TCTTTGCTTTTTT
64645 TCTTTGCTCTTTTT
1 TCTTTGCT-TTTTT
*
64659 TTTTTGCTTTTTCT
1 TCTTTGCTTTTT-T
*
64673 TCTTTGCTATTTT
1 TCTTTGCTTTTTT
64686 TCTTTG-TTTTT
1 TCTTTGCTTTTT
64697 ATCCTCGCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
10 10 0.19
12 10 0.19
13 11 0.21
14 22 0.42
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (13 bp):
TCTTTGCTTTTTT
Found at i:65966 original size:22 final size:22
Alignment explanation
Indices: 65938--65980 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
65928 ATAGATACTA
* *
65938 ATGCAAATATGCTCATGCAAAG
1 ATGCAAAGACGCTCATGCAAAG
65960 ATGCAAAGACGCTCATGCAAA
1 ATGCAAAGACGCTCATGCAAA
65981 TACAAAGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (22 bp):
ATGCAAAGACGCTCATGCAAAG
Found at i:69778 original size:20 final size:19
Alignment explanation
Indices: 69753--69794 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
69743 TTTTATTTTA
69753 TAATTATATATTATTTAAAT
1 TAATTATA-ATTATTTAAAT
* *
69773 TAATTATAATTTTTTTAAT
1 TAATTATAATTATTTAAAT
69792 TAA
1 TAA
69795 AAAACATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTATAATTATTTAAAT
Found at i:69963 original size:15 final size:15
Alignment explanation
Indices: 69943--69971 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
69933 AAAAAAAGTT
69943 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
69958 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
69972 CGGTTCGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:80810 original size:22 final size:22
Alignment explanation
Indices: 80784--80843 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
80774 ATTACAAGTG
*
80784 TAATGCAAGAGTTACATAGCTT
1 TAATGCAAGAGTTACAGAGCTT
* *
80806 TAATGTAAGAGTTACAGAGTTT
1 TAATGCAAGAGTTACAGAGCTT
* *
80828 TATTGCATGAGTTACA
1 TAATGCAAGAGTTACA
80844 AACTATTGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (22 bp):
TAATGCAAGAGTTACAGAGCTT
Found at i:81570 original size:23 final size:22
Alignment explanation
Indices: 81544--81607 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
81534 CAGCTCATAT
81544 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
81567 AATTGCACCGGAGTACCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
81590 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
81608 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:81752 original size:103 final size:103
Alignment explanation
Indices: 81615--81840 Score: 389
Period size: 103 Copynumber: 2.2 Consensus size: 103
81605 CCATATAATA
* *
81615 ATGTCCAGAAATACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCGAAAGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
81680 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
* *
81718 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTG
1 ATGTCCCGAAAGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
* * *
81783 TCTCGCCATACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
81821 ATGTCCCGAAAGACCACATA
1 ATGTCCCGAAAGACCACATA
81841 GACCCTCTAC
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (103 bp):
ATGTCCCGAAAGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
Found at i:82407 original size:21 final size:21
Alignment explanation
Indices: 82383--82425 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
82373 TCATATTCGT
*
82383 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
82404 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
82425 T
1 T
82426 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:88306 original size:23 final size:22
Alignment explanation
Indices: 88253--88317 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
88243 TTGTTGTAGG
88253 TTTAATGCAAGAGTTACAAAGC
1 TTTAATGCAAGAGTTACAAAGC
* *
88275 TTTAATGCAAGAGTTACAGAGGT
1 TTTAATGCAAGAGTTACA-AAGC
* *
88298 TTTATTGCATGAGTTACAAA
1 TTTAATGCAAGAGTTACAAA
88318 CTGCATGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (22 bp):
TTTAATGCAAGAGTTACAAAGC
Found at i:91344 original size:21 final size:19
Alignment explanation
Indices: 91312--91350 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
91302 TGGAATATTC
*
91312 ATATTTTTAAAATTAATTA
1 ATATTTTTAAAAATAATTA
91331 ATATTATTGTAAAAATAATT
1 ATATT-TT-TAAAAATAATT
91351 TTATGCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATATTTTTAAAAATAATTA
Found at i:92151 original size:40 final size:39
Alignment explanation
Indices: 92107--92198 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 39
92097 TTAATATTAA
* *
92107 ATTTTGAAAACGATGAATCAATTCTTAAAGTCTCTTTTGG
1 ATTTTTAAAAC-ATGAATCAATTCTTAAAGTCTCTTCTGG
*
92147 ATTTTATAAATTACATGAATCAATTCTTAGAGTCTCTTCTGG
1 ATTTT-TAAA--ACATGAATCAATTCTTAAAGTCTCTTCTGG
92189 ATTTTTAAAA
1 ATTTTTAAAA
92199 ATAATTTAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
39 1 0.02
40 5 0.11
41 7 0.15
42 31 0.67
43 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (39 bp):
ATTTTTAAAACATGAATCAATTCTTAAAGTCTCTTCTGG
Found at i:92166 original size:42 final size:41
Alignment explanation
Indices: 92119--92197 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 41
92109 TTTGAAAACG
*
92119 ATGAATCAATTCTTAAAGTCTCTTTTGGATTTTATAAATTAC
1 ATGAATCAATTCTTAAAGTCTCTTCTGGATTTT-TAAATTAC
*
92161 ATGAATCAATTCTTAGAGTCTCTTCTGGATTTTTAAA
1 ATGAATCAATTCTTAAAGTCTCTTCTGGATTTTTAAA
92198 AATAATTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 4 0.11
42 31 0.89
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (41 bp):
ATGAATCAATTCTTAAAGTCTCTTCTGGATTTTTAAATTAC
Found at i:92415 original size:42 final size:42
Alignment explanation
Indices: 92356--92441 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
92346 CCTTCTTAAA
92356 TAATATGAGAGGGTTAAAAGGTAATATTTATTCATACTCTTT
1 TAATATGAGAGGGTTAAAAGGTAATATTTATTCATACTCTTT
*
92398 TAATATGAGATGGTTAAAAGGTAATATTTATTCATACTCTTT
1 TAATATGAGAGGGTTAAAAGGTAATATTTATTCATACTCTTT
92440 TA
1 TA
92442 TAATTATTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (42 bp):
TAATATGAGAGGGTTAAAAGGTAATATTTATTCATACTCTTT
Found at i:95020 original size:2 final size:2
Alignment explanation
Indices: 95015--95047 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
95005 CTCAAACAAA
95015 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
95048 CGAACAGATC
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:95848 original size:15 final size:15
Alignment explanation
Indices: 95809--95850 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
95799 AAAAAATTAT
*
95809 TTTAAT-TATTATAA
1 TTTAATATATTAAAA
95823 TTT-A-ATATTAAAA
1 TTTAATATATTAAAA
95836 TTTAATATATTAAAA
1 TTTAATATATTAAAA
95851 ATAACATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.46
14 4 0.17
15 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAATATATTAAAA
Found at i:96539 original size:20 final size:20
Alignment explanation
Indices: 96510--96557 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
96500 AATAACTCAA
*
96510 AATTAAATATTATTTTA-AAT
1 AATTATATATT-TTTTACAAT
96530 AATTATATATTTTTTACAAT
1 AATTATATATTTTTTACAAT
*
96550 AATAATAT
1 AATTATAT
96558 TTCCACCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTATATATTTTTTACAAT
Found at i:99211 original size:31 final size:31
Alignment explanation
Indices: 99176--99237 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
99166 CAATACTGTT
* *
99176 TCCTAATATTTAGTCTGTTTGTAATATGGTC
1 TCCTAACATTTAGTCTGTTTGCAATATGGTC
*
99207 TCCTAACATTTAGTTTGTTTGCAATATGGTC
1 TCCTAACATTTAGTCTGTTTGCAATATGGTC
99238 CCTGACCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.47
Consensus pattern (31 bp):
TCCTAACATTTAGTCTGTTTGCAATATGGTC
Found at i:101387 original size:22 final size:23
Alignment explanation
Indices: 101354--101399 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
101344 CCGTCATTCA
*
101354 AAAAGTTATATTAAAATTTTAAG
1 AAAAGTTATATTAAAATTGTAAG
*
101377 AAAA-TTATATTAAACTTGTAAG
1 AAAAGTTATATTAAAATTGTAAG
101399 A
1 A
101400 GTACAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (23 bp):
AAAAGTTATATTAAAATTGTAAG
Found at i:101857 original size:21 final size:21
Alignment explanation
Indices: 101833--101881 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
101823 TTATCGAAAA
101833 TATTATTATTTT-TATCGATTT
1 TATTATT-TTTTCTATCGATTT
101854 TATTATTTTTTCTATCGATTT
1 TATTATTTTTTCTATCGATTT
101875 TATTATT
1 TATTATT
101882 GTTAGACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (21 bp):
TATTATTTTTTCTATCGATTT
Found at i:102398 original size:19 final size:19
Alignment explanation
Indices: 102341--102398 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
102331 AAAGCTTTAC
*
102341 TATTTTTTAT-TTCTA-AA
1 TATTTTTTATATTTTATAA
*
102358 TATTTTTTCA-ATTTT-TAG
1 TATTTTTT-ATATTTTATAA
102376 TATTTTTTATATTTTATAA
1 TATTTTTTATATTTTATAA
102395 TATT
1 TATT
102399 GTAAAATTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
17 9 0.27
18 18 0.55
19 6 0.18
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTTATATTTTATAA
Found at i:105497 original size:21 final size:20
Alignment explanation
Indices: 105472--105544 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
105462 TCTCTGGCTC
*
105472 AAAGGATCGATCTCTTTGACT
1 AAAGGATCGATCCCTTTGA-T
* *
105493 AAAGGATCGATCCCCTTGAA
1 AAAGGATCGATCCCTTTGAT
* *
105513 AAAGGATTGATCCCTTTGGT
1 AAAGGATCGATCCCTTTGAT
105533 ATAAGGATCGAT
1 A-AAGGATCGAT
105545 TTCTTGTGCC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (20 bp):
AAAGGATCGATCCCTTTGAT
Found at i:114240 original size:15 final size:15
Alignment explanation
Indices: 114220--114249 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
114210 TGTATCGTCA
114220 CATTCAAATTTTCAT
1 CATTCAAATTTTCAT
*
114235 CATTCACATTTTCAT
1 CATTCAAATTTTCAT
114250 TAGAAAGTTC
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:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (15 bp):
CATTCAAATTTTCAT
Found at i:116176 original size:30 final size:30
Alignment explanation
Indices: 116131--116215 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
116121 TAATGATGCA
* *
116131 TGACTGATTTGTAACAAACAATAACGTTAG
1 TGACTAATTTATAACAAACAATAACGTTAG
**
116161 TGACTAATTTATAACAAATTATAACGTTAG
1 TGACTAATTTATAACAAACAATAACGTTAG
* * *
116191 TGACCAATTTATAATAAACGATAAC
1 TGACTAATTTATAACAAACAATAAC
116216 ATTAATGGTC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.32
Consensus pattern (30 bp):
TGACTAATTTATAACAAACAATAACGTTAG
Found at i:116744 original size:21 final size:21
Alignment explanation
Indices: 116718--116757 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
116708 GATGTATGAA
* *
116718 TTTTTAATTATATTTAAATTT
1 TTTTTAATAAAATTTAAATTT
116739 TTTTTAATAAAATTTAAAT
1 TTTTTAATAAAATTTAAAT
116758 GCTTAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTAATAAAATTTAAATTT
Found at i:117867 original size:3 final size:3
Alignment explanation
Indices: 117859--117889 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
117849 TGATTTCTAC
*
117859 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
117890 GTTGAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:119901 original size:60 final size:59
Alignment explanation
Indices: 119833--119947 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 59
119823 GTTGGGAGGC
* *
119833 CAAATTGATAGCATAAACTCTTAAATGGCCTCATTGTTTGATAGGGTATAGTTGAGTGGA
1 CAAATTGATAGCAAAAACTCTTAAATGGCCACA-TGTTTGATAGGGTATAGTTGAGTGGA
* * * * *
119893 CAAATTGATAGTAAAAATTCTTAGATGGCCACATGTTTGGTAGGGTTTAGTTGAG
1 CAAATTGATAGCAAAAACTCTTAAATGGCCACATGTTTGATAGGGTATAGTTGAG
119948 CGACCATAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 20 0.42
60 28 0.58
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (59 bp):
CAAATTGATAGCAAAAACTCTTAAATGGCCACATGTTTGATAGGGTATAGTTGAGTGGA
Found at i:122719 original size:15 final size:15
Alignment explanation
Indices: 122699--122733 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
122689 GGTAAAATAC
*
122699 AGTATATATTATTGA
1 AGTATAGATTATTGA
122714 AGTATAGATTATTGA
1 AGTATAGATTATTGA
122729 AGTAT
1 AGTAT
122734 GTTGAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (15 bp):
AGTATAGATTATTGA
Found at i:126108 original size:21 final size:21
Alignment explanation
Indices: 126060--126099 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
126050 ATCCATTTCC
*
126060 AAAAGGATCGATCCCTCGAAA
1 AAAAAGATCGATCCCTCGAAA
126081 AAAAAGATCGATCCCTCGA
1 AAAAAGATCGATCCCTCGA
126100 CCGAAAAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (21 bp):
AAAAAGATCGATCCCTCGAAA
Found at i:126116 original size:92 final size:92
Alignment explanation
Indices: 126020--126191 Score: 263
Period size: 92 Copynumber: 1.9 Consensus size: 92
126010 AAAATGATCG
* * *
126020 ATCCCAAACTTTTTGTTTTGCAAAGGATCGATCCATTTCCAAAAGGATCGATCCCTCGAAAAAAA
1 ATCCCAAACTTTCTGTTGTGCAAAGGATCAATCCATTTCCAAAAGGATCGATCCCTCGAAAAAAA
*
126085 AGATCGATCCCTCGACCGAAAAGACCA
66 AGATCAATCCCTCGACCGAAAAGACCA
* * ***
126112 ATCCCAAACTTTCTGTTGTGCAAAGGATCAATCCCTTTTCAAAAGGATCGATCCCTCGGGGAAAA
1 ATCCCAAACTTTCTGTTGTGCAAAGGATCAATCCATTTCCAAAAGGATCGATCCCTCGAAAAAAA
126177 AGATCAATCCCTCGA
66 AGATCAATCCCTCGA
126192 AAGAAAGGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 71 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (92 bp):
ATCCCAAACTTTCTGTTGTGCAAAGGATCAATCCATTTCCAAAAGGATCGATCCCTCGAAAAAAA
AGATCAATCCCTCGACCGAAAAGACCA
Found at i:126478 original size:5 final size:5
Alignment explanation
Indices: 126468--126764 Score: 333
Period size: 5 Copynumber: 59.4 Consensus size: 5
126458 TACTCTAGCA
126468 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
126518 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
126568 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
* * * * * * * * * *
126618 CTATG CTATG CTATG CTATG CTATG CTATG CTATG CTATG CTATG CTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
* * * * * * * * * *
126668 CTATG CTATG CTATG CTATG CTATG CTATG CTATG CTATG CTATG CTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
* * * * * * * * *
126718 CTATG CTATG CTATG CTATG CTATG CTATG CTATG CTATG CTATG TT
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TT
126765 GATATCGGGA
Statistics
Matches: 290, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 290 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.51
Consensus pattern (5 bp):
TTATG
Found at i:135874 original size:36 final size:36
Alignment explanation
Indices: 135833--135941 Score: 166
Period size: 36 Copynumber: 3.0 Consensus size: 36
135823 CAATCAGTAA
* *
135833 AATAAATAATTAATTGAAA-AAAATTTAAATTTCAAG
1 AATAAATAATTAAGT-AAAGAAAATTTGAATTTCAAG
*
135869 AATAAATAATTTAGTAAAGAAAATTTGAATTTCAAG
1 AATAAATAATTAAGTAAAGAAAATTTGAATTTCAAG
*
135905 AATAAATAATTAAGTAAAGAAAATTTGTATTTCAAG
1 AATAAATAATTAAGTAAAGAAAATTTGAATTTCAAG
135941 A
1 A
135942 TGCATCCACT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 3 0.04
36 64 0.96
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (36 bp):
AATAAATAATTAAGTAAAGAAAATTTGAATTTCAAG
Found at i:148390 original size:13 final size:13
Alignment explanation
Indices: 148372--148404 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
148362 AATGGGCAAT
148372 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
148385 TTTGAAAACAAGG
1 TTTGAAAACAAGG
148398 TTTGAAA
1 TTTGAAA
148405 GTCAATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:148957 original size:23 final size:23
Alignment explanation
Indices: 148905--148957 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
148895 CGATTCCCTA
148905 AAGGGGGGAATCAGTTCCCATTC
1 AAGGGGGGAATCAGTTCCCATTC
* * * *
148928 AAAGGGGGAATCGGTTCCCCTTT
1 AAGGGGGGAATCAGTTCCCATTC
148951 AAGGGGG
1 AAGGGGG
148958 TATCGATTGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.21
Consensus pattern (23 bp):
AAGGGGGGAATCAGTTCCCATTC
Found at i:152882 original size:34 final size:32
Alignment explanation
Indices: 152820--152889 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
152810 ACCTTACAAC
* *
152820 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
152852 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
152886 TCCC
1 TCCC
152890 CTTTACAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:153443 original size:29 final size:31
Alignment explanation
Indices: 153411--153470 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
153401 AAATTTTGAA
*
153411 TAAATTCAATT-AAGCCCAAATA-CATTTTG
1 TAAATTCAATTCAAGCCCAAAAACCATTTTG
*
153440 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGCCCAAAAACCATTTTG
153471 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 9 0.33
31 7 0.26
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGCCCAAAAACCATTTTG
Found at i:164366 original size:13 final size:13
Alignment explanation
Indices: 164348--164375 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
164338 AGGAACGTTT
164348 AATGAAAATGAGA
1 AATGAAAATGAGA
164361 AATGAAAATGAGA
1 AATGAAAATGAGA
164374 AA
1 AA
164376 AGATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.14
Consensus pattern (13 bp):
AATGAAAATGAGA
Found at i:169633 original size:20 final size:22
Alignment explanation
Indices: 169580--169634 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
169570 TACTCAGTAA
169580 AGTATCGATACCATAGGAAGGG
1 AGTATCGATACCATAGGAAGGG
* *
169602 AGTACCGATACC-TAGGTA-GG
1 AGTATCGATACCATAGGAAGGG
*
169622 AGTATCGGTACCA
1 AGTATCGATACCA
169635 ACTTGATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 12 0.43
21 5 0.18
22 11 0.39
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (22 bp):
AGTATCGATACCATAGGAAGGG
Found at i:176470 original size:67 final size:65
Alignment explanation
Indices: 176382--176518 Score: 195
Period size: 67 Copynumber: 2.1 Consensus size: 65
176372 TGTTTCTCTC
*
176382 GAAAC-AAATTTTGACTCTCTTGAGATAGTTTCTCTTGAAATAAAAATCTTTGAGTTTATTTCCC
1 GAAACAAAATTTTGACTCTCTTGAGATAATTTCTCTTG-AA-AAAAATCTTTGAGTTTATTTCCC
176446 TT
64 TT
* * * * *
176448 GAAACAAAATTTTGTCTTTCTTGAGATAATTTCTCTTGAAACACATCTTTGAGTTTGTTTCCCTT
1 GAAACAAAATTTTGACTCTCTTGAGATAATTTCTCTTGAAAAAAATCTTTGAGTTTATTTCCCTT
176513 GAAACA
1 GAAACA
176519 TTATCCCTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 28 0.44
66 7 0.11
67 29 0.45
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (65 bp):
GAAACAAAATTTTGACTCTCTTGAGATAATTTCTCTTGAAAAAAATCTTTGAGTTTATTTCCCTT
Found at i:176848 original size:83 final size:83
Alignment explanation
Indices: 176674--176864 Score: 215
Period size: 83 Copynumber: 2.3 Consensus size: 83
176664 GATGGCCAGC
* * **
176674 CGTCCTCATTACATAGGAACCATGTCATACACCGACCAGATCTCCTCATCACGTAGGAGACGCAT
1 CGTCCTCATCACGTAGGAACTGTGTCATACACCGACCAGATCTCCTCATCACGTAGGAGACGCAT
* *
176739 CACCCCTAGATAAATAGT
66 CACCCCTAGATAAACAGA
* * * *
176757 CGTACTCATCACGTAGGAACTGTGTCATCCACTGGCCAGATCTCCTCATCACGTAGGAG-C-CAT
1 CGTCCTCATCACGTAGGAACTGTGTCATACACCGACCAGATCTCCTCATCACGTAGGAGACGCA-
* **
176820 GTCACCCTTAGATAGCCAGA
65 -TCACCCCTAGATAAACAGA
* *
176840 CTTCCTCATCACGTAAGAACTGTGT
1 CGTCCTCATCACGTAGGAACTGTGT
176865 TATCTCCAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
81 2 0.02
82 1 0.01
83 87 0.97
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (83 bp):
CGTCCTCATCACGTAGGAACTGTGTCATACACCGACCAGATCTCCTCATCACGTAGGAGACGCAT
CACCCCTAGATAAACAGA
Found at i:177101 original size:3 final size:3
Alignment explanation
Indices: 177095--177137 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
177085 TTTGTTGTTG
177095 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
177138 GCATTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:179939 original size:24 final size:25
Alignment explanation
Indices: 179833--179939 Score: 73
Period size: 24 Copynumber: 4.4 Consensus size: 25
179823 AAATGAAGAT
179833 ATCAGAAATCA-AATCAGAATTC-AG
1 ATCAGAAATCATAA-CAGAATTCAAG
* * *
179857 ATCAGATATCATAACA-AAATCCAG
1 ATCAGAAATCATAACAGAATTCAAG
* * * *
179881 ATAAGAAATCAGAACATAATT-TAG
1 ATCAGAAATCATAACAGAATTCAAG
* *
179905 GTCATG-TATCATAACAGAATTCAAG
1 ATCA-GAAATCATAACAGAATTCAAG
179930 -TCAGAAATCA
1 ATCAGAAATCA
179940 GATAAAATAT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
23 5 0.08
24 50 0.79
25 8 0.13
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (25 bp):
ATCAGAAATCATAACAGAATTCAAG
Found at i:180293 original size:27 final size:27
Alignment explanation
Indices: 180263--180323 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
180253 ATTCTTATCC
180263 ATAGATCATCTTCGAAATCATCACTGA
1 ATAGATCATCTTCGAAATCATCACTGA
180290 ATAGATCATCTTCGAAATCATCACTGA
1 ATAGATCATCTTCGAAATCATCACTGA
180317 ATAGATC
1 ATAGATC
180324 TTAAGGAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (27 bp):
ATAGATCATCTTCGAAATCATCACTGA
Found at i:186940 original size:35 final size:35
Alignment explanation
Indices: 186892--187002 Score: 141
Period size: 35 Copynumber: 3.2 Consensus size: 35
186882 TCTAAACCTT
* * * *
186892 AAATTGAAGTATTTTAGAATTTGGGGTTTATAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
* *
186927 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATA
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
* * *
186962 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
186997 AAATTG
1 AAATTG
187003 GGACTATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
Found at i:188231 original size:11 final size:11
Alignment explanation
Indices: 188212--188246 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
188202 ATACAGAATC
188212 TATTAAATATA
1 TATTAAATATA
*
188223 TATTCAATATA
1 TATTAAATATA
188234 TATATAAATATA
1 TAT-TAAATATA
188246 T
1 T
188247 TATTTAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (11 bp):
TATTAAATATA
Found at i:197512 original size:17 final size:18
Alignment explanation
Indices: 197492--197555 Score: 73
Period size: 17 Copynumber: 3.7 Consensus size: 18
197482 GATTTTCAAT
197492 TATCAGAT-ATTTATAGA
1 TATCAGATGATTTATAGA
*
197509 TATCA-ATGATTTTTA-A
1 TATCAGATGATTTATAGA
197525 TTATCAGAT-ATTTATAGA
1 -TATCAGATGATTTATAGA
*
197543 TATTAGATGATTT
1 TATCAGATGATTT
197556 TTGGTTACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 3 0.08
17 29 0.74
18 7 0.18
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (18 bp):
TATCAGATGATTTATAGA
Found at i:197527 original size:34 final size:35
Alignment explanation
Indices: 197478--197616 Score: 151
Period size: 34 Copynumber: 4.1 Consensus size: 35
197468 TACAGTTATT
197478 AGATGATTTTCAATTATCAGATATTTATAGATATC
1 AGATGATTTTCAATTATCAGATATTTATAGATATC
* *
197513 A-ATGATTTTTAATTATCAGATATTTATAGATATT
1 AGATGATTTTCAATTATCAGATATTTATAGATATC
*** * *
197547 AGATGATTTTTGGTTACCAAATATTTAT--ATATC
1 AGATGATTTTCAATTATCAGATATTTATAGATATC
* * * *
197580 ATATGA-TTACAATTATCATATATTTACAGATATC
1 AGATGATTTTCAATTATCAGATATTTATAGATATC
197614 AGA
1 AGA
197617 CCTTTTACAG
Statistics
Matches: 85, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
32 14 0.16
33 9 0.11
34 39 0.46
35 23 0.27
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (35 bp):
AGATGATTTTCAATTATCAGATATTTATAGATATC
Found at i:197860 original size:46 final size:46
Alignment explanation
Indices: 197793--197883 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
197783 GTTGGTGCTT
* *
197793 AGGTTATGATTACACTGAAGTGCATCATATCGCAGTTTCAGTTATA
1 AGGTTATGATTACACTGAAGTGCATCATATCACAGTTTCAATTATA
* *
197839 AGGTTATGATTGCACTGAAGTGCATCATATCATAGTTTCAATTAT
1 AGGTTATGATTACACTGAAGTGCATCATATCACAGTTTCAATTAT
197884 GATTCGACAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (46 bp):
AGGTTATGATTACACTGAAGTGCATCATATCACAGTTTCAATTATA
Found at i:209085 original size:20 final size:20
Alignment explanation
Indices: 209060--209106 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
209050 CTTCTAATCC
209060 ATTTCCACTTAAATTCTAAA
1 ATTTCCACTTAAATTCTAAA
209080 ATTTCCACTTAAATTCTAAA
1 ATTTCCACTTAAATTCTAAA
209100 ATTTCCA
1 ATTTCCA
209107 TATTCAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTCCACTTAAATTCTAAA
Found at i:214714 original size:200 final size:202
Alignment explanation
Indices: 214386--214750 Score: 506
Period size: 200 Copynumber: 1.8 Consensus size: 202
214376 TGTCATGAAC
* ** * * *
214386 ATGTCTATCAAGCCATGTTAGCTTATTCTTCATGTAGAAAACTAAGCTTTGGAACCATTTTGAAC
1 ATGTCTATCAAACCATGTTAGCTTATTCTTCATACACAAAACTAAGCTTTGAAACCATTTTCAAC
* * * * *
214451 GTGATTTTTACCCTTCTTACAATATCTCATATGTACCTATATTACCCTGAATTGAAAGATAAATT
66 ATGATTTTAACCCGTCTTACAATATCTCATATGTACCTATATTACCCTCAACTGAAAGATAAATT
214516 -ATAATACTACGCCTCTAATCTTATAAATGACGAAATTTTTTAGATTAACTACCCAAAAAAAACC
131 CA-AATACTACGCCTCTAATCTTATAAATGACGAAATTTTTTAGATTAACTACCCAAAAAAAACC
214580 CCTCGAAT
195 CCTCGAAT
* *
214588 ATGTCTATCAAACCATTTTAGCATT-TTCTTCATACACAAAAC-AAGTTTTGAAACCATTTTCAA
1 ATGTCTATCAAACCATGTTAGC-TTATTCTTCATACACAAAACTAAGCTTTGAAACCATTTTCAA
* * **
214651 CATGATTTTAACCCGT-TTACAATATCTCGTATGT-CTTGATATTGGCCTCAACTGAAAGATAAA
65 CATGATTTTAACCCGTCTTACAATATCTCATATGTACCT-ATATTACCCTCAACTGAAAGATAAA
*
214714 TTCAAATACTACGCCTCTAATCTTATAAATTACGAAA
129 TTCAAATACTACGCCTCTAATCTTATAAATGACGAAA
214751 AATTTGAGAT
Statistics
Matches: 142, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
199 2 0.01
200 72 0.51
201 32 0.23
202 34 0.24
203 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (202 bp):
ATGTCTATCAAACCATGTTAGCTTATTCTTCATACACAAAACTAAGCTTTGAAACCATTTTCAAC
ATGATTTTAACCCGTCTTACAATATCTCATATGTACCTATATTACCCTCAACTGAAAGATAAATT
CAAATACTACGCCTCTAATCTTATAAATGACGAAATTTTTTAGATTAACTACCCAAAAAAAACCC
CTCGAAT
Found at i:218575 original size:20 final size:20
Alignment explanation
Indices: 218550--218589 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
218540 ACAATAAATG
* *
218550 AAAAAAGAAGTCAAATAACA
1 AAAAAACAAGTCAAAAAACA
*
218570 AAAAAACATGTCAAAAAACA
1 AAAAAACAAGTCAAAAAACA
218590 TAAGAAAATA
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:0.70, C:0.12, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAACAAGTCAAAAAACA
Found at i:218602 original size:22 final size:20
Alignment explanation
Indices: 218559--218604 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
218549 GAAAAAAGAA
*
218559 GTCAAATAACAAAAAAACAT
1 GTCAAAAAACAAAAAAACAT
*
218579 GTCAAAAAACATAAGAAAATAT
1 GTCAAAAAACA-AA-AAAACAT
218601 GTCA
1 GTCA
218605 TAGAGATAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.61, C:0.13, G:0.09, T:0.17
Consensus pattern (20 bp):
GTCAAAAAACAAAAAAACAT
Found at i:219400 original size:24 final size:24
Alignment explanation
Indices: 219368--219417 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
219358 GAAAGATCAC
219368 CGACAATCAAATATTAGAGTTCAA
1 CGACAATCAAATATTAGAGTTCAA
219392 CGACAATCAAATATTAGAGTTCAA
1 CGACAATCAAATATTAGAGTTCAA
219416 CG
1 CG
219418 TCGTGAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (24 bp):
CGACAATCAAATATTAGAGTTCAA
Found at i:220084 original size:23 final size:23
Alignment explanation
Indices: 220043--220086 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
220033 GATAAATTTT
*
220043 TAAATTTAATACCTCAAAATAAG
1 TAAATTTAACACCTCAAAATAAG
220066 TAAATTTAACACACT-AAAATA
1 TAAATTTAACAC-CTCAAAATA
220087 TATATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAATTTAACACCTCAAAATAAG
Found at i:221434 original size:18 final size:16
Alignment explanation
Indices: 221411--221446 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 16
221401 CACAATAAAA
221411 TATTATTAATTTTTTCAT
1 TATTA-TAATTTTTT-AT
221429 TATTATAATTTTTTAT
1 TATTATAATTTTTTAT
221445 TA
1 TA
221447 GTGACGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 9 0.50
18 5 0.28
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATAATTTTTTAT
Found at i:222786 original size:22 final size:22
Alignment explanation
Indices: 222754--222804 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
222744 CGATCTCAAA
* *
222754 AAACTACAGCTCGATTGAAGCTC
1 AAACT-CAGCTAGATTCAAGCTC
*
222777 AAACTCAGCTAGGTTCAAGCTC
1 AAACTCAGCTAGATTCAAGCTC
*
222799 GAACTC
1 AAACTC
222805 GAGTTCGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (22 bp):
AAACTCAGCTAGATTCAAGCTC
Found at i:225824 original size:20 final size:20
Alignment explanation
Indices: 225795--225833 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
225785 CAATATCGGC
*
225795 GCGTGAAGGATCCGATGAGA
1 GCGTGAAGGAGCCGATGAGA
*
225815 GCGTGTAGGAGCCGATGAG
1 GCGTGAAGGAGCCGATGAG
225834 TTGCCTTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.44, T:0.15
Consensus pattern (20 bp):
GCGTGAAGGAGCCGATGAGA
Found at i:226179 original size:19 final size:19
Alignment explanation
Indices: 226139--226181 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
226129 AATATAAAAC
*
226139 TAATAATAATATATAGTGA
1 TAATAATAATAAATAGTGA
*
226158 TAATATATAATAAATTGT-A
1 TAATA-ATAATAAATAGTGA
226177 TAATA
1 TAATA
226182 CTTGTAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (19 bp):
TAATAATAATAAATAGTGA
Found at i:228495 original size:3 final size:3
Alignment explanation
Indices: 228487--228667 Score: 102
Period size: 3 Copynumber: 57.7 Consensus size: 3
228477 ATACTAATGC
228487 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
228535 ACTT AGT AAAT AAT -AT ATAT CAAT AAT -GT ATAT AA- AAT AACT AAAT
1 A-AT AAT -AAT AAT AAT A-AT -AAT AAT AAT A-AT AAT AAT AA-T -AAT
* * * * * ** *
228581 AGT AAC AAT AGT AAT ATAT TAG AAT AAT GTT AAT -CT AAAT AAAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT
*
228628 AAT ACT AAT AAT AA- AATT GAAT AAT AAT AAGT AAT AAT AA
1 AAT AAT AAT AAT AAT AA-T -AAT AAT AAT AA-T AAT AAT AA
228668 CATTGAAAAA
Statistics
Matches: 138, Mismatches: 23, Indels: 34
0.71 0.12 0.17
Matches are distributed among these distances:
2 8 0.06
3 102 0.74
4 23 0.17
5 5 0.04
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:228672 original size:26 final size:25
Alignment explanation
Indices: 228622--228674 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
228612 AATCTAAATA
228622 AATAATAATACTAATAATAAAATTG
1 AATAATAATACTAATAATAAAATTG
* *
228647 AATAATAATAAGTAATAATAACATTG
1 AATAATAAT-ACTAATAATAAAATTG
228673 AA
1 AA
228675 AAAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (25 bp):
AATAATAATACTAATAATAAAATTG
Found at i:230455 original size:35 final size:36
Alignment explanation
Indices: 230414--230494 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 36
230404 AACACAATCA
* *
230414 TCAATTACATTTTAAACCCCAAAATC-TAAAATGCT
1 TCAATTACATTTTAAACCCCAAAATCAAAAAATACT
* * *
230449 TCAATTATATTTTAAACCTCAAATTCAAAAAATACT
1 TCAATTACATTTTAAACCCCAAAATCAAAAAATACT
230485 TCAATTACAT
1 TCAATTACAT
230495 GCTCAACCCC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 23 0.59
36 16 0.41
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.35
Consensus pattern (36 bp):
TCAATTACATTTTAAACCCCAAAATCAAAAAATACT
Found at i:230508 original size:36 final size:36
Alignment explanation
Indices: 230414--230511 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 36
230404 AACACAATCA
* * *
230414 TCAATTACATTTTAAACCCCAAAATC-TAAAATGCT
1 TCAATTACATTTTAAACCCCAAATTCAAAAAATACT
* *
230449 TCAATTATATTTTAAACCTCAAATTCAAAAAATACT
1 TCAATTACATTTTAAACCCCAAATTCAAAAAATACT
** *
230485 TCAATTACATGCTCAACCCCAAATTCA
1 TCAATTACATTTTAAACCCCAAATTCA
230512 TAATCCATTC
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
35 23 0.44
36 29 0.56
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (36 bp):
TCAATTACATTTTAAACCCCAAATTCAAAAAATACT
Found at i:230860 original size:148 final size:148
Alignment explanation
Indices: 230668--230956 Score: 499
Period size: 148 Copynumber: 2.0 Consensus size: 148
230658 ACTCAATTCG
* *
230668 GTTTATAAAATAGTTGACTCAAATTTTTTTCGATTTGAGTTTATAAAATTTAAGTCAAGTTGAAT
1 GTTTATAAAATAGTTGACTCAAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAAT
* *
230733 TGAATTGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATCATATTATAATATTATT
66 TGAATTGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATT
230798 TGATTCTAATTCAGTTCA
131 TGATTCTAATTCAGTTCA
*
230816 GTTTATAAAATAGTTGTCTCGAAA-TTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAA
1 GTTTATAAAATAGTTGACTC-AAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAA
* *
230880 TTGAATTGAATTTTTGAGTTTTTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTAT
65 TTGAATTGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTAT
230945 TTGATTCTAATT
130 TTGATTCTAATT
230957 TAAATAGTTT
Statistics
Matches: 133, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
148 130 0.98
149 3 0.02
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (148 bp):
GTTTATAAAATAGTTGACTCAAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAAT
TGAATTGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATT
TGATTCTAATTCAGTTCA
Found at i:231764 original size:20 final size:20
Alignment explanation
Indices: 231739--231778 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
231729 TATTAGATAT
*
231739 AATAATAATTAATAACAATA
1 AATAATAAATAATAACAATA
*
231759 AATAATAAATAGTAACAATA
1 AATAATAAATAATAACAATA
231779 TAAAAACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
AATAATAAATAATAACAATA
Found at i:231947 original size:21 final size:19
Alignment explanation
Indices: 231923--231973 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
231913 AATGCTATCT
231923 TAATAAATAATATATATAAAG
1 TAATAAATAATA-ATA-AAAG
231944 TAAT-AATAA-AATAAAAG
1 TAATAAATAATAATAAAAG
231961 TAA-ATAATAATAA
1 TAATA-AATAATAA
231974 GTAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.26
18 8 0.30
19 3 0.11
20 5 0.19
21 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
TAATAAATAATAATAAAAG
Done.