Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009000.1 Hibiscus syriacus cultivar Beakdansim tig00112382_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: 1742898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:553461 original size:67 final size:67
Alignment explanation
Indices: 553289--553499 Score: 200
Period size: 67 Copynumber: 3.1 Consensus size: 67
553279 AAAATTTATT
* * * *
553289 GTTTCAAAGAAAAACACAA-TCAAAGTTTTTTGTGTTTCAAGAGAAACTGTCTCTAGGGAGACAA
1 GTTTC-AAGAGAAACA-AATTCAAAG-ATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
553353 AATTC
63 AATTC
* * * *
553358 AG-TTCAAGAGAAAC-GATCTCAAAGATCGGTT-T-TTTCAAGGGAAACTATCTCAAGAGAGACA
1 -GTTTCAAGAGAAACAAAT-TCAAAGAT--TTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
553419 AAATTC
62 AAATTC
* *
553425 GTTTCAAGAGAAACAAATTCAAAGATTTTGTGTTTCAAGAGAAAATGTCTCCAACA-AGACAAAA
1 GTTTCAAGAGAAACAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCT-CAAGAGAGACAAAA
*
553489 TTT
65 TTC
*
553492 ATTTCAAG
1 GTTTCAAG
553500 GGCAACTGTC
Statistics
Matches: 116, Mismatches: 16, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
65 2 0.02
66 3 0.03
67 84 0.72
68 21 0.18
69 5 0.04
70 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (67 bp):
GTTTCAAGAGAAACAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
TC
Found at i:553787 original size:21 final size:20
Alignment explanation
Indices: 553754--553814 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
553744 GTTTCAAGGG
553754 AAACTGTCTCAAGAGAGACA
1 AAACTGTCTCAAGAGAGACA
*
553774 AAACTCGTTTCAAG-G-G---
1 AAACT-GTCTCAAGAGAGACA
*
553790 AAACTGTCTCAAGAAAGACA
1 AAACTGTCTCAAGAGAGACA
553810 AAACT
1 AAACT
553815 AGTTTCAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
15 7 0.22
16 5 0.16
17 1 0.03
19 1 0.03
20 11 0.34
21 7 0.22
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (20 bp):
AAACTGTCTCAAGAGAGACA
Found at i:553931 original size:36 final size:37
Alignment explanation
Indices: 553888--553990 Score: 129
Period size: 36 Copynumber: 2.8 Consensus size: 37
553878 TGGTGTTTCA
*
553888 AGTAAAAAATGACTCAAATGAGACGAAATTTGTTTTG
1 AGTAAAAAATGTCTCAAATGAGACGAAATTTGTTTTG
* * *
553925 AG--AAAAATAGTCTCAAAAGAGACAAAACTTGTTTTG
1 AGTAAAAAAT-GTCTCAAATGAGACGAAATTTGTTTTG
* *
553961 AGTAAAAATTGTCTCAAGTGAGACGAAATT
1 AGTAAAAAATGTCTCAAATGAGACGAAATT
553991 CATTTTTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
35 6 0.11
36 25 0.46
37 18 0.33
38 5 0.09
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (37 bp):
AGTAAAAAATGTCTCAAATGAGACGAAATTTGTTTTG
Found at i:554166 original size:90 final size:89
Alignment explanation
Indices: 554037--554490 Score: 611
Period size: 90 Copynumber: 5.0 Consensus size: 89
554027 AAAATCAGGC
* * *
554037 TTCTAAAAACTCATTTGAAAACATCTTGCACTGAAGGTCTTATGAATGGCCCGAATGACTTACAA
1 TTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
* ** * *
554102 ATCAAGAAATCCCTAAAAATAAGGC
66 ATCAAGAAACCCCTAAAGCTTA-GT
* * * *
554127 TTATAAAAACTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAA
1 TTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
* *
554192 ATCAAGAAACCCTCGAAGGCTTAGT
66 ATCAAGAAACCC-CTAAAGCTTAGT
* *
554217 TTCTAAAATGTCATTTGAAAACATCCTGCTCTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
1 TTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
* *
554282 ATCAAGAAACCCCCGAAGGCTTAGT
66 ATCAAGAAA-CCCCTAAAGCTTAGT
* * *** *
554307 TTCTAAAATCTCATTTGAAAACATCCTGCATTGAAGGTCTTATGAATGGTTTGAAGGACTTACAA
1 TTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
*
554372 ATCAAGAAACCCCCAAAGGCTTAGT
66 ATCAAGAAACCCCTAAA-GCTTAGT
*
554397 TTCTAAAATCTCATTTGAAAACATCTTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
1 TTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
* *
554462 ATCAAGAAACCCCCGAAGGCTTAGT
66 ATCAAGAAA-CCCCTAAAGCTTAGT
554487 TTCT
1 TTCT
554491 TTGAAAGTTT
Statistics
Matches: 324, Mismatches: 36, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
89 6 0.02
90 304 0.94
91 14 0.04
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (89 bp):
TTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
ATCAAGAAACCCCTAAAGCTTAGT
Found at i:554322 original size:180 final size:180
Alignment explanation
Indices: 554037--554490 Score: 694
Period size: 180 Copynumber: 2.5 Consensus size: 180
554027 AAAATCAGGC
* *
554037 TTCTAAAAACTCATTTGAAAACATCTTGCACTGAAGGTCTTATGAATGGCCCGAATGACTTACAA
1 TTCTAAAATCTCATTTGAAAACATCTTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
* * *** * * *
554102 ATCAAGAAA-TCCCTAAAAATAAGGCTTATAAAAACTCATTTGAAAACATCATGCACTGAAGGTC
66 ATCAAGAAACCCCCGAAGGCTTA-GTTTCTAAAAACTCATTTGAAAACATCATGCACTGAAGGTC
* * *
554166 TTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCTCGAAGGCTTAGT
130 TTATGAATGGCCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGT
* * *
554217 TTCTAAAATGTCATTTGAAAACATCCTGCTCTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
1 TTCTAAAATCTCATTTGAAAACATCTTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
* * *
554282 ATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCATTGAAGGTCT
66 ATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCATGCACTGAAGGTCT
***
554347 TATGAATGGTTTGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGT
131 TATGAATGGCCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGT
554397 TTCTAAAATCTCATTTGAAAACATCTTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
1 TTCTAAAATCTCATTTGAAAACATCTTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
554462 ATCAAGAAACCCCCGAAGGCTTAGTTTCT
66 ATCAAGAAACCCCCGAAGGCTTAGTTTCT
554491 TTGAAAGTTT
Statistics
Matches: 248, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
180 241 0.97
181 7 0.03
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (180 bp):
TTCTAAAATCTCATTTGAAAACATCTTGCACTGAAGGTCTTATGGATGGCCCGAATGACTTACAA
ATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCATGCACTGAAGGTCT
TATGAATGGCCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGT
Found at i:561073 original size:15 final size:15
Alignment explanation
Indices: 561053--561084 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
561043 ATATATATTA
561053 AAATTAAAAGGTAAG
1 AAATTAAAAGGTAAG
*
561068 AAATTAAAAGGTTAG
1 AAATTAAAAGGTAAG
561083 AA
1 AA
561085 CATCAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (15 bp):
AAATTAAAAGGTAAG
Found at i:563550 original size:13 final size:13
Alignment explanation
Indices: 563534--563606 Score: 56
Period size: 14 Copynumber: 5.4 Consensus size: 13
563524 CTTTTTGAAC
563534 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
*
563547 TTTTCTTTTCTTCT
1 TTTTTTTTTCTT-T
* *
563561 TTTCTTTTTCTGAT
1 TTTTTTTTTCT-TT
* *
563575 TTATTTCTTCTTT
1 TTTTTTTTTCTTT
* *
563588 TGTCTTTTTCTTT
1 TTTTTTTTTCTTT
563601 CTTTTT
1 -TTTTT
563607 GCACTCCAAT
Statistics
Matches: 43, Mismatches: 14, Indels: 5
0.69 0.23 0.08
Matches are distributed among these distances:
13 21 0.49
14 22 0.51
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:564355 original size:19 final size:21
Alignment explanation
Indices: 564312--564363 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
564302 GAAACCCCTT
564312 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
564333 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
564352 TGAAGATACATG
1 TGAAAATACATG
564364 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:567823 original size:13 final size:13
Alignment explanation
Indices: 567807--567832 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
567797 TTTTGAACTT
567807 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
567820 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
567833 CTGATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:568618 original size:19 final size:21
Alignment explanation
Indices: 568575--568626 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
568565 GAAACCCCTT
568575 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
568596 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
568615 TGAAGATACATG
1 TGAAAATACATG
568627 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:570218 original size:30 final size:30
Alignment explanation
Indices: 570170--570234 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
570160 CATTGCTACA
* *
570170 GCGACCACCATAGATCTCCAGGAGCACATG
1 GCGACCACCACAGATCTCCAGGAGCACAAG
* *
570200 GCGACCTCCACAGGTCTCCAGGAGCACAAG
1 GCGACCACCACAGATCTCCAGGAGCACAAG
570230 GCGAC
1 GCGAC
570235 TTATGGAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.35, G:0.26, T:0.11
Consensus pattern (30 bp):
GCGACCACCACAGATCTCCAGGAGCACAAG
Found at i:570244 original size:19 final size:19
Alignment explanation
Indices: 570220--570262 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
570210 CAGGTCTCCA
570220 GGAGCACAAGGCGACTTAT
1 GGAGCACAAGGCGACTTAT
**
570239 GGAGCACTTGGCGACTTAT
1 GGAGCACAAGGCGACTTAT
570258 GGAGC
1 GGAGC
570263 TGTAACATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.35, T:0.19
Consensus pattern (19 bp):
GGAGCACAAGGCGACTTAT
Found at i:571210 original size:16 final size:18
Alignment explanation
Indices: 571183--571215 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
571173 TGATGTTGAT
571183 AAAAATGATTTT-GATTA
1 AAAAATGATTTTAGATTA
571200 AAAAATG-TTTTAGATT
1 AAAAATGATTTTAGATT
571216 CGCCATCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
AAAAATGATTTTAGATTA
Found at i:571215 original size:17 final size:17
Alignment explanation
Indices: 571168--571215 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
571158 ATTTGGCGAG
*
571168 AAAAATGATGTTGA-T-
1 AAAAATGATTTTGATTA
571183 AAAAATGATTTTGATTA
1 AAAAATGATTTTGATTA
571200 AAAAATG-TTTTAGATT
1 AAAAATGATTTT-GATT
571216 CGCCATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 13 0.45
16 5 0.17
17 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (17 bp):
AAAAATGATTTTGATTA
Found at i:571673 original size:23 final size:22
Alignment explanation
Indices: 571641--571688 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
571631 CTTTAATATT
* *
571641 AAAAAATAAATAAATATTAATA
1 AAAAAATAAATAAAAATAAATA
571663 AAAAAATTAAATAAAAATAAATA
1 AAAAAA-TAAATAAAAATAAATA
571686 AAA
1 AAA
571689 TATAGTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAATAAATAAAAATAAATA
Found at i:572689 original size:17 final size:17
Alignment explanation
Indices: 572667--572724 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
572657 TAAAGTATTG
572667 AAAATAATAATAGAAAT
1 AAAATAATAATAGAAAT
* *
572684 AAAATAA-AATTGCAAT
1 AAAATAATAATAGAAAT
* *
572700 TACATAATAATCA-AAAT
1 AAAATAATAAT-AGAAAT
572717 AAAATAAT
1 AAAATAAT
572725 TAAAATTATA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATAATAATAGAAAT
Found at i:573814 original size:23 final size:23
Alignment explanation
Indices: 573784--573827 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
573774 GAACATGACA
573784 GTAGAGCAGTTAGAGTAGAGGCG
1 GTAGAGCAGTTAGAGTAGAGGCG
*
573807 GTAGAGCAGTTGGAGTAGAGG
1 GTAGAGCAGTTAGAGTAGAGG
573828 TGGCGTCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.45, T:0.18
Consensus pattern (23 bp):
GTAGAGCAGTTAGAGTAGAGGCG
Found at i:574071 original size:3 final size:3
Alignment explanation
Indices: 574063--574122 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
574053 TTATTTATTA
* **
574063 AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT TTT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
574109 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
574123 AACGAAATGA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:574409 original size:78 final size:78
Alignment explanation
Indices: 574248--574566 Score: 534
Period size: 78 Copynumber: 4.1 Consensus size: 78
574238 GATGGAAATG
* * * *
574248 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC-GAAGGTTTTGAAAAAAACATCAAAAA
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTG-AGGGTTT-AAGAAAACATCAAAAA
*
574312 GCTCCTGAAGGCTTT
64 GCTCCCGAAGGCTTT
574327 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGGTTTAAGAAAACATCAAAAAGC
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGGTTTAAGAAAACATCAAAAAGC
*
574392 TCCTGAAGGCTTT
66 TCCCGAAGGCTTT
*
574405 TTGAAAACATCATGCATTGTAGGTCTTACAGATGACCCTGAGGGTTTAAGAAAACATCAAAAAGC
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGGTTTAAGAAAACATCAAAAAGC
574470 TCCCGAAGGCTTT
66 TCCCGAAGGCTTT
*
574483 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGGTTTAA-AAAACATCATAAAGC
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGGTTTAAGAAAACATCAAAAAGC
574547 TCCCGAAGGCTTT
66 TCCCGAAGGCTTT
574560 TTGAAAA
1 TTGAAAA
574567 AAAAATATCA
Statistics
Matches: 231, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
77 34 0.15
78 154 0.67
79 42 0.18
80 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (78 bp):
TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGGTTTAAGAAAACATCAAAAAGC
TCCCGAAGGCTTT
Found at i:574582 original size:36 final size:37
Alignment explanation
Indices: 574530--574603 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
574520 CTGAGGGTTT
*
574530 AAAAAACATCATAAAGCTCCCGAAGGC-TTTTTGAAA
1 AAAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGAAA
* *
574566 AAAAAATATCAAAAAGCTCTCGAAGGCTTTTTTGAAA
1 AAAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGAAA
574603 A
1 A
574604 CATCATGCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 24 0.71
37 10 0.29
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (37 bp):
AAAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGAAA
Found at i:574622 original size:192 final size:185
Alignment explanation
Indices: 574376--574894 Score: 851
Period size: 192 Copynumber: 2.8 Consensus size: 185
574366 GAGGGTTTAA
574376 GAAAACATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCA-TTGTAGGTCTTACAGATGA
1 GAAAACATCAAAAAGCTCC-GAAGGCTTTTTGAAAACATCATGCACTT-TAGGTCTTACAGATGA
574440 CCCTGAGGGTTTAAGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
64 CCCTGAGGGTTTAAGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
* *
574505 GTCTTACAGATGACCCTGAGGGTTTAAAAAACATCATAAAGCTCCCGAAGGCTTTTT
129 GTCTTACAGATGACCCTGAGGGTTTAAAAAAAATCAAAAAGCTCCCGAAGGCTTTTT
*
574562 GAAAAAAAAATATCAAAAAGCTCTCGAAGGCTTTTTTGAAAACATCATGCACTTTAGGTCTTACA
1 G-----AAAACATCAAAAAGCTC-CGAAGGC-TTTTTGAAAACATCATGCACTTTAGGTCTTACA
*
574627 GATGACCCTGAGGGTTTAAGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAATATCATGCAC
59 GATGACCCTGAGGGTTTAAGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCAC
574692 TGTAGGTCTTACAGATGACCCTGAGGGTTTAAAAAAAATCAAAAAGCTCCCGAAGGCTTTTT
124 TGTAGGTCTTACAGATGACCCTGAGGGTTTAAAAAAAATCAAAAAGCTCCCGAAGGCTTTTT
* * * *
574754 GAAAACATCAAAAAGCTCCCGAATGCTTTTTGAAAACATCATGTACTGTAGGTCTTATAGATGAC
1 GAAAACATCAAAAAGCT-CCGAAGGCTTTTTGAAAACATCATGCACTTTAGGTCTTACAGATGAC
* *
574819 CCTAAGGGTTTAAGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTAGG
65 CCTGAGGGTTTAAGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
574884 TCTTACAGATG
130 TCTTACAGATG
574895 TGGGAAATAG
Statistics
Matches: 312, Mismatches: 12, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
186 110 0.35
187 21 0.07
188 1 0.00
191 22 0.07
192 156 0.50
193 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (185 bp):
GAAAACATCAAAAAGCTCCGAAGGCTTTTTGAAAACATCATGCACTTTAGGTCTTACAGATGACC
CTGAGGGTTTAAGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGT
CTTACAGATGACCCTGAGGGTTTAAAAAAAATCAAAAAGCTCCCGAAGGCTTTTT
Found at i:574703 original size:78 final size:77
Alignment explanation
Indices: 574565--574763 Score: 335
Period size: 78 Copynumber: 2.5 Consensus size: 77
574555 GCTTTTTGAA
* *
574565 AAAAAAATATCAAAAAGCTCTCGAAGGCTTTTTTGAAAACATCATGCACTTTAGGTCTTACAGAT
1 AAAAAAA-ATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGCACTGTAGGTCTTACAGAT
574630 GACCCTGAGGGTTT
64 GACCCTGAGGGTTT
* *
574644 AAGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAATATCATGCACTGTAGGTCTTACAGATG
1 AA-AAAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
574709 ACCCTGAGGGTTT
65 ACCCTGAGGGTTT
574722 AAAAAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCA
1 AAAAAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCA
574764 AAAAGCTCCC
Statistics
Matches: 113, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
77 38 0.34
78 50 0.44
79 21 0.19
80 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (77 bp):
AAAAAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
CCCTGAGGGTTT
Found at i:574764 original size:31 final size:31
Alignment explanation
Indices: 574724--574794 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
574714 GAGGGTTTAA
*
574724 AAAAAATCAAAAAGCTCCCGAAGGCTTTTTG
1 AAAACATCAAAAAGCTCCCGAAGGCTTTTTG
*
574755 AAAACATCAAAAAGCTCCCGAATGCTTTTTG
1 AAAACATCAAAAAGCTCCCGAAGGCTTTTTG
574786 AAAACATCA
1 AAAACATCA
574795 TGTACTGTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.23
Consensus pattern (31 bp):
AAAACATCAAAAAGCTCCCGAAGGCTTTTTG
Found at i:574782 original size:108 final size:109
Alignment explanation
Indices: 574646--574872 Score: 384
Period size: 108 Copynumber: 2.1 Consensus size: 109
574636 GAGGGTTTAA
*
574646 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAATATCATGCACTGTAGGTCTTACAGATGAC
1 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGAC
*
574711 CCTGAGGGTTTAA-AAAAAATCAAAAAGCTCCCGAAGGCTTTTT
66 CCTAAGGGTTTAAGAAAAAATCAAAAAGCTCCCGAAGGCTTTTT
* * *
574754 GAAAACATCAAAAAGCTCCCGAATGCTTTTTGAAAACATCATGTACTGTAGGTCTTATAGATGAC
1 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGAC
* *
574819 CCTAAGGGTTTAAGAAAACATCAAAAAGCTCCTGAAGGCTTTTT
66 CCTAAGGGTTTAAGAAAAAATCAAAAAGCTCCCGAAGGCTTTTT
574863 GAAAACATCA
1 GAAAACATCA
574873 TGCACTGTAG
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
108 73 0.66
109 38 0.34
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (109 bp):
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGAC
CCTAAGGGTTTAAGAAAAAATCAAAAAGCTCCCGAAGGCTTTTT
Found at i:575561 original size:22 final size:22
Alignment explanation
Indices: 575536--575658 Score: 176
Period size: 22 Copynumber: 5.6 Consensus size: 22
575526 AATAAAGCTT
*
575536 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
575558 TCATCTTTGAAGATAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
575580 TCATCTTTGAAGAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
575602 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
575624 TCATCTTTGAA-AAATGAATGTA
1 TCATCTTTGAAGAGA-GAATCTA
*
575646 TCATATTTGAAGA
1 TCATCTTTGAAGA
575659 ATATAGATGT
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
21 2 0.02
22 88 0.97
23 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:577005 original size:70 final size:72
Alignment explanation
Indices: 576892--577140 Score: 220
Period size: 75 Copynumber: 3.4 Consensus size: 72
576882 CATAATGTCG
* * * * *
576892 TGGGCCTTCAGCATGCCCCAGCATTTACTGATATGAACGTTCAAAAT-G-TTATTCCAATTTCTG
1 TGGGCTTTCAGCATGCCCCAGCATTTGCTAATAAGAACGTTCAAAATAGCATATTCCAATTTCTG
576955 ATTGAAA
66 ATTGAAA
*
576962 TGGGCTTTCAGCATGCCCCAACATTTGCTAATACAG-ACGTTCAAAATACGCCAATATTCCAATT
1 TGGGCTTTCAGCATGCCCCAGCATTTGCTAATA-AGAACGTTCAAAATA-G-C-ATATTCCAATT
*
577026 TTTGATTGAAA
62 TCTGATTGAAA
* * * *** * *
577037 TGGGATTTCAGCATGCCCCAGCATTTGTTGACGTGAACATTCAAAACGT-GTCAATATTCCTGA-
1 TGGGCTTTCAGCATGCCCCAGCATTTGCTAATAAGAACGTTCAAAA--TAG-C-ATATTCC-AAT
*
577100 TTATGATTGAAA
61 TTCTGATTGAAA
* *
577112 TGGGCTTTCAGCATACCCCATCATTTGCT
1 TGGGCTTTCAGCATGCCCCAGCATTTGCT
577141 TCTTGTTGAT
Statistics
Matches: 147, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
70 40 0.27
71 1 0.01
72 1 0.01
74 1 0.01
75 102 0.69
76 1 0.01
77 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (72 bp):
TGGGCTTTCAGCATGCCCCAGCATTTGCTAATAAGAACGTTCAAAATAGCATATTCCAATTTCTG
ATTGAAA
Found at i:579861 original size:9 final size:8
Alignment explanation
Indices: 579828--579857 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
579818 TTTGATTCAA
579828 TTTTTTCT
1 TTTTTTCT
*
579836 TTTTTTCC
1 TTTTTTCT
579844 TTTTTTCT
1 TTTTTTCT
579852 TTTTTT
1 TTTTTT
579858 TCTTCTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTCT
Found at i:585294 original size:12 final size:11
Alignment explanation
Indices: 585278--585357 Score: 51
Period size: 11 Copynumber: 7.2 Consensus size: 11
585268 ATAAAGGGTA
585278 ATAATAAAAAT
1 ATAATAAAAAT
585289 AGTAATAAAAA-
1 A-TAATAAAAAT
585300 AT-ATAAAAAT
1 ATAATAAAAAT
*
585310 ATATGATTAATAAT
1 ATA--A-TAAAAAT
*
585324 A-ATTAAAAAT
1 ATAATAAAAAT
585334 AATAAT-AAAAT
1 -ATAATAAAAAT
* *
585345 CTAATTAAAAT
1 ATAATAAAAAT
585356 AT
1 AT
585358 TAAAGTTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
9 7 0.13
10 13 0.24
11 14 0.26
12 11 0.20
13 2 0.04
14 7 0.13
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (11 bp):
ATAATAAAAAT
Found at i:585336 original size:13 final size:12
Alignment explanation
Indices: 585276--585343 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 12
585266 ATATAAAGGG
585276 TAATAATAAAAA
1 TAATAATAAAAA
*
585288 TAGTAAT-AAAA
1 TAATAATAAAAA
585299 -AAT-ATAAAAA
1 TAATAATAAAAA
**
585309 T-AT-ATGATTAA
1 TAATAAT-AAAAA
585320 TAATAATTAAAAA
1 TAATAA-TAAAAA
585333 TAATAATAAAA
1 TAATAATAAAA
585344 TCTAATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
9 2 0.05
10 10 0.23
11 8 0.18
12 13 0.30
13 10 0.23
14 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
TAATAATAAAAA
Found at i:586106 original size:19 final size:19
Alignment explanation
Indices: 586073--586113 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
586063 TTTGAGGGAC
*
586073 TAAATCTATTATTTACT-A
1 TAAATATATTATTTACTGA
586091 TAAATATATATATTTACTGA
1 TAAATATAT-TATTTACTGA
586111 TAA
1 TAA
586114 TGACTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (19 bp):
TAAATATATTATTTACTGA
Found at i:586979 original size:23 final size:23
Alignment explanation
Indices: 586952--586997 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
586942 GAACATGACA
*
586952 GCGGAGCAGTTAGAGTATAGGCG
1 GCGGAGCAGTTAGAGTAGAGGCG
*
586975 GCGGAGCAGTTGGAGTAGAGGCG
1 GCGGAGCAGTTAGAGTAGAGGCG
586998 TCGCCGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.48, T:0.15
Consensus pattern (23 bp):
GCGGAGCAGTTAGAGTAGAGGCG
Found at i:587238 original size:3 final size:3
Alignment explanation
Indices: 587230--587282 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
587220 TTATTTATTA
* **
587230 AAT AAT AAT AAT -AT ATAT AAT ATT AAT AAT AAT AAT TTT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
587275 AAT AAT AA
1 AAT AAT AA
587283 AACGAAATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:587264 original size:15 final size:15
Alignment explanation
Indices: 587230--587281 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
587220 TTATTTATTA
*
587230 AATAATAATAAT-AT
1 AATAATATTAATAAT
587244 ATATAATATTAATAAT
1 A-ATAATATTAATAAT
*
587260 AATAATTTTAATAAT
1 AATAATATTAATAAT
587275 AATAATA
1 AATAATA
587282 AAACGAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 1 0.03
15 29 0.88
16 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAATATTAATAAT
Found at i:589553 original size:31 final size:30
Alignment explanation
Indices: 589512--589570 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
589502 GGATAAATTT
*
589512 TATATTTAATATATAAATTATCAATTTTGA
1 TATATTTAATATATAAATTATAAATTTTGA
* *
589542 TATATTTTAATATTTAAATTTTAAATTTT
1 TATA-TTTAATATATAAATTATAAATTTT
589571 TTAAAATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TATATTTAATATATAAATTATAAATTTTGA
Found at i:592452 original size:13 final size:13
Alignment explanation
Indices: 592436--592460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
592426 TTAGTATTTT
592436 ATTTTATTTATTG
1 ATTTTATTTATTG
592449 ATTTTATTTATT
1 ATTTTATTTATT
592461 CAGATAAAAA
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
ATTTTATTTATTG
Found at i:601683 original size:65 final size:63
Alignment explanation
Indices: 601564--601773 Score: 212
Period size: 65 Copynumber: 3.3 Consensus size: 63
601554 TTTTTCAGAG
* * *
601564 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
601626 ATT
61 ATT
* * *
601629 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATAGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
601693 T
63 T
* * * * *
601694 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
601758 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
601774 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 46 0.37
65 68 0.55
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:601791 original size:129 final size:130
Alignment explanation
Indices: 601564--601799 Score: 302
Period size: 129 Copynumber: 1.8 Consensus size: 130
601554 TTTTTCAGAG
* * *
601564 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTGAACATCGAATGCATT
1 TGATGCACCGATGCACCAAGCCATGCATCGATGCACCATGAACTAAATTGAACATCGAATGCACT
* *
601629 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAAAACATAGAATGCATT
66 TCATGCATCGATGCACATACCATGCACCAATGCACTAAGGATTTTATGAAAACATAGAATGCATT
* * **
601694 TGATGCATCGATGCACC-AGCCATGCATCGATGCACTC-TG-GCTATTTTGAAACATCGAATGCA
1 TGATGCACCGATGCACCAAGCCATGCATCGATGCAC-CATGAACTAAATTG-AACATCGAATGCA
* *
601756 CTTGATGCATCGATGCAC-T-CTTAGTGCACCAATGCACTAAGGAT
64 CTTCATGCATCGATGCACATAC-CA-TGCACCAATGCACTAAGGAT
601800 CCAACGGTCA
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
127 1 0.01
128 7 0.08
129 66 0.73
130 17 0.19
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (130 bp):
TGATGCACCGATGCACCAAGCCATGCATCGATGCACCATGAACTAAATTGAACATCGAATGCACT
TCATGCATCGATGCACATACCATGCACCAATGCACTAAGGATTTTATGAAAACATAGAATGCATT
Found at i:604012 original size:2 final size:2
Alignment explanation
Indices: 604007--604078 Score: 60
Period size: 2 Copynumber: 35.5 Consensus size: 2
603997 ACACACACAC
*
604007 AT AT AT AT AGT -T TT AT A- AT AT AT AT AT AT AT AT AT AT AGT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
604049 AGT -T TT GAA AT AT AT AT AT AT AT AT AT AT A
1 A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT A
604079 ATTTGGAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
1 3 0.05
2 52 0.88
3 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:604053 original size:34 final size:33
Alignment explanation
Indices: 604007--604078 Score: 119
Period size: 34 Copynumber: 2.2 Consensus size: 33
603997 ACACACACAC
604007 ATATATATAGTTTT-ATAATATATATATATATAT
1 ATATATATAGTTTTGA-AATATATATATATATAT
604040 ATATAGTATAGTTTTGAAATATATATATATATAT
1 ATATA-TATAGTTTTGAAATATATATATATATAT
604074 ATATA
1 ATATA
604079 ATTTGGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
33 5 0.14
34 31 0.84
35 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (33 bp):
ATATATATAGTTTTGAAATATATATATATATAT
Found at i:604066 original size:24 final size:24
Alignment explanation
Indices: 604034--604147 Score: 89
Period size: 23 Copynumber: 4.9 Consensus size: 24
604024 ATATATATAT
*
604034 ATATATATATAGTATAGTTTTGAA
1 ATATATATATAATATAGTTTTGAA
*
604058 ATATATATAT-ATATA--TAT-ATA
1 ATATATATATAATATAGTTTTGA-A
* *
604079 ATTTGGAAATA-AATATAGTTTTGAA
1 ATAT--ATATATAATATAGTTTTGAA
* *
604104 AAATATA-ATAAGTATAATTTTGAA
1 ATATATATATAA-TATAGTTTTGAA
604128 A-ATATATATAATATAGTTTT
1 ATATATATATAATATAGTTTT
604148 ATAAAATAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
20 1 0.01
21 6 0.09
22 1 0.01
23 30 0.43
24 26 0.37
25 5 0.07
26 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (24 bp):
ATATATATATAATATAGTTTTGAA
Found at i:604129 original size:23 final size:22
Alignment explanation
Indices: 604090--604160 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 22
604080 TTTGGAAATA
604090 AATATAGTTTTGAAAAATATAAT
1 AATATAGTTTTG-AAAATATAAT
*
604113 AAGTATAATTTTGAAAATATATAT
1 AA-TATAGTTTTGAAAATATA-AT
604137 AATATAGTTTT-ATAAA-ATAAT
1 AATATAGTTTTGA-AAATATAAT
604158 AAT
1 AAT
604161 TTGGAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 5 0.12
22 4 0.09
23 21 0.49
24 13 0.30
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
AATATAGTTTTGAAAATATAAT
Found at i:604171 original size:39 final size:40
Alignment explanation
Indices: 604117--604194 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
604107 TATAATAAGT
* * *
604117 ATAATTTTGAAAATATATAT-AATATAGTTTTATAAAATA
1 ATAATTTGGAAAATATATATAAATATAATTTTAGAAAATA
604156 ATAATTTGGAAAATATATATACAATATAATTTTAGAAAA
1 ATAATTTGGAAAATATATATA-AATATAATTTTAGAAAA
604195 CATAGTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 19 0.56
41 15 0.44
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (40 bp):
ATAATTTGGAAAATATATATAAATATAATTTTAGAAAATA
Found at i:604193 original size:26 final size:27
Alignment explanation
Indices: 604147--604203 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
604137 AATATAGTTT
* *
604147 TATAAAATAATAATTTGGAAAATATA-
1 TATAAAATAATAATTTAGAAAACATAG
*
604173 TATACAAT-ATAATTTTAGAAAACATAG
1 TATAAAATAATAA-TTTAGAAAACATAG
604200 TATA
1 TATA
604204 TGATTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 4 0.15
26 18 0.69
27 4 0.15
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (27 bp):
TATAAAATAATAATTTAGAAAACATAG
Found at i:604709 original size:21 final size:21
Alignment explanation
Indices: 604680--604727 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
604670 CCCAACCACC
604680 TCACCGGCCACCCCTGATGAG
1 TCACCGGCCACCCCTGATGAG
* * *
604701 TCACTGGCCGCCCCTGGTGAG
1 TCACCGGCCACCCCTGATGAG
604722 TCACCG
1 TCACCG
604728 CCATAGACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.42, G:0.27, T:0.17
Consensus pattern (21 bp):
TCACCGGCCACCCCTGATGAG
Found at i:605473 original size:8 final size:8
Alignment explanation
Indices: 605462--605487 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
605452 TTTATATTTG
605462 TATGTATA
1 TATGTATA
605470 TATGTATA
1 TATGTATA
605478 TATGTATA
1 TATGTATA
605486 TA
1 TA
605488 AATTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
TATGTATA
Found at i:607638 original size:21 final size:24
Alignment explanation
Indices: 607612--607656 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
607602 ATACAATGTC
607612 TACTTTGGC-CAA-AAGA-AAAGA
1 TACTTTGGCACAAGAAGAGAAAGA
*
607633 TACTTTTGCACAAGAAGAGAAAGA
1 TACTTTGGCACAAGAAGAGAAAGA
607657 GCTCAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 4 0.20
24 5 0.25
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (24 bp):
TACTTTGGCACAAGAAGAGAAAGA
Found at i:612009 original size:42 final size:42
Alignment explanation
Indices: 611932--612020 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
611922 TAAAGGTCCG
* * * *
611932 TATCATCCAAAAGTATTAATGTGGGGTACTATTGAAGGTTCT
1 TATCATCCAAAAGTATTAATGTAGGGCACTATTGAAGGCTCA
* *
611974 TATCATCCAGAAGTATTAATGTTAGGGCA-TTTTGAAGGCTCA
1 TATCATCCAAAAGTATTAATG-TAGGGCACTATTGAAGGCTCA
612016 TATCA
1 TATCA
612021 GCAAGAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
42 35 0.88
43 5 0.12
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (42 bp):
TATCATCCAAAAGTATTAATGTAGGGCACTATTGAAGGCTCA
Found at i:613278 original size:67 final size:66
Alignment explanation
Indices: 613201--613554 Score: 404
Period size: 67 Copynumber: 5.3 Consensus size: 66
613191 GAATTCTTCA
* * * * *
613201 TGAAATGAAGTCAATCTTTGTTATTCCTAACTCCCTCATGAAGAGGATTCAATCATTGACTTCCT
1 TGAAAAGAAGTCAATCTTTGTTATTCCTAA-TCCCTCACGAAGAGGAGTCAATCCTTGATTTCCT
613266 CG
65 CG
* ** * *
613268 TGAAAAGAAGTCAACCTTTGTTATTCCTGAATCCCTCGTGAAGAGGAGTTAATCCTTGATTTCTT
1 TGAAAAGAAGTCAATCTTTGTTATTCCT-AATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCT
613333 CG
65 CG
* * *
613335 TGAAGAGAGGTTAATCTTTGTTATTCCTGAATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCT
1 TGAAAAGAAGTCAATCTTTGTTATTCCT-AATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCT
*
613400 CA
65 CG
* * * * * * * *
613402 TTAAGAGAAGTCAATCTTTTTTTTTCTTGATTCCCTCACGAAGAGGAGTCAATCCTTGACTTCAT
1 TGAAAAGAAGTCAATCTTTGTTATTCCT-AATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCT
613467 CG
65 CG
* * * *
613469 TGAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCCTCGATTTCCT
1 TGAAAAGAAGTCAATCTTTGTTATTCCT-AATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCT
*
613534 CA
65 CG
613536 T-AAAGAGAAGTCAATCTTT
1 TGAAA-AGAAGTCAATCTTT
613555 TAGATATGGT
Statistics
Matches: 247, Mismatches: 38, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
66 2 0.01
67 243 0.98
68 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (66 bp):
TGAAAAGAAGTCAATCTTTGTTATTCCTAATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCTC
G
Found at i:613323 original size:28 final size:29
Alignment explanation
Indices: 613287--613350 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
613277 GTCAACCTTT
*
613287 GTTATTCC-TGAATCCCTCGTGAAGAG-G
1 GTTAATCCTTGAATCCCTCGTGAAGAGAG
* * *
613314 AGTTAATCCTTGATTTCTTCGTGAAGAGAG
1 -GTTAATCCTTGAATCCCTCGTGAAGAGAG
613344 GTTAATC
1 GTTAATC
613351 TTTGTTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 7 0.23
29 22 0.73
30 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (29 bp):
GTTAATCCTTGAATCCCTCGTGAAGAGAG
Found at i:613437 original size:134 final size:134
Alignment explanation
Indices: 613207--613555 Score: 477
Period size: 134 Copynumber: 2.6 Consensus size: 134
613197 TTCATGAAAT
* * * * *
613207 GAAGTCAATCTTTGTTATTCCT-AACTCCCTCATGAAGAGGATTCAATCATTGACTTCCTCGTGA
1 GAAGTCAATCTTTGTTATTCCTGAA-TCCCTCACGAAGAGGAGTCAATCCTTGATTTCCTCAT-A
* * ** * * *
613271 AA-AGAAGTCAACCTTTGTTATTCCTGAATCCCTCGTGAAGAGGAGTTAATCCTTGATTTCTTCG
64 AAGAGAAGTCAATCTTTTTTATTCCTGAATCCCTCACGAAGAGGAGTCAATCCTTGACTTCATCG
613335 TGAAGA
129 TGAAGA
* * *
613341 GAGGTTAATCTTTGTTATTCCTGAATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCTCATTAA
1 GAAGTCAATCTTTGTTATTCCTGAATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCTCATAAA
* * *
613406 GAGAAGTCAATCTTTTTTTTTCTTGATTCCCTCACGAAGAGGAGTCAATCCTTGACTTCATCGTG
66 GAGAAGTCAATCTTTTTTATTCCTGAATCCCTCACGAAGAGGAGTCAATCCTTGACTTCATCGTG
613471 AAGA
131 AAGA
* * *
613475 GAAGTCAATCTTTGTTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCCTCGATTTCCTCATAAA
1 GAAGTCAATCTTTGTTATTCCTGAATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCTCATAAA
613540 GAGAAGTCAATCTTTT
66 GAGAAGTCAATCTTTT
613556 AGATATGGTC
Statistics
Matches: 189, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
133 2 0.01
134 185 0.98
135 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (134 bp):
GAAGTCAATCTTTGTTATTCCTGAATCCCTCACGAAGAGGAGTCAATCCTTGATTTCCTCATAAA
GAGAAGTCAATCTTTTTTATTCCTGAATCCCTCACGAAGAGGAGTCAATCCTTGACTTCATCGTG
AAGA
Found at i:613879 original size:88 final size:88
Alignment explanation
Indices: 613779--613949 Score: 218
Period size: 88 Copynumber: 1.9 Consensus size: 88
613769 AATTTTCCTT
*
613779 GAGTCTGATCTCCCCTAAAGAGCAATGGAGAAGATTCTTCTT-ATTTAAGATTTGGTCTTCCTGA
1 GAGTCTGATCTCCCCTAAAGAGCAACGGAGAAGATTCTT-TTCATTTAAGATTTGGTCTTCCTGA
613843 AGACCAGCGAAGCAAATCAATCTC
65 AGACCAGCGAAGCAAATCAATCTC
* * * * * * **
613867 GAGTCTGATCTCCCTTAAAGAGTAGCGGAGCATATTCTTTTCCTTTTTGATTTGGTCTTCCTGAA
1 GAGTCTGATCTCCCCTAAAGAGCAACGGAGAAGATTCTTTTCATTTAAGATTTGGTCTTCCTGAA
* * *
613932 TAGCAGCGAAGTAAATCA
66 GACCAGCGAAGCAAATCA
613950 CGTTTGATTC
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
87 2 0.03
88 68 0.97
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (88 bp):
GAGTCTGATCTCCCCTAAAGAGCAACGGAGAAGATTCTTTTCATTTAAGATTTGGTCTTCCTGAA
GACCAGCGAAGCAAATCAATCTC
Found at i:613881 original size:135 final size:135
Alignment explanation
Indices: 613556--613861 Score: 461
Period size: 135 Copynumber: 2.3 Consensus size: 135
613546 TCAATCTTTT
* * *
613556 AGATATGGTCTTCCTGAAGAGCAGAGAAGCAAATCACGTTTGATTCAATCTTCCTTGAAGAGTAG
1 AGATTTGGTCTTCCTGAAGAGCAGAGAAGCAAATCACGTTTGATTCAATCTTCCCTGAAAAGTAG
* *
613621 CAAAGTGGATCAAAAGTTTCCTTGAGTCTGATCTCCCCTAAAGAATAATGGAGCAGATTCTTCTT
66 CAAAGTGGATCAAAAGTTTCCTTGAGTCTGATCTCCCCTAAAGAACAATGGAGAAGATTCTTCTT
*
613686 ATTTC
131 ATTTA
* * *
613691 AGATTTGCTCTTCCTAAAGAG-AAATGAAGCAAATCACGTTTGATTCAATCTTCCCTGAAAAGTA
1 AGATTTGGTCTTCCTGAAGAGCAGA-GAAGCAAATCACGTTTGATTCAATCTTCCCTGAAAAGTA
** * *
613755 GTGAAGTGGATCAAAATTTTCCTTGAGTCTGATCTCCCCTAAAGAGCAATGGAGAAGATTCTTCT
65 GCAAAGTGGATCAAAAGTTTCCTTGAGTCTGATCTCCCCTAAAGAACAATGGAGAAGATTCTTCT
613820 TATTTA
130 TATTTA
* *
613826 AGATTTGGTCTTCCTGAAGACCAGCGAAGCAAATCA
1 AGATTTGGTCTTCCTGAAGAGCAGAGAAGCAAATCA
613862 ATCTCGAGTC
Statistics
Matches: 151, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
134 2 0.01
135 148 0.98
136 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (135 bp):
AGATTTGGTCTTCCTGAAGAGCAGAGAAGCAAATCACGTTTGATTCAATCTTCCCTGAAAAGTAG
CAAAGTGGATCAAAAGTTTCCTTGAGTCTGATCTCCCCTAAAGAACAATGGAGAAGATTCTTCTT
ATTTA
Found at i:614041 original size:223 final size:222
Alignment explanation
Indices: 613644--614254 Score: 817
Period size: 223 Copynumber: 2.7 Consensus size: 222
613634 AAGTTTCCTT
* * * * *
613644 GAGTCTGATCTCCCCTAAAGAATAATGGAGCAGATTCTTCTTATTTCAGATTTGCTCTTCCTAAA
1 GAGTCTGATCTCCCCTAAAGAGTAACGGAGCAGATTCTT-TTCTTTCAGATTTGGTCTTCCTGAA
* ** * *
613709 GAGAAATGAAGCAAATCACGTTTGATTCAATCTTCCCTGAAAAGTAGTGAAGTGGATCAAAATTT
65 GAGCAGCGAAGCAAATCACGTTTGATTCAATCTTCCCTGAAGAGTAGTGAAGTGGATCAAAAATT
* *
613774 TCCTTGAGTCTGATCTCCCCTAAAGAGCAATGGAGAAGATTCTTCTTATTTAAGATTTGGTCTTC
130 TCCTTGAGTCTGATCTCCCCTAAAGAGTAGTGGAGAAGATTCTTCTTATTTAAGATTTGGTCTTC
613839 CTGAAGACCAGCGAAGCAAATCAATCTC
195 CTGAAGACCAGCGAAGCAAATCAATCTC
* * * **
613867 GAGTCTGATCTCCCTTAAAGAGTAGCGGAGCATATTCTTTTCCTTTTTGATTTGGTCTTCCTGAA
1 GAGTCTGATCTCCCCTAAAGAGTAACGGAGCAGATTCTTTT-CTTTCAGATTTGGTCTTCCTGAA
* * *
613932 TAGCAGCGAAGTAAATCACGTTTGATTCAATCTTCCCTGAAGAGTAGCGAAGTGGATCAAAAATT
65 GAGCAGCGAAGCAAATCACGTTTGATTCAATCTTCCCTGAAGAGTAGTGAAGTGGATCAAAAATT
* * * *
613997 TCCTTGAGTCTGATCTACCCTAAAGAGTAGTGGAGCATATTCTTCTTATTTCAGATTTGGTCTTC
130 TCCTTGAGTCTGATCTCCCCTAAAGAGTAGTGGAGAAGATTCTTCTTATTTAAGATTTGGTCTTC
* * *
614062 CTGGAGAGCAGTGAAGCAAATCAATCTC
195 CTGAAGACCAGCGAAGCAAATCAATCTC
* * *
614090 GATTCTGATCTCCCCTAAAGAGTAACAGAGCAGATTCTTTTTCTTTCCGATTTGGTCTTCCTGAA
1 GAGTCTGATCTCCCCTAAAGAGTAACGGAGCAGATTC-TTTTCTTTCAGATTTGGTCTTCCTGAA
* * * * * * *
614155 GAGCAGCGAAGCAAATCAAGTTTGATTCAATTTTCTCTTAAGAGAAGTGGAGTGGATCAACAATT
65 GAGCAGCGAAGCAAATCACGTTTGATTCAATCTTCCCTGAAGAGTAGTGAAGTGGATCAAAAATT
* * * * *
614220 TTCTTAAGTCTCATATCCCCTAAAGATTAGTGGAG
130 TCCTTGAGTCTGATCTCCCCTAAAGAGTAGTGGAG
614255 TAGACCCGTC
Statistics
Matches: 336, Mismatches: 50, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
222 2 0.01
223 330 0.98
224 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (222 bp):
GAGTCTGATCTCCCCTAAAGAGTAACGGAGCAGATTCTTTTCTTTCAGATTTGGTCTTCCTGAAG
AGCAGCGAAGCAAATCACGTTTGATTCAATCTTCCCTGAAGAGTAGTGAAGTGGATCAAAAATTT
CCTTGAGTCTGATCTCCCCTAAAGAGTAGTGGAGAAGATTCTTCTTATTTAAGATTTGGTCTTCC
TGAAGACCAGCGAAGCAAATCAATCTC
Found at i:614094 original size:135 final size:136
Alignment explanation
Indices: 613867--614113 Score: 322
Period size: 135 Copynumber: 1.8 Consensus size: 136
613857 AATCAATCTC
* **
613867 GAGTCTGATCTCCCTTAAAGAGTAGCGGAGCATATTCTTTTCCTTTTTGATTTGGTCTTCCTGAA
1 GAGTCTGATCTCCCTTAAAGAGTAGCGGAGCATATTCTTTTCATTTCAGATTTGGTCTTCCTGAA
* * * * * *
613932 TAGCAGCGAAGTAAATCACGTTTGATTC-AATCTTCCCTGAAGAGTAGCGAAGTGGATCAAAAAT
66 GAGCAGCGAAGCAAATCACATTCGATTCTAATCTCCCCTAAAGAGTAGCGAAGTGGATCAAAAAT
613996 TTCCTT
131 TTCCTT
*
614002 GAGTCTGATCTACCC-TAAAGAGTAGTGGAGCATATTCTTCTT-ATTTCAGATTTGGTCTTCCTG
1 GAGTCTGATCT-CCCTTAAAGAGTAGCGGAGCATATTCTT-TTCATTTCAGATTTGGTCTTCCTG
* * *
614065 GAGAGCAGTGAAGCAAATCA-ATCTCGATTCTGATCTCCCCTAAAGAGTA
64 AAGAGCAGCGAAGCAAATCACAT-TCGATTCTAATCTCCCCTAAAGAGTA
614114 ACAGAGCAGA
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
134 1 0.01
135 74 0.78
136 20 0.21
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (136 bp):
GAGTCTGATCTCCCTTAAAGAGTAGCGGAGCATATTCTTTTCATTTCAGATTTGGTCTTCCTGAA
GAGCAGCGAAGCAAATCACATTCGATTCTAATCTCCCCTAAAGAGTAGCGAAGTGGATCAAAAAT
TTCCTT
Found at i:614158 original size:88 final size:88
Alignment explanation
Indices: 614005--614173 Score: 248
Period size: 88 Copynumber: 1.9 Consensus size: 88
613995 TTTCCTTGAG
*** * *
614005 TCTGATCTACCCTAAAGAGTAGTGGAGCATATTCTTCTTATTTCAGATTTGGTCTTCCTGGAGAG
1 TCTGATCTACCCTAAAGAGTAACAGAGCAGATTCTTCTTATTTCAGATTTGGTCTTCCTGAAGAG
*
614070 CAGTGAAGCAAATCAATCTCGAT
66 CAGCGAAGCAAATCAATCTCGAT
* * * *
614093 TCTGATCTCCCCTAAAGAGTAACAGAGCAGATTCTTTTTCTTTCCGATTTGGTCTTCCTGAAGAG
1 TCTGATCTACCCTAAAGAGTAACAGAGCAGATTCTTCTTATTTCAGATTTGGTCTTCCTGAAGAG
614158 CAGCGAAGCAAATCAA
66 CAGCGAAGCAAATCAA
614174 GTTTGATTCA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 71 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (88 bp):
TCTGATCTACCCTAAAGAGTAACAGAGCAGATTCTTCTTATTTCAGATTTGGTCTTCCTGAAGAG
CAGCGAAGCAAATCAATCTCGAT
Found at i:614626 original size:10 final size:11
Alignment explanation
Indices: 614601--614625 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
614591 TTTCATTTCC
614601 TTTTGTTTTAT
1 TTTTGTTTTAT
614612 TTTTGTTTTAT
1 TTTTGTTTTAT
614623 TTT
1 TTT
614626 GGTTATATAT
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:0.08, T:0.84
Consensus pattern (11 bp):
TTTTGTTTTAT
Found at i:614679 original size:23 final size:22
Alignment explanation
Indices: 614629--614695 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
614619 TTATTTTGGT
614629 TATATATATAGTTTT-ATAAA-A
1 TATATATATAGTTTTGA-AAATA
614650 TA-A-ATATAGTTTTGAAATATA
1 TATATATATAGTTTTGAAA-ATA
614671 TATATATATAGTTTTGAAAA-A
1 TATATATATAGTTTTGAAAATA
614692 TATA
1 TATA
614696 ATAAGTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
19 12 0.29
20 3 0.07
21 10 0.24
22 2 0.05
23 14 0.34
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (22 bp):
TATATATATAGTTTTGAAAATA
Found at i:614694 original size:19 final size:19
Alignment explanation
Indices: 614630--614695 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
614620 TATTTTGGTT
614630 ATATATATAGTTTT-ATAAA
1 ATATATATAGTTTTGA-AAA
*
614649 ATAAATATAGTTTTGAAATATA
1 ATATATATAGTTTTG-AA-A-A
614671 TATATATATAGTTTTGAAAA
1 -ATATATATAGTTTTGAAAA
614691 ATATA
1 ATATA
614696 ATAAGTATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 18 0.45
20 2 0.05
21 3 0.08
22 3 0.08
23 14 0.35
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (19 bp):
ATATATATAGTTTTGAAAA
Found at i:614711 original size:42 final size:42
Alignment explanation
Indices: 614629--614714 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 42
614619 TTATTTTGGT
* *
614629 TATATATATAGTTTTATAAAATAAATATAGTTTTGAAATATA
1 TATATATATAGTTTTATAAAATAAATATAGTTATAAAATATA
614671 TATATATATAGTTTTGA-AAAATATAATA-AG-TATAATAATATA
1 TATATATATAGTTTT-ATAAAATA-AATATAGTTATAA-AATATA
614713 TA
1 TA
614715 ATAGTAACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
41 3 0.08
42 31 0.79
43 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (42 bp):
TATATATATAGTTTTATAAAATAAATATAGTTATAAAATATA
Found at i:618047 original size:7 final size:8
Alignment explanation
Indices: 618028--618062 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
618018 TCACCTTGAA
618028 AAAAAAGG
1 AAAAAAGG
618036 AAAAAAGG
1 AAAAAAGG
618044 AAAAAAGG
1 AAAAAAGG
*
618052 AAAAAAAG
1 AAAAAAGG
618060 AAA
1 AAA
618063 CTAGGGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:618581 original size:53 final size:53
Alignment explanation
Indices: 618461--618776 Score: 377
Period size: 53 Copynumber: 6.0 Consensus size: 53
618451 ATAAGAGTTA
* * * * * **
618461 GGGTCAGAGAAGATGAACAAAAATAGAAGATGAAGATGCTCAATTT-ATTTTG
1 GGGTTAGAGAAGATGAATAAAGATAGAAGATGAAGAGGCTCAGTTTGGGTTTG
*
618513 GGGTTAGAGAAGATGAATAAAGACAGAAGATGAAGAGGCTCAGTTTGGGTTTG
1 GGGTTAGAGAAGATGAATAAAGATAGAAGATGAAGAGGCTCAGTTTGGGTTTG
* * * *
618566 GGGTTAGAGAAGATGAATATAGATAGAAGATGAAAAGGCTCAATTTGGGTTTA
1 GGGTTAGAGAAGATGAATAAAGATAGAAGATGAAGAGGCTCAGTTTGGGTTTG
* * * *
618619 GGGTTAGAGAATATGAATATAGACAGAAGATGAAGAGGCTCATTTTGGGTTTG
1 GGGTTAGAGAAGATGAATAAAGATAGAAGATGAAGAGGCTCAGTTTGGGTTTG
* **
618672 GGGTTAGAGAAGATAAATAAAGATAGAAGATGAAGAGGCT-AGGTTAAGGTTTG
1 GGGTTAGAGAAGATGAATAAAGATAGAAGATGAAGAGGCTCA-GTTTGGGTTTG
* * * * *
618725 GGATTAAAGAAGATGAACAGAGATAGAA-AGTGAAGAGGCTCAGTTAGGGTTT
1 GGGTTAGAGAAGATGAATAAAGATAGAAGA-TGAAGAGGCTCAGTTTGGGTTT
618777 AGGTTTGGGT
Statistics
Matches: 229, Mismatches: 31, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
52 42 0.18
53 186 0.81
54 1 0.00
ACGTcount: A:0.39, C:0.05, G:0.32, T:0.24
Consensus pattern (53 bp):
GGGTTAGAGAAGATGAATAAAGATAGAAGATGAAGAGGCTCAGTTTGGGTTTG
Found at i:619173 original size:98 final size:100
Alignment explanation
Indices: 619020--619205 Score: 279
Period size: 98 Copynumber: 1.9 Consensus size: 100
619010 AGGGTTGAAT
* **
619020 TTTTAGGTGTTTGATCAAGAGAAAAATGAGTTTAGGTTTTGGTGTTTGTGAATATCAATTGAGGG
1 TTTTAGGTGTTTGATCAAGAGAAAAATGAGTTTAGGTTTTAGTGTTTGTGAATATCAAAAGAGGG
*
619085 TTTTTGGGATGAACACAAATGAACAATGATTTAAA
66 TTTTTAGGATGAACACAAATGAACAATGATTTAAA
* *
619120 TTTTGGGTGTTTGATCAA-A-AAAACATG-GTTTGGGTTTTAGTGTTTGTGAATATCAAAAGAGG
1 TTTTAGGTGTTTGATCAAGAGAAAA-ATGAGTTTAGGTTTTAGTGTTTGTGAATATCAAAAGAGG
*
619182 GTTTTTAGGATGAACACAGATGAA
65 GTTTTTAGGATGAACACAAATGAA
619206 ATTTTAGAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
98 57 0.73
99 4 0.05
100 17 0.22
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (100 bp):
TTTTAGGTGTTTGATCAAGAGAAAAATGAGTTTAGGTTTTAGTGTTTGTGAATATCAAAAGAGGG
TTTTTAGGATGAACACAAATGAACAATGATTTAAA
Found at i:619565 original size:25 final size:26
Alignment explanation
Indices: 619518--619576 Score: 111
Period size: 25 Copynumber: 2.3 Consensus size: 26
619508 CAATTCATTC
619518 AATTAATATATATGTTTATATTAATA
1 AATTAATATATATGTTTATATTAATA
619544 AATTAATATATA-GTTTATATTAATA
1 AATTAATATATATGTTTATATTAATA
619569 AATTAATA
1 AATTAATA
619577 AAAAATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 21 0.64
26 12 0.36
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (26 bp):
AATTAATATATATGTTTATATTAATA
Found at i:620975 original size:26 final size:26
Alignment explanation
Indices: 620952--621120 Score: 338
Period size: 26 Copynumber: 6.5 Consensus size: 26
620942 GCAATCAATT
620952 TGTAAATTGTAATAATGCTATCAACC
1 TGTAAATTGTAATAATGCTATCAACC
620978 TGTAAATTGTAATAATGCTATCAACC
1 TGTAAATTGTAATAATGCTATCAACC
621004 TGTAAATTGTAATAATGCTATCAACC
1 TGTAAATTGTAATAATGCTATCAACC
621030 TGTAAATTGTAATAATGCTATCAACC
1 TGTAAATTGTAATAATGCTATCAACC
621056 TGTAAATTGTAATAATGCTATCAACC
1 TGTAAATTGTAATAATGCTATCAACC
621082 TGTAAATTGTAATAATGCTATCAACC
1 TGTAAATTGTAATAATGCTATCAACC
621108 TGTAAATTGTAAT
1 TGTAAATTGTAAT
621121 TGATTATTTA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 143 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (26 bp):
TGTAAATTGTAATAATGCTATCAACC
Found at i:621319 original size:19 final size:20
Alignment explanation
Indices: 621268--621319 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
621258 ATGATCTACC
621268 TTTTGTTTATA-TTATTGGAT
1 TTTTGTTTATATTTATT-GAT
* *
621288 TTTTATTTTTATTTATT-AT
1 TTTTGTTTATATTTATTGAT
621307 TTTTGTTTATATT
1 TTTTGTTTATATT
621320 ATTTTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.48
20 9 0.33
21 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (20 bp):
TTTTGTTTATATTTATTGAT
Found at i:626516 original size:15 final size:16
Alignment explanation
Indices: 626482--626518 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
626472 AATCTAGAGT
626482 AGAGTCAGAGGGAAAC
1 AGAGTCAGAGGGAAAC
*
626498 AGAGTCAGAGGG-CAC
1 AGAGTCAGAGGGAAAC
626513 AGAGTC
1 AGAGTC
626519 CTCGAGGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.38, C:0.16, G:0.38, T:0.08
Consensus pattern (16 bp):
AGAGTCAGAGGGAAAC
Found at i:631399 original size:20 final size:20
Alignment explanation
Indices: 631376--631427 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
631366 CTAAAATATG
*
631376 AGTATCGATACTCTTA-AGTC
1 AGTATCGATACTCATAGA-TC
* * *
631396 AGTATTGTTACTGATAGATC
1 AGTATCGATACTCATAGATC
631416 AGTATCGATACT
1 AGTATCGATACT
631428 ATCTCAGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
AGTATCGATACTCATAGATC
Found at i:644164 original size:3 final size:3
Alignment explanation
Indices: 644156--644277 Score: 235
Period size: 3 Copynumber: 40.7 Consensus size: 3
644146 TTTTGATCCC
644156 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
644204 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
644252 TCT TCT TAT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
644278 AAGCTCTTGT
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:650498 original size:33 final size:33
Alignment explanation
Indices: 650460--650526 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
650450 TAGAGATGTC
650460 AGAATTGATACATGATTATATTGTTAGAGAACA
1 AGAATTGATACATGATTATATTGTTAGAGAACA
650493 AGAATTGATACATGATTATATTGTTAGAGAACA
1 AGAATTGATACATGATTATATTGTTAGAGAACA
650526 A
1 A
650527 TGTATTGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (33 bp):
AGAATTGATACATGATTATATTGTTAGAGAACA
Found at i:653190 original size:21 final size:21
Alignment explanation
Indices: 653166--653208 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
653156 GCTTCACTGC
* *
653166 AAGATTTTATGGCCTCGACAA
1 AAGATTTCATGGCCTCAACAA
*
653187 AAGATTTCATGGCTTCAACAA
1 AAGATTTCATGGCCTCAACAA
653208 A
1 A
653209 GGCCCTACTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (21 bp):
AAGATTTCATGGCCTCAACAA
Found at i:657126 original size:20 final size:20
Alignment explanation
Indices: 657072--657133 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
657062 TTTGGGAAAA
* *
657072 TTAACACAGTATTGATACTC
1 TTAACATAGTATCGATACTC
*
657092 TT-ACCTAGGGTATCGATACTC
1 TTAACATA--GTATCGATACTC
657113 TTAACATAGTATCGATACTC
1 TTAACATAGTATCGATACTC
657133 T
1 T
657134 CGTGATTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 3 0.09
20 15 0.43
21 13 0.37
22 4 0.11
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (20 bp):
TTAACATAGTATCGATACTC
Found at i:662886 original size:19 final size:19
Alignment explanation
Indices: 662837--662887 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
662827 AAAGTTACAG
662837 AATTTAAAT-ATTTATATT
1 AATTTAAATAATTTATATT
*
662855 AATAT-AATAAATTTAT-TGT
1 AATTTAAAT-AATTTATAT-T
662874 AATTTAAATAATTT
1 AATTTAAATAATTT
662888 TCTATAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.11
18 5 0.19
19 16 0.59
20 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
AATTTAAATAATTTATATT
Found at i:663359 original size:16 final size:16
Alignment explanation
Indices: 663256--663362 Score: 83
Period size: 16 Copynumber: 6.6 Consensus size: 16
663246 CTCAACCCAT
*
663256 ATTATACCCAATCCAAA
1 ATTA-ACCCAAACCAAA
*
663273 ATTTAA-CAAAACCAAA
1 A-TTAACCCAAACCAAA
*
663289 A-TAAACCAGAACCAAA
1 ATTAACCCA-AACCAAA
* *
663305 ATTTACCCAAACTAAA
1 ATTAACCCAAACCAAA
*
663321 ATTAACTCAAACCAAA
1 ATTAACCCAAACCAAA
** *
663337 AGAAACCCGAACCAAA
1 ATTAACCCAAACCAAA
*
663353 TTTAACCCAA
1 ATTAACCCAA
663363 CACGAAAACA
Statistics
Matches: 69, Mismatches: 17, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
14 3 0.04
15 2 0.03
16 54 0.78
17 7 0.10
18 3 0.04
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (16 bp):
ATTAACCCAAACCAAA
Found at i:663459 original size:18 final size:18
Alignment explanation
Indices: 663436--663492 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
663426 AATAATAAAT
*
663436 TAATTTAAATAAAATTAA
1 TAATTTAAATAAAAATAA
* *
663454 TAATTT-ATTAAAAATAT
1 TAATTTAAATAAAAATAA
663471 TATATTTATAATAAAAATAA
1 TA-ATTTA-AATAAAAATAA
663491 TA
1 TA
663493 GAAAACAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 10 0.32
18 10 0.32
20 11 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATTTAAATAAAAATAA
Found at i:663485 original size:20 final size:19
Alignment explanation
Indices: 663434--663489 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
663424 TCAATAATAA
*
663434 ATTAATTTA-AATAAAATT
1 ATTAATTTATAATAAAAAT
*
663452 AATAATTTAT--TAAAAAT
1 ATTAATTTATAATAAAAAT
663469 ATTATATTTATAATAAAAAT
1 ATTA-ATTTATAATAAAAAT
663489 A
1 A
663490 ATAGAAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.29
18 14 0.45
20 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTAATTTATAATAAAAAT
Found at i:663662 original size:18 final size:18
Alignment explanation
Indices: 663607--663662 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
663597 TATTATTTTT
*
663607 TAAAA-TTTATTAAAAATA
1 TAAAATTTTAATAAAAA-A
* * *
663625 TTAAATTTATAATTAGAAA
1 TAAAATTT-TAATAAAAAA
663644 TAAAATTTTAATAAAAAA
1 TAAAATTTTAATAAAAAA
663662 T
1 T
663663 TTATTTCTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 13 0.45
19 10 0.34
20 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAAATTTTAATAAAAAA
Found at i:668880 original size:19 final size:20
Alignment explanation
Indices: 668856--668906 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
668846 AATGACCAAT
668856 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
668875 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
668895 AAAATCGCAACG
1 AAAATCGCAACG
668907 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:668900 original size:20 final size:20
Alignment explanation
Indices: 668856--669133 Score: 139
Period size: 20 Copynumber: 13.6 Consensus size: 20
668846 AATGACCAAT
* *
668856 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
668875 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
668895 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
668915 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
668935 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
668956 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
668979 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
668999 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
669019 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
669039 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
669059 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
669082 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
669102 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
669122 AGAATCGCAACG
1 AAAATCGCAACG
669134 TTAAAAAGAA
Statistics
Matches: 204, Mismatches: 43, Indels: 23
0.76 0.16 0.09
Matches are distributed among these distances:
19 17 0.08
20 144 0.71
21 14 0.07
23 29 0.14
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:669034 original size:40 final size:40
Alignment explanation
Indices: 668981--669131 Score: 187
Period size: 40 Copynumber: 3.7 Consensus size: 40
668971 TTTAGAAGAA
* *
668981 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
* *
669021 AATCGCAATGCGATTTATATAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
* * *
669061 AGTCGCAACGCGATTTAGA-AGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-TT-GATAG--AATCGCAATGCGATTGAGAG
*
669104 AATCGCAATGCGATTTATAGAATCGCAA
1 AATCGCAATGCGATTGATAGAATCGCAA
669132 CGTTAAAAAG
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
40 55 0.59
41 4 0.04
42 5 0.05
43 30 0.32
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (40 bp):
AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
Found at i:669147 original size:20 final size:20
Alignment explanation
Indices: 669124--669163 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
669114 CGATTTATAG
*
669124 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
669144 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
669164 TAGTTAAAAA
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:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:669148 original size:103 final size:103
Alignment explanation
Indices: 668917--669153 Score: 298
Period size: 103 Copynumber: 2.3 Consensus size: 103
668907 TTAAAAAGAA
* * *
668917 AATCGCAACGGTCAAAAGAAAATCGCAACGCGAGCTTCCAAGTTCGCAACGCGATTTAGAAGAAA
1 AATCGCAACGCTAAAAAGAAAATCGCAACGCGA-CTTCCAAGGTCGCAACGCGATTTAGAAGAAA
* *
668982 ATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAG
65 ATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAG
* * *** * * * *
669021 AATCGCAATGCGATTTATATAATCGCAATGCGA-TT-GAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAACGCTAAAAAGAAAATCGCAACGCGACTTCCA-AG-GTCGCAACGCGATTTAGAAGAA
669084 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAG
64 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAG
*
669124 AATCGCAACGTTAAAAAGAAAATCGCAACG
1 AATCGCAACGCTAAAAAGAAAATCGCAACG
669154 GTCAAAAGAA
Statistics
Matches: 108, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
101 1 0.01
102 4 0.04
103 80 0.74
104 23 0.21
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (103 bp):
AATCGCAACGCTAAAAAGAAAATCGCAACGCGACTTCCAAGGTCGCAACGCGATTTAGAAGAAAA
TCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAG
Found at i:669252 original size:6 final size:6
Alignment explanation
Indices: 669241--669285 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
669231 GACACGTATT
669241 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
669286 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:669992 original size:6 final size:6
Alignment explanation
Indices: 669976--670103 Score: 249
Period size: 6 Copynumber: 21.5 Consensus size: 6
669966 TCTCGTCTCG
669976 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
670023 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
670071 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
670104 AATACGTGTC
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.04
6 117 0.96
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:670206 original size:20 final size:20
Alignment explanation
Indices: 670181--670224 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
670171 TTTTTAACTA
*
670181 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
670201 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
670221 TTCT
1 TTCT
670225 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:670234 original size:20 final size:20
Alignment explanation
Indices: 670211--670424 Score: 194
Period size: 20 Copynumber: 10.4 Consensus size: 20
670201 TTCTTTTTAA
*
670211 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTCTCTAAATCG
* *
670231 CGTTGGGATTCTCTCAATCG
1 CGTTGCGATTCTCTAAATCG
* *
670251 CATTGCGATTCTATAAATCG
1 CGTTGCGATTCTCTAAATCG
* * *
670271 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTCTAAATCG
* * *
670291 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTCTAAATCG
*
670311 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTAAATCG
* *
670334 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTCTCTAAATCG
* *
670354 CATTGCGATTCTATAAATCG
1 CGTTGCGATTCTCTAAATCG
* * *
670374 CATTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTAAATCG
*
670394 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTAAATCG
670417 CGTTGCGA
1 CGTTGCGA
670425 ACTTGGAAGC
Statistics
Matches: 165, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
20 129 0.78
21 2 0.01
22 6 0.04
23 28 0.17
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTCTCTAAATCG
Found at i:670257 original size:40 final size:40
Alignment explanation
Indices: 670213--670424 Score: 226
Period size: 40 Copynumber: 5.2 Consensus size: 40
670203 CTTTTTAACG
* * * *
670213 TTGCGATTTTCTAAATCGCGTTGGGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCGCA
* * *
670253 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCGCA
* * *
670293 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCATTGCGA--TTC-TCTAAATCGCA
* * *
670336 TTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCGCA
* * *
670376 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCATTGCGA--TTC-TCTAAATCGCA
670419 TTGCGA
1 TTGCGA
670425 ACTTGGAAGC
Statistics
Matches: 147, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
40 91 0.62
41 3 0.02
42 6 0.04
43 47 0.32
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCGCA
Found at i:670353 original size:83 final size:83
Alignment explanation
Indices: 670246--670424 Score: 277
Period size: 83 Copynumber: 2.2 Consensus size: 83
670236 GGATTCTCTC
* * * * * * *
670246 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCG
1 AATCGCGTTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
670311 CATTGCGATTTTCTTCTA
66 CATTGCGATTTTCTTCTA
* *
670329 AATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
1 AATCGCGTTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
670394 CATTGCGATTTTCTTCTA
66 CATTGCGATTTTCTTCTA
670412 AATCGCGTTGCGA
1 AATCGCGTTGCGA
670425 ACTTGGAAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (83 bp):
AATCGCGTTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
CATTGCGATTTTCTTCTA
Found at i:670463 original size:20 final size:20
Alignment explanation
Indices: 670438--670491 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
670428 TGGAAGCTCG
*
670438 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
670458 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
670478 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
670492 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:671177 original size:24 final size:24
Alignment explanation
Indices: 671150--671202 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
671140 AGGTTATTAG
*
671150 TTAATTGATAAATAAAT-ATTTTTA
1 TTAATTGATAAA-AAATAATATTTA
* *
671174 TTAATTTATTAAAAATAATATTTA
1 TTAATTGATAAAAAATAATATTTA
671198 TTAAT
1 TTAAT
671203 CTAGAGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTAATTGATAAAAAATAATATTTA
Found at i:671993 original size:45 final size:44
Alignment explanation
Indices: 671938--672041 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 44
671928 GCACCAATCC
671938 ATGCATCGATGCAC-CA-TTGAATAAATTGAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGTTGAATAAA---AACATCGAATGCATTTT
** *
671983 ATGCATCGATGCACTCAGGTTTTATGAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCA-GTTGAATAAAAACATCGAATGCATTTT
672028 ATGCATCGATGCAC
1 ATGCATCGATGCAC
672042 AGACCATGTG
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
45 45 0.85
46 2 0.04
48 6 0.11
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (44 bp):
ATGCATCGATGCACTCAGTTGAATAAAAACATCGAATGCATTTT
Found at i:672808 original size:32 final size:34
Alignment explanation
Indices: 672742--672810 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
672732 TTTGTAAAGA
* *
672742 GGAAATGTTCTAGCTTAGCCCGTGTAAAAACTAG
1 GGAAAGGTTCTAGCTTAGCCCGAGTAAAAACTAG
*
672776 GGAAAGGTTCTAGTTTAGCCC-AG-AAAAACTAG
1 GGAAAGGTTCTAGCTTAGCCCGAGTAAAAACTAG
672808 GGA
1 GGA
672811 GTTTATAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 12 0.38
33 1 0.03
34 19 0.59
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (34 bp):
GGAAAGGTTCTAGCTTAGCCCGAGTAAAAACTAG
Found at i:673694 original size:19 final size:20
Alignment explanation
Indices: 673670--673717 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
673660 AATGATTTTC
*
673670 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
673689 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
673709 TTTTGAAAA
1 TTTTGAAAA
673718 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:684705 original size:10 final size:10
Alignment explanation
Indices: 684690--684717 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
684680 ATTGATCAAT
684690 AACAAGAAAC
1 AACAAGAAAC
684700 AACAAGAAAC
1 AACAAGAAAC
684710 AACAAGAA
1 AACAAGAA
684718 TCAAGAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.18, G:0.11, T:0.00
Consensus pattern (10 bp):
AACAAGAAAC
Found at i:688602 original size:34 final size:28
Alignment explanation
Indices: 688563--688655 Score: 71
Period size: 34 Copynumber: 3.0 Consensus size: 28
688553 AATAATAATA
688563 TATTTTAATTTAAAATATTCAAAAGATAT
1 TATTTTAATTT-AAATATTCAAAAGATAT
* *
688592 TGACACATTTTACTATTTAAA-CTTAAAAAGATAT
1 T-----ATTTTA--ATTTAAATATTCAAAAGATAT
688626 TATTTTAATTTTAAATATTCAAAAGGATAT
1 TATTTTAA-TTTAAATATTCAAAA-GATAT
688656 AATTATCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 19
0.68 0.05 0.26
Matches are distributed among these distances:
27 1 0.02
28 6 0.12
29 13 0.26
30 5 0.10
34 18 0.36
35 3 0.06
36 4 0.08
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (28 bp):
TATTTTAATTTAAATATTCAAAAGATAT
Found at i:689908 original size:23 final size:23
Alignment explanation
Indices: 689873--689920 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
689863 ATAAAGTACA
* *
689873 ATAACATATTAGGTAGCGGTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
689896 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
689919 AT
1 AT
689921 TGACATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:690430 original size:23 final size:23
Alignment explanation
Indices: 690395--690467 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
690385 ATACTTTACA
690395 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
690418 ATATAAACTCTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
690441 ATATAAGCGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATT
690464 ATAT
1 ATAT
690468 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:690911 original size:23 final size:23
Alignment explanation
Indices: 690885--690957 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
690875 ATATTTTACA
*
690885 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
690908 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
690931 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
690954 ATAT
1 ATAT
690958 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:691409 original size:23 final size:23
Alignment explanation
Indices: 691374--691446 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
691364 ATACTTTACA
*
691374 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
691397 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
691420 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
691443 ATAT
1 ATAT
691447 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:691470 original size:489 final size:488
Alignment explanation
Indices: 689994--691632 Score: 2926
Period size: 490 Copynumber: 3.4 Consensus size: 488
689984 TTATAATATG
*
689994 TTGAAAGTGTTCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAA-TTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
**
690058 TTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTCGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
690122 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
690187 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* * ** *
690252 ACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACT
260 ACTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACT
* * *
690317 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATATATACTTTTATAAAAATGA
325 CAAAAGATAA-CTTAAATTAATGTTTTCCACAGTGAAATAAGTATGTACACTTTTATAAAAAAGA
* *
690382 TCGATACTTTACAATATAAGCACTACCTATTACATTATATAAACTCTACCTATTACATTATATAA
389 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
690447 GCGCTACCTATTACATCATATTTTTACCTATTATA
454 GCGCTACCTATTACATCATATTTTTACCTATTATA
690482 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
690547 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
*
690612 AAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
690677 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
690742 A-TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCAC
260 ACT-GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCAC
690806 TCAAAAGATAATCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGTACACTTTTATAAAAAAG
324 TCAAAAGATAA-CTTAAATTAATGTTTTCCACAGTGAAATAAGTATGTACACTTTTATAAAAAAG
*
690871 ATAGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
388 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
690936 AGCGCTACCTATTACATCATATTTTTACCTATTATA
453 AGCGCTACCTATTACATCATATTTTTACCTATTATA
*
690972 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
691037 TCAATTTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* **
691102 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGGTTTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
691167 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATT-TTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
691231 ACTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ACTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACT
* * *
691296 CAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAAC-TTAAATTAATGTTTTCCACAGTGAAATAAGTATGTACACTTTTATAAAAAAGA
*
691361 TAAATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
389 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
691426 GCGCTACCTATTACATCATATTTTTACCTATTATA
454 GCGCTACCTATTACATCATATTTTTACCTATTATA
* *
691461 TTGAAAGTGTTCATACTTTTTATAAAAGGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
691526 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
691591 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
691633 AATTTGGGTC
Statistics
Matches: 1111, Mismatches: 34, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
487 32 0.03
488 137 0.12
489 309 0.28
490 633 0.57
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (488 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACTC
AAAAGATAACTTAAATTAATGTTTTCCACAGTGAAATAAGTATGTACACTTTTATAAAAAAGATA
GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
GCTACCTATTACATCATATTTTTACCTATTATA
Found at i:694548 original size:120 final size:120
Alignment explanation
Indices: 694335--694581 Score: 422
Period size: 120 Copynumber: 2.1 Consensus size: 120
694325 TTTTTCTTTC
* * *
694335 ATTCTGGACATAAAGTACCGACACAATATTAAAATGTGTCAACATAGGTTGTAGACCTATTCGTT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCAACATAGGTTGTAGACCTATTCGCT
694400 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
* *
694455 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCAACATAGGTTGTAGACCTATTCGCT
* * *
694520 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
694575 ATTCTGG
1 ATTCTGG
694582 GTTCGATGTG
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCAACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:694721 original size:302 final size:303
Alignment explanation
Indices: 694170--694948 Score: 1420
Period size: 302 Copynumber: 2.6 Consensus size: 303
694160 TTAAAATTAG
* * *
694170 CGACACAATATTAAAAAGTGTTGATATAGGTTATAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
694235 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
694300 CACTTTTTGACAAGGTATCGATACATTTTTCTTTCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* *
694365 AAAATGTGTCAACATAGGTTGTAGACCTATTCGTTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAATGTGTCAACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCCGTTATA
694430 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
694473 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
694538 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT-CGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
694602 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTATGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* * *
694667 AACAA-GTGTCGACATAGGTTGTAGACCTATTCGCTAATAACACTGGTATACTTATACCCGTTAT
196 AA-AATGTGTCAACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCCGTTAT
694731 ATTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
260 ATTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
*
694775 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
694840 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGT-AATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
694904 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
694949 CAATATTAAA
Statistics
Matches: 461, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
302 342 0.74
303 119 0.26
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
AAAATGTGTCAACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCCGTTATA
TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
Found at i:694854 original size:120 final size:120
Alignment explanation
Indices: 694641--694883 Score: 414
Period size: 120 Copynumber: 2.0 Consensus size: 120
694631 TCTTCCATTA
* *
694641 TGGACATAAAGTACCGACACAATATTAACAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
1 TGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
*
694706 ACACTGGTATACTTATACCCGTTATATTACAAAATTATCTAGTACATTATAATTC
66 AAACTGGTATACTTATACCCGTTATATTACAAAATTATCTAGTACATTATAATTC
* *
694761 TGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
* * *
694826 AAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTC
66 AAACTGGTATACTTATACCCGTTATATTACAAAATTATCTAGTACATTATAATTC
694881 TGG
1 TGG
694884 GTTCCGATGT
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 115 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (120 bp):
TGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
AAACTGGTATACTTATACCCGTTATATTACAAAATTATCTAGTACATTATAATTC
Found at i:696176 original size:3 final size:3
Alignment explanation
Indices: 696168--696221 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
696158 ACTTGTTTGG
*
696168 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
696216 TTC ATC
1 ATC ATC
696222 GTCAGCTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.30, C:0.33, G:0.02, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:698059 original size:200 final size:200
Alignment explanation
Indices: 697735--698698 Score: 1730
Period size: 200 Copynumber: 4.8 Consensus size: 200
697725 AACATTAAAC
697735 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
697800 AAAATTACCTAATACATTATACTTATGGGTTTAGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
697865 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCAATCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
697930 ACAAA
196 ACAAA
*
697935 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
698000 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGAAACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
698065 GATCGACACTTTATTGTTGCACCATGTTTGCCATTCATTCTGGACCAAAAATATCGACAGAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
*
698130 AAAAA
196 ACAAA
* *
698135 AGTGTCGAAAAATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
698200 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
698265 GATCGACACTTTATTGTTGCACCTTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
698330 ACAAA
196 ACAAA
698335 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
698400 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * *
698465 GATCGACACTTTATTGTTGCACCCTGTTTGTCATTCATTCTGGACCAAAAGTATCGACAAAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
698530 ACAAA
196 ACAAA
*
698535 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
698600 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTCTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
698665 GATCGACACTTTATGGTTGCACCCTGTTTTCCAT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCAT
698699 ATTGTAAATT
Statistics
Matches: 735, Mismatches: 29, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 735 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:698943 original size:18 final size:18
Alignment explanation
Indices: 698920--698980 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
698910 TCTCATTCAT
*
698920 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
698938 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
698957 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
698976 AATTA
1 AATTA
698981 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:698956 original size:19 final size:19
Alignment explanation
Indices: 698932--698980 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
698922 TTATATTCAC
698932 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
698951 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
698970 ATACAAAATTA
1 ATACAAAATTA
698981 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:700804 original size:33 final size:33
Alignment explanation
Indices: 700767--700832 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
700757 CATCTTAATA
*
700767 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
700800 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
700833 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:700891 original size:21 final size:21
Alignment explanation
Indices: 700866--700930 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
700856 CCCCTTATGC
* *
700866 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
700887 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
700908 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
700929 CT
1 CT
700931 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:703162 original size:20 final size:20
Alignment explanation
Indices: 703134--703186 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
703124 GGTATCGTTT
*
703134 TACCGGTTTTATCAT-TTTGA
1 TACCTGTTTTATCATATTT-A
*
703154 TACCTGTTTTATCATATTTT
1 TACCTGTTTTATCATATTTA
*
703174 TACCTGTTATATC
1 TACCTGTTTTATC
703187 GTTGTGGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (20 bp):
TACCTGTTTTATCATATTTA
Found at i:703358 original size:20 final size:19
Alignment explanation
Indices: 703312--703358 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
703302 TCCGGTAACG
703312 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
703331 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
703352 TTTTACC
1 TTTTACC
703359 TGGTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:703402 original size:181 final size:182
Alignment explanation
Indices: 703098--703561 Score: 725
Period size: 181 Copynumber: 2.6 Consensus size: 182
703088 CGTACTTACG
* *
703098 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCTGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
703163 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
703228 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
703279 AAAGTATCGACTCTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
703344 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
703409 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * **
703461 AAAGTA-CTGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTT
1 AAAGTATC-GACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTT
* *
703525 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGA
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGA
703562 CACGAACCGA
Statistics
Matches: 259, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
181 169 0.65
182 90 0.35
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:704752 original size:147 final size:142
Alignment explanation
Indices: 704456--704822 Score: 364
Period size: 147 Copynumber: 2.5 Consensus size: 142
704446 TATTTTTATC
* * * *
704456 GTTCAATAATTAACCAAATTTGGTCGATAAATTATATGTT-ATCAAAGATAAAATGAGACAAATC
1 GTTCAATAATTAACCAAATTTGGTCGATAACTTATAAGTTCAT-AAAGATAAAATAAGAGAAATC
* ** * * * * * *
704520 CGATTCCAATTCATTATAAAATACTTTTATCATTTGCTTAATATTTATTTTATCGTTTAGATATT
65 CGACTCTTATTTATTATAAAATACTTTTATCATTTACTCAATATTTATTTCATCGCTTAAATATT
704585 TCAAATTATGATA
130 TCAAATTATGATA
* * * *
704598 CTTCAATAATTAATCAAATTCGGTCGATAACGTATAAGTTCATAAAGATAAAATAAGAGAAATCC
1 GTTCAATAATTAACCAAATTTGGTCGATAACTTATAAGTTCATAAAGATAAAATAAGAGAAATCC
* * ** *
704663 AACTCTTATTTATTTTAGAATTGCATACTTTTATTGTTTACTCAATATTTATTTCATTGCTTAAA
66 GACTCTTATTTATTATA-AA----ATACTTTTATCATTTACTCAATATTTATTTCATCGCTTAAA
704728 TATTTCAAATCT-TCG-TA
126 TATTTCAAAT-TAT-GATA
*** * * **
704745 GTTCAATAATTAACCAAATTTAACCAATAACTTACAAGTTCCCAAA-ATTAAAATAAGAGAAATC
1 GTTCAATAATTAACCAAATTTGGTCGATAACTTATAAGTTCATAAAGA-TAAAATAAGAGAAATC
704809 CGACTCTTATTTAT
65 CGACTCTTATTTAT
704823 CTAAATTTAT
Statistics
Matches: 182, Mismatches: 34, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
142 65 0.36
143 4 0.02
146 1 0.01
147 110 0.60
148 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (142 bp):
GTTCAATAATTAACCAAATTTGGTCGATAACTTATAAGTTCATAAAGATAAAATAAGAGAAATCC
GACTCTTATTTATTATAAAATACTTTTATCATTTACTCAATATTTATTTCATCGCTTAAATATTT
CAAATTATGATA
Found at i:704917 original size:118 final size:118
Alignment explanation
Indices: 704709--704939 Score: 295
Period size: 118 Copynumber: 2.0 Consensus size: 118
704699 TTTACTCAAT
*
704709 ATTTATTTCATTGCTTAAATATTTCAAATCTTCGTAGTTCAATAATTAACCAAATTTAACCAATA
1 ATTTATTTCATTGCTTAAATATTTCAAATCATCGTAGTTCAATAATTAACCAAATTTAACCAATA
* * *
704774 ACTTACAAGTTCCCAAAATTAAAATAAGAGAAATCCGACTCTTATTTATCTAA
66 ACATACAAGTTCCCAAAATTAAAATAAGAAAAATCCGACTCCTATTTATCTAA
* * * * * * *
704827 ATTTATTTTATTG-TCTAGATATTTCAAATCATGGTAGTTCAATATTTAACTAAATTTGACCGAT
1 ATTTATTTCATTGCT-TAAATATTTCAAATCATCGTAGTTCAATAATTAACCAAATTTAACCAAT
** * *
704891 AACATACAAGTT-CTTAAATATAAAATATGAAAAATTCGACTCCTATTTA
65 AACATACAAGTTCCCAAAAT-TAAAATAAGAAAAATCCGACTCCTATTTA
704940 AAAAAAACGC
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
117 6 0.06
118 90 0.94
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (118 bp):
ATTTATTTCATTGCTTAAATATTTCAAATCATCGTAGTTCAATAATTAACCAAATTTAACCAATA
ACATACAAGTTCCCAAAATTAAAATAAGAAAAATCCGACTCCTATTTATCTAA
Found at i:716289 original size:137 final size:137
Alignment explanation
Indices: 716038--716823 Score: 1031
Period size: 137 Copynumber: 5.7 Consensus size: 137
716028 TTAGGGAACA
* *
716038 TCATCCTTAGATAACCAAACGTCCTCGTCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGA
1 TCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGA
* * * *
716103 TGACCAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACCCCTCATCACGAAGG
66 TGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCTACCGATCAGAACTCCTCATCACGAAGG
716168 AGTC-GCG
131 AG-CAGCG
* * ** * * *
716175 TCATTCTTAGATAACCAGACGTCCTCATCATGAAGGAACTATGTTATCTTAGATATCTTCAAAGA
1 TCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGA
* ** * *
716240 TGGCCAGACGTCCTCATCACGAAGGAACAACGTCATCTACTAATCAGAACTCCTTATCATGAAGG
66 TGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCTACCGATCAGAACTCCTCATCACGAAGG
*
716305 AGTC-GTG
131 AG-CAGCG
* * *
716312 TCATCCTTAGATAACCAGACGCCCTCATCACGATGGAACTGTGTTATCTCAAATATCTTTAAAGA
1 TCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGA
*
716377 TGGCCAGATGTCCTCATCACGAAGGAACAATGTCATCTACCGATCAGAACTCCTCATCACGAAGG
66 TGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCTACCGATCAGAACTCCTCATCACGAAGG
* *
716442 AGCAACA
131 AGCAGCG
** * *
716449 TCATCCTTAGATAGTCAGATGTCCTCATCACGAAAGAACCGTGTTATCTCAAATATCTTTAAAGA
1 TCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGA
* * * *
716514 TGGCCAAACGTTCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCATGAAGG
66 TGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCTACCGATCAGAACTCCTCATCACGAAGG
* *
716579 AGCAACA
131 AGCAGCG
* * * *
716586 TCATCCTTAGATAGCTAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGA
1 TCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGA
* * * * * * *
716651 TGGCTAGACATCCTCATCACGGAA-GAATAATGTCATCCACTGA-CTAGAACTCCTAATCACGTA
66 TGGCCAGACGTCCTCATCAC-GAAGGAACAATGTCATCTACCGATC-AGAACTCCTCATCACGAA
* * *
716714 GGAACTGAG
129 GGAGCAGCG
* * * *
716723 TCACCCTCAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTCAAAGA
1 TCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGA
716788 TGGCCAGACGTCCTCATCACGAAGGAACAATGTCAT
66 TGGCCAGACGTCCTCATCACGAAGGAACAATGTCAT
716824 ACAACAGTTG
Statistics
Matches: 572, Mismatches: 73, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
136 5 0.01
137 564 0.99
138 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (137 bp):
TCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGA
TGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCTACCGATCAGAACTCCTCATCACGAAGG
AGCAGCG
Found at i:717548 original size:20 final size:20
Alignment explanation
Indices: 717523--717569 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
717513 ATAATGACTG
*
717523 AAATAGTAACCGACGGTGGT
1 AAATAGTAACCGACGATGGT
* **
717543 AAATAGTGACCGGTGATGGT
1 AAATAGTAACCGACGATGGT
717563 AAATAGT
1 AAATAGT
717570 GATCGACAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (20 bp):
AAATAGTAACCGACGATGGT
Found at i:723877 original size:45 final size:45
Alignment explanation
Indices: 723803--723908 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 45
723793 TGTTGGATTT
* *
723803 CCAACTTATTT-CTCACACTATGTTAGAGCTATTACCAACACTAC
1 CCAACTTATTTCCTAAAACTATGTTAGAGCTATTACCAACACTAC
* * * *
723847 TCAACTTATTTCCTAAAACTATGTTGGAGCTATTACCAGCATTAC
1 CCAACTTATTTCCTAAAACTATGTTAGAGCTATTACCAACACTAC
*
723892 CCAACTTATTTCGTAAA
1 CCAACTTATTTCCTAAA
723909 TCTTTTTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 10 0.19
45 43 0.81
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.34
Consensus pattern (45 bp):
CCAACTTATTTCCTAAAACTATGTTAGAGCTATTACCAACACTAC
Found at i:724802 original size:36 final size:36
Alignment explanation
Indices: 724751--724820 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
724741 CTGGAGCATC
*
724751 CTCTTCCTCAGTAATGTTAGCCTCTTCAGATTCCTT
1 CTCTTCCTCAATAATGTTAGCCTCTTCAGATTCCTT
724787 CTCTTCCTCAATAATGTTAGCCTCTTCAGATTCC
1 CTCTTCCTCAATAATGTTAGCCTCTTCAGATTCC
724821 ACTACAAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.19, C:0.31, G:0.10, T:0.40
Consensus pattern (36 bp):
CTCTTCCTCAATAATGTTAGCCTCTTCAGATTCCTT
Found at i:726994 original size:3 final size:3
Alignment explanation
Indices: 726979--727037 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
726969 TACTTATATA
* * **
726979 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
727023 AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT A
727038 TTGCAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:727046 original size:26 final size:28
Alignment explanation
Indices: 726987--727048 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
726977 TAAATAATAA
*
726987 AAATAATAATAATGAAATAATAATTAAAGC
1 AAATAATAATAATAAAATAATAATT--AGC
727017 -AATAATAATAATAAAATAAT-ATT-GC
1 AAATAATAATAATAAAATAATAATTAGC
727042 AAATAAT
1 AAATAAT
727049 GATTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
28 3 0.10
29 19 0.63
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATAATAATAATAAAATAATAATTAGC
Found at i:728334 original size:3 final size:3
Alignment explanation
Indices: 728326--728382 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
728316 AATTATTTTT
*
728326 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
728371 TAA TAA TAA TAA
1 TAA TAA TAA TAA
728383 AATGGGTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Done.