Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008392.1 Hibiscus syriacus cultivar Beakdansim tig00111157_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: 522134
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:201064 original size:3 final size:3
Alignment explanation
Indices: 201056--201124 Score: 83
Period size: 3 Copynumber: 23.3 Consensus size: 3
201046 ATAAAAAATA
201056 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT AAT
201104 -AT AAT -AT AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
201125 TTTTTATAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 8 0.13
3 42 0.69
4 11 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:201917 original size:14 final size:14
Alignment explanation
Indices: 201898--201928 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
201888 TTATTCCGTA
*
201898 GACTTAGTTTACTT
1 GACTTAGTTGACTT
201912 GACTTAGTTGACTT
1 GACTTAGTTGACTT
201926 GAC
1 GAC
201929 CTCTTTGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (14 bp):
GACTTAGTTGACTT
Found at i:203556 original size:72 final size:72
Alignment explanation
Indices: 203434--203585 Score: 196
Period size: 72 Copynumber: 2.1 Consensus size: 72
203424 GATGTTTCAG
* ** *
203434 AAAATCAATTAAATGGTACTCTTCCTCCAAATTTTGGAAAATTGGCAAATTTAGAAACTCTAGAT
1 AAAATAAATTAAATGGTACTCTTCCTCCAAATTTTGGAAAATTGAAAAATTTAGAAACTCTAAAT
*
203499 ATTTGGA
66 ATTGGGA
* * * * ** *
203506 AAAATAAATTAAATGGTCCTCTTCCTCCAAGTTTTGGACAGTTGAAAAATTTAGAAGTTGTAAAT
1 AAAATAAATTAAATGGTACTCTTCCTCCAAATTTTGGAAAATTGAAAAATTTAGAAACTCTAAAT
203571 ATTGGGA
66 ATTGGGA
203578 AAAATAAA
1 AAAATAAA
203586 ATGGAAGGAG
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (72 bp):
AAAATAAATTAAATGGTACTCTTCCTCCAAATTTTGGAAAATTGAAAAATTTAGAAACTCTAAAT
ATTGGGA
Found at i:205235 original size:31 final size:31
Alignment explanation
Indices: 205197--205266 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
205187 TTGGGCTACT
205197 AAATGTATCTAGTTCCAAGAGGAAACAAATA
1 AAATGTATCTAGTTCCAAGAGGAAACAAATA
205228 AAATGTATCTAGTTCCAAGAGGAAACAAATA
1 AAATGTATCTAGTTCCAAGAGGAAACAAATA
205259 AAATGTAT
1 AAATGTAT
205267 AATTAATGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (31 bp):
AAATGTATCTAGTTCCAAGAGGAAACAAATA
Found at i:205579 original size:21 final size:21
Alignment explanation
Indices: 205555--205596 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
205545 TGTTAGAACA
*
205555 TAAATTTGTATATATTTTGAT
1 TAAATTTCTATATATTTTGAT
* *
205576 TAAATTTCTATGTGTTTTGAT
1 TAAATTTCTATATATTTTGAT
205597 GATCTAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (21 bp):
TAAATTTCTATATATTTTGAT
Found at i:207482 original size:40 final size:38
Alignment explanation
Indices: 207438--207571 Score: 110
Period size: 40 Copynumber: 3.3 Consensus size: 38
207428 GGTTTTCAAC
*
207438 AAACGCCGTAAAATCGCGTACTTTAGTGGCATTTTTAAAG
1 AAACGCCGCAAAATCGCGTACTTTAGTGGCATTTTT--AG
* * *
207478 AAACGTCGCTACAAA-CTCGTACTATAGTGGCATTTTGTAG
1 AAACGCCGC-A-AAATCGCGTACTTTAGTGGCATTTT-TAG
* * *
207518 ATAACTGCCACAAAAT-GCGTACTTTAGCGGCGTTTTTGGAG
1 A-AAC-GCCGCAAAATCGCGTACTTTAGTGGCATTTTT--AG
207559 AAACGCCGCAAAA
1 AAACGCCGCAAAA
207572 GTATTAATAT
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
39 9 0.12
40 32 0.43
41 27 0.36
42 7 0.09
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (38 bp):
AAACGCCGCAAAATCGCGTACTTTAGTGGCATTTTTAG
Found at i:207709 original size:21 final size:21
Alignment explanation
Indices: 207685--207724 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
207675 GCCCGGATCA
*
207685 TCGCGCCTCCGGTCACCATTG
1 TCGCGCCTCCGATCACCATTG
* *
207706 TCGCTCCTCTGATCACCAT
1 TCGCGCCTCCGATCACCAT
207725 CGTCTCTCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.42, G:0.17, T:0.28
Consensus pattern (21 bp):
TCGCGCCTCCGATCACCATTG
Found at i:208886 original size:21 final size:22
Alignment explanation
Indices: 208860--208910 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
208850 AATTTTTCGT
208860 TTATTATTAATAAA-ATTATTA
1 TTATTATTAATAAATATTATTA
208881 TTATTATT-ATAAATATTATTA
1 TTATTATTAATAAATATTATTA
208902 TTATTATTA
1 TTATTATTA
208911 TTATTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATTATTAATAAATATTATTA
Found at i:208915 original size:18 final size:18
Alignment explanation
Indices: 208860--208919 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
208850 AATTTTTCGT
* *
208860 TTATTATTAATAAAATTA
1 TTATTATTATTATAATTA
*
208878 TTATTATTATTATAAATA
1 TTATTATTATTATAATTA
*
208896 TTATTATTATTATTATTA
1 TTATTATTATTATAATTA
208914 TTATTA
1 TTATTA
208920 AATATATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTATTATTATAATTA
Found at i:208927 original size:12 final size:13
Alignment explanation
Indices: 208860--208931 Score: 62
Period size: 12 Copynumber: 5.7 Consensus size: 13
208850 AATTTTTCGT
208860 TTATTATT-AATA
1 TTATTATTAAATA
** *
208872 AAATTATT-ATTA
1 TTATTATTAAATA
208884 TTATTA-TAAATA
1 TTATTATTAAATA
*
208896 TTATTATTATTATTA
1 TTATTATTA--AATA
208911 TTATTATTAAATA
1 TTATTATTAAATA
208924 -TATTATTA
1 TTATTATTA
208932 CAAGCCCAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.02
12 30 0.62
13 5 0.10
15 12 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTATTAAATA
Found at i:208927 original size:18 final size:16
Alignment explanation
Indices: 208876--208931 Score: 73
Period size: 15 Copynumber: 3.7 Consensus size: 16
208866 TTAATAAAAT
208876 TATTATTATTATTATA
1 TATTATTATTATTATA
*
208892 -AATATTATTATTAT-
1 TATTATTATTATTATA
*
208906 TATTATTATTATTAAA
1 TATTATTATTATTATA
208922 TA-TATTATTA
1 TATTATTATTA
208932 CAAGCCCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 33 0.94
16 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTATTATTATA
Found at i:208931 original size:3 final size:3
Alignment explanation
Indices: 208860--208919 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
208850 AATTTTTCGT
* ** * *
208860 TTA TTA TTA ATA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
208908 TTA TTA TTA TTA
1 TTA TTA TTA TTA
208920 AATATATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:217471 original size:114 final size:114
Alignment explanation
Indices: 217271--217490 Score: 368
Period size: 114 Copynumber: 1.9 Consensus size: 114
217261 CACGTTCTCG
** *
217271 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGGAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTC
* * *
217336 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GATAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
*
217385 TAGTAGAAATAAGGAGACTCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTC
*
217450 GATAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GATAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
217491 CTGCATGATC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTC
GATAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:218731 original size:76 final size:76
Alignment explanation
Indices: 218592--218759 Score: 187
Period size: 76 Copynumber: 2.2 Consensus size: 76
218582 ACAAATGTTG
* * * * * *
218592 GGGCATGCTGAAA-ACCCTTGTCAATCAGAATCAGGAATGTTGATGTATCCTGAATGTTTATATC
1 GGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATGTTAATGTATCCTGAACGCTCATATC
218656 AGTAAAATGCTA
66 A-TAAAATGCTA
* * **
218668 GGGCATACTGAAAGCCCCTT-TCAATCAGAATGAAGAATGTTAATGTATTTTGAACGCTCATATC
1 GGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATGTTAATGTATCCTGAACGCTCATATC
* * *
218732 ATCAAATGTTG
66 ATAAAATGCTA
*
218743 GGGCATGCTGAAGGCCC
1 GGGCATGCTGAAAGCCC
218760 ACAACATCCT
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
75 22 0.29
76 49 0.64
77 5 0.07
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (76 bp):
GGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATGTTAATGTATCCTGAACGCTCATATC
ATAAAATGCTA
Found at i:219759 original size:50 final size:53
Alignment explanation
Indices: 219624--219768 Score: 165
Period size: 54 Copynumber: 2.8 Consensus size: 53
219614 TAATTGAGAA
219624 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACAGAAAA-GATGAATGTGTTGTCAAATGCTTTACGAAC
* * * *
219678 ATCTGAGCAGAAGCCACA-AGAAAGAAAGAATGTGTTTTCAAATGTTTTAC-ATC
1 ATCTGAGCAGAAGCCACAGA-AAAG-ATGAATGTGTTGTCAAATGCTTTACGAAC
* *
219731 -TC-GA-CAGAAACCACAGGAAAAGATGAATGTATTGTCAA
1 ATCTGAGCAGAAGCCACA-GAAAAGATGAATGTGTTGTCAA
219769 CCAGTGATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
50 23 0.29
51 6 0.08
52 3 0.04
53 4 0.05
54 43 0.54
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (53 bp):
ATCTGAGCAGAAGCCACAGAAAAGATGAATGTGTTGTCAAATGCTTTACGAAC
Found at i:220166 original size:22 final size:22
Alignment explanation
Indices: 220132--220188 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
220122 GCATCTACAA
*
220132 TCTTCAAATATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
220154 TTTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
220176 TCTTCAAAGATGA
1 TCTTCAAAGATGA
220189 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:221458 original size:76 final size:76
Alignment explanation
Indices: 220863--221424 Score: 1043
Period size: 76 Copynumber: 7.4 Consensus size: 76
220853 CTATTTCCTA
*
220863 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
220928 AGCCTTAGGGT
66 AGCCTTAGGGT
220939 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
221004 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
221015 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCTTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
221080 AGCCTTAGGGT
66 AGCCTTAGGGT
*
221091 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
221156 AGCCTTAGGGT
66 AGCCTTAGGGT
221167 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
221232 AGCCTTAGGGT
66 AGCCTTAGGGT
*
221243 CATCTGTAAGTCCTACAGGGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
221308 AGCCTTAGGGT
66 AGCCTTAGGGT
**
221319 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
221384 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
221395 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
221425 TTAAGACCTC
Statistics
Matches: 472, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 472 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:221596 original size:21 final size:22
Alignment explanation
Indices: 221570--221620 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
221560 AATTTTTCGT
221570 TTATTATTAATAAA-ATTATTA
1 TTATTATTAATAAATATTATTA
221591 TTATTATT-ATAAATATTATTA
1 TTATTATTAATAAATATTATTA
221612 TTATTATTA
1 TTATTATTA
221621 TTATTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATTATTAATAAATATTATTA
Found at i:221625 original size:18 final size:18
Alignment explanation
Indices: 221570--221629 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
221560 AATTTTTCGT
* *
221570 TTATTATTAATAAAATTA
1 TTATTATTATTATAATTA
*
221588 TTATTATTATTATAAATA
1 TTATTATTATTATAATTA
*
221606 TTATTATTATTATTATTA
1 TTATTATTATTATAATTA
221624 TTATTA
1 TTATTA
221630 AATATATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTATTATTATAATTA
Found at i:221637 original size:12 final size:13
Alignment explanation
Indices: 221570--221641 Score: 62
Period size: 12 Copynumber: 5.7 Consensus size: 13
221560 AATTTTTCGT
221570 TTATTATT-AATA
1 TTATTATTAAATA
** *
221582 AAATTATT-ATTA
1 TTATTATTAAATA
221594 TTATTA-TAAATA
1 TTATTATTAAATA
*
221606 TTATTATTATTATTA
1 TTATTATTA--AATA
221621 TTATTATTAAATA
1 TTATTATTAAATA
221634 -TATTATTA
1 TTATTATTA
221642 CAAGCCCAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.02
12 30 0.62
13 5 0.10
15 12 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTATTAAATA
Found at i:221637 original size:18 final size:16
Alignment explanation
Indices: 221586--221641 Score: 73
Period size: 15 Copynumber: 3.7 Consensus size: 16
221576 TTAATAAAAT
221586 TATTATTATTATTATA
1 TATTATTATTATTATA
*
221602 -AATATTATTATTAT-
1 TATTATTATTATTATA
*
221616 TATTATTATTATTAAA
1 TATTATTATTATTATA
221632 TA-TATTATTA
1 TATTATTATTA
221642 CAAGCCCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 33 0.94
16 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTATTATTATA
Found at i:221641 original size:3 final size:3
Alignment explanation
Indices: 221570--221629 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
221560 AATTTTTCGT
* ** * *
221570 TTA TTA TTA ATA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
221618 TTA TTA TTA TTA
1 TTA TTA TTA TTA
221630 AATATATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:222901 original size:9 final size:10
Alignment explanation
Indices: 222885--222909 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
222875 TTTATATTTA
222885 ATTTTTTTTT
1 ATTTTTTTTT
222895 ATTTTTTTTT
1 ATTTTTTTTT
222905 ATTTT
1 ATTTT
222910 ACTCATTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:223975 original size:19 final size:19
Alignment explanation
Indices: 223951--224005 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
223941 TAGTTTTAAT
223951 CTAAGTCCTAGATTTAACC
1 CTAAGTCCTAGATTTAACC
*
223970 CTAAG---T---TTTAA-T
1 CTAAGTCCTAGATTTAACC
223982 CTAAGTCCTAGATTTAACC
1 CTAAGTCCTAGATTTAACC
224001 CTAAG
1 CTAAG
224006 GATAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 14
0.63 0.05 0.33
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
15 1 0.04
16 1 0.04
18 5 0.19
19 10 0.37
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (19 bp):
CTAAGTCCTAGATTTAACC
Found at i:223980 original size:31 final size:31
Alignment explanation
Indices: 223942--224005 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
223932 GCTGAAATAT
223942 AGTTTTAATCTAAGTCCTAGATTTAACCCTA
1 AGTTTTAATCTAAGTCCTAGATTTAACCCTA
223973 AGTTTTAATCTAAGTCCTAGATTTAACCCTA
1 AGTTTTAATCTAAGTCCTAGATTTAACCCTA
224004 AG
1 AG
224006 GATAATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (31 bp):
AGTTTTAATCTAAGTCCTAGATTTAACCCTA
Found at i:224022 original size:31 final size:31
Alignment explanation
Indices: 223947--224023 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
223937 AATATAGTTT
* **
223947 TAATCTAAGTCCTAGATTTAACCCTAAGTTT
1 TAATCTAAATCCTAGATTTAACCCTAAGTGA
*
223978 TAATCTAAGTCCTAGATTTAACCCTAAG-GA
1 TAATCTAAATCCTAGATTTAACCCTAAGTGA
*
224008 TAATTTATAATCCTAG
1 TAATCTA-AATCCTAG
224024 CCATCTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 6 0.15
31 35 0.85
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (31 bp):
TAATCTAAATCCTAGATTTAACCCTAAGTGA
Found at i:224959 original size:42 final size:43
Alignment explanation
Indices: 224894--225273 Score: 299
Period size: 42 Copynumber: 8.9 Consensus size: 43
224884 TAATTAGTGA
* * * *
224894 CGTTTGTATCAAAAAACACCGCTATAGATCT-AACCTTTTATGG
1 CGTTTGT-TCCAAAAACGCCGCTATAGATCTCGACCTTTTACGG
* * *
224937 CGTTTGTTCTAAAAACGCCGCTATATATCT-GACCTTTTACGA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTACGG
* * * *
224979 CGTTTGTTCCAAAAATGCTGCTATAGATCTCGATCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTACGG
** * * * *
225022 CGTTTGTTCCAAAAATTCCGCTATAGCTCTCAATCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTACGG
* * * * *
225065 CGTTTGTTCCAAAAATGACGCTATAAATCT-GACTTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTACGG
** * * * *
225107 TTTTTGTTCCAAAAACACCAC--TAGATAT-GACATTTTGA-GG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT-ACGG
* * * * *
225147 AGTTTGTTCCAAAAACGCCGCTATAGATATCGACGTTTTGCAG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTACGG
* * * * *
225190 CGTTTATTCC-AAAACGCCGCTATATATATCAACCTTTTACGA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTACGG
* * *
225232 CGTTTGTTCCAAAAAAATGCCGCCATAGATATCGACCTTTTA
1 CGTTTGTTCC--AAAAACGCCGCTATAGATCTCGACCTTTTA
225274 GAAATCGACC
Statistics
Matches: 274, Mismatches: 54, Indels: 16
0.80 0.16 0.05
Matches are distributed among these distances:
40 31 0.11
42 121 0.44
43 97 0.35
45 25 0.09
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (43 bp):
CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTACGG
Found at i:225036 original size:85 final size:85
Alignment explanation
Indices: 224913--225246 Score: 308
Period size: 85 Copynumber: 4.0 Consensus size: 85
224903 CAAAAAACAC
* * ** * *
224913 CGCTATAGATCT-AACCTTTTATGGCGTTTGTTCTAAAAACGCCGCTATATATCT-GACCTTTTA
1 CGCTATAGATCTCGACGTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATATATCTCAACCTTTTA
224976 CGACGTTTGTTCCAAAAATG
66 CGACGTTTGTTCCAAAAATG
** ** *
224996 CTGCTATAGATCTCGATC-TTTTGCGGCGTTTGTTCCAAAAATTCCGCTATAGCTCTCAATCTTT
1 C-GCTATAGATCTCGA-CGTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATATATCTCAACCTTT
* *
225060 TGCGGCGTTTGTTCCAAAAATG
64 TACGACGTTTGTTCCAAAAATG
* * ** * * * * *
225082 ACGCTATAAATCT-GACTTTTTGCGGTTTTTGTTCCAAAAACACCACTAGATA--T-GACATTTT
1 -CGCTATAGATCTCGACGTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATATATCTCAACCTTTT
* *
225143 GAGGA-GTTTGTTCCAAAAACG
65 -ACGACGTTTGTTCCAAAAATG
* * * *
225164 CCGCTATAGATATCGACGTTTTGCAGCGTTTATTCC-AAAACGCCGCTATATATATCAACCTTTT
1 -CGCTATAGATCTCGACGTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATATATCTCAACCTTTT
225228 ACGACGTTTGTTCCAAAAA
65 ACGACGTTTGTTCCAAAAA
225247 AATGCCGCCA
Statistics
Matches: 197, Mismatches: 42, Indels: 22
0.75 0.16 0.08
Matches are distributed among these distances:
82 43 0.22
83 20 0.10
84 16 0.08
85 81 0.41
86 36 0.18
87 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (85 bp):
CGCTATAGATCTCGACGTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATATATCTCAACCTTTTA
CGACGTTTGTTCCAAAAATG
Found at i:225238 original size:125 final size:128
Alignment explanation
Indices: 224895--225246 Score: 310
Period size: 125 Copynumber: 2.8 Consensus size: 128
224885 AATTAGTGAC
* * * * *** * *
224895 GTTTGTATCAAAAAACACCGCTATAGATCT-AACCTTTTATGGCGTTTGTTCTAAAAACGCCGCT
1 GTTTGT-TCCAAAAACGCCGCTATAGATATCAATCTTTTGCAGCGTTTATTCCAAAAACGCCGCT
* * * * * *
224959 ATATATCT-GACCTTTTACGACGTTTGTTCCAAAAATGCTGCTATAGATCTCGATCTTTTGCGGC
65 ATATATATCGACCTTTTACGACGTTTGTTCCAAAAA-GCTACCATAGATATCGATCTTTTGAGGA
** * * * * * *
225023 GTTTGTTCCAAAAATTCCGCTATAGCTCTCAATCTTTTGCGGCGTTTGTTCCAAAAATGACGCTA
1 GTTTGTTCCAAAAACGCCGCTATAGATATCAATCTTTTGCAGCGTTTATTCCAAAAACGCCGCTA
* * ***
225088 TA-A-ATCTGACTTTTTGCGGTTTTTGTTCCAAAAA-C-ACCACTAGATAT-GA-CATTTTGAGG
66 TATATATC-GACCTTTTACGACGTTTGTTCCAAAAAGCTACCA-TAGATATCGATC-TTTTGAGG
225147 A
128 A
*
225148 GTTTGTTCCAAAAACGCCGCTATAGATATCGA-CGTTTTGCAGCGTTTATTCC-AAAACGCCGCT
1 GTTTGTTCCAAAAACGCCGCTATAGATATCAATC-TTTTGCAGCGTTTATTCCAAAAACGCCGCT
*
225211 ATATATATCAACCTTTTACGACGTTTGTTCCAAAAA
65 ATATATATCGACCTTTTACGACGTTTGTTCCAAAAA
225247 AATGCCGCCA
Statistics
Matches: 180, Mismatches: 36, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
124 14 0.08
125 76 0.42
126 11 0.06
127 20 0.11
128 59 0.33
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (128 bp):
GTTTGTTCCAAAAACGCCGCTATAGATATCAATCTTTTGCAGCGTTTATTCCAAAAACGCCGCTA
TATATATCGACCTTTTACGACGTTTGTTCCAAAAAGCTACCATAGATATCGATCTTTTGAGGA
Found at i:227084 original size:65 final size:65
Alignment explanation
Indices: 226997--227150 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 65
226987 ACTAGGAGTA
* * *
226997 CATCGGTACAC-TAATTACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATG-GTATG
1 CATCGGTACACAAAATGA-ATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGACT-TG
227060 TG
64 TG
* **
227062 CATCGGTACACAAAATGAATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGACTTGTG
1 CATCGGTACACAAAATGAATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGACTTGTG
* *
227127 CATCGGTGCACAAAATGCATTCGA
1 CATCGGTACACAAAATGAATTCGA
227151 AATGGGTGTG
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 74 0.94
66 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (65 bp):
CATCGGTACACAAAATGAATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGACTTGTG
Found at i:237881 original size:23 final size:24
Alignment explanation
Indices: 237851--237903 Score: 99
Period size: 23 Copynumber: 2.2 Consensus size: 24
237841 ATAATAACAT
237851 AAAAACATCAACCATTAATTAAA-
1 AAAAACATCAACCATTAATTAAAC
237874 AAAAACATCAACCATTAATTAAAC
1 AAAAACATCAACCATTAATTAAAC
237898 AAAAAC
1 AAAAAC
237904 TTAATCATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (24 bp):
AAAAACATCAACCATTAATTAAAC
Found at i:249226 original size:17 final size:17
Alignment explanation
Indices: 249199--249242 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
249189 TATCCAACAG
249199 AAAAG-AAAAAATCATA
1 AAAAGTAAAAAATCATA
**
249215 AAAAGTAAAAAATGTTA
1 AAAAGTAAAAAATCATA
249232 AAAA-TAAAAAA
1 AAAAGTAAAAAA
249243 AATAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (17 bp):
AAAAGTAAAAAATCATA
Found at i:251917 original size:22 final size:23
Alignment explanation
Indices: 251892--251940 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
251882 TGAACCACAC
251892 TTAGGAAACT-TAATGGATTACT
1 TTAGGAAACTATAATGGATTACT
* *
251914 TTA-GCAAGTGATAATGGATTACT
1 TTAGGAAACT-ATAATGGATTACT
251937 TTAG
1 TTAG
251941 CAAATCACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 15 0.68
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (23 bp):
TTAGGAAACTATAATGGATTACT
Found at i:255113 original size:30 final size:30
Alignment explanation
Indices: 255077--255138 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
255067 CGTCTTGCAT
*
255077 GTTTGTTCGATCTGTGTTCCCATCATGCTG
1 GTTTGTTCGATCAGTGTTCCCATCATGCTG
* *
255107 GTTTGTTTGATCAGTGTTCCCATCATGTTG
1 GTTTGTTCGATCAGTGTTCCCATCATGCTG
255137 GT
1 GT
255139 CGTTTGGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.45
Consensus pattern (30 bp):
GTTTGTTCGATCAGTGTTCCCATCATGCTG
Found at i:258898 original size:41 final size:41
Alignment explanation
Indices: 258841--258961 Score: 158
Period size: 41 Copynumber: 3.0 Consensus size: 41
258831 TCGGGTCGGG
*
258841 TTTTTTAAA-TGTGATATTCAGGCCGAGTCGGGTTGGGTTT
1 TTTTTTAAAGTGTGATATTCAGGCCGGGTCGGGTTGGGTTT
** * *
258881 TTTTTTAAAGTGTGATATTTGGGTCGGGTCGGGTTTGG-TT
1 TTTTTTAAAGTGTGATATTCAGGCCGGGTCGGGTTGGGTTT
*
258921 TTTTTT-AAGTGTAATATTCAGGCCGGGTCGGGTTCGGGTTT
1 TTTTTTAAAGTGTGATATTCAGGCCGGGTCGGGTT-GGGTTT
258962 AGGGTGAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 24 0.35
40 19 0.28
41 25 0.37
ACGTcount: A:0.15, C:0.09, G:0.32, T:0.44
Consensus pattern (41 bp):
TTTTTTAAAGTGTGATATTCAGGCCGGGTCGGGTTGGGTTT
Found at i:258923 original size:39 final size:40
Alignment explanation
Indices: 258841--258961 Score: 156
Period size: 39 Copynumber: 3.0 Consensus size: 40
258831 TCGGGTCGGG
*
258841 TTTTTTAAA-TGTGATATTCAGGCCGAGTCGGGTTGGGTTT
1 TTTTTTAAAGTGTGATATTCAGGCCGGGTCGGGTTGGG-TT
** * *
258881 TTTTTTAAAGTGTGATATTTGGGTCGGGTCGGGTTTGGTT
1 TTTTTTAAAGTGTGATATTCAGGCCGGGTCGGGTTGGGTT
*
258921 TTTTTT-AAGTGTAATATTCAGGCCGGGTCGGGTTCGGGTT
1 TTTTTTAAAGTGTGATATTCAGGCCGGGTCGGGTT-GGGTT
258961 T
1 T
258962 AGGGTGAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 24 0.35
40 22 0.32
41 23 0.33
ACGTcount: A:0.15, C:0.09, G:0.32, T:0.44
Consensus pattern (40 bp):
TTTTTTAAAGTGTGATATTCAGGCCGGGTCGGGTTGGGTT
Found at i:262903 original size:21 final size:21
Alignment explanation
Indices: 262874--262917 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
262864 GCATGACTAC
*
262874 TTAATTATTG-TCTTATATATT
1 TTAACTATTGATCTTATA-ATT
*
262895 TTAACTATTGATCTTTTAATT
1 TTAACTATTGATCTTATAATT
262916 TT
1 TT
262918 GTAAATCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (21 bp):
TTAACTATTGATCTTATAATT
Found at i:266823 original size:32 final size:32
Alignment explanation
Indices: 266782--266888 Score: 171
Period size: 32 Copynumber: 3.3 Consensus size: 32
266772 CCTAAGGTGA
266782 CCTTGGGTAGGCTTTCAGGCCCCAAGACATTT
1 CCTTGGGTAGGCTTTCAGGCCCCAAGACATTT
266814 CCTTGGGTAGGCTTTCAGGCCCCAAGACATTT
1 CCTTGGGTAGGCTTTCAGGCCCCAAGACATTT
* *
266846 CCTTGGGTAGGCTTTAAGGCCCCAATG-TATTT
1 CCTTGGGTAGGCTTTCAGGCCCCAA-GACATTT
*
266878 CCTTGGATAGG
1 CCTTGGGTAGG
266889 TTCTTAGGCC
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
32 70 0.99
33 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (32 bp):
CCTTGGGTAGGCTTTCAGGCCCCAAGACATTT
Found at i:266898 original size:32 final size:31
Alignment explanation
Indices: 266782--266939 Score: 131
Period size: 32 Copynumber: 5.0 Consensus size: 31
266772 CCTAAGGTGA
* * *
266782 CCTTGGGTAGGCTTTCAGGCCCCAAGACATTT
1 CCTTGGATAGGCTTTTAGGCCCCAAG-TATTT
* * *
266814 CCTTGGGTAGGCTTTCAGGCCCCAAGACATTT
1 CCTTGGATAGGCTTTTAGGCCCCAAG-TATTT
* *
266846 CCTTGGGTAGGCTTTAAGGCCCCAATGTATTT
1 CCTTGGATAGGCTTTTAGGCCCCAA-GTATTT
** *
266878 CCTTGGATAGG-TTCTTAGGCCATAAGT-TCTC
1 CCTTGGATAGGCTT-TTAGGCCCCAAGTAT-TT
* *
266909 CCTTGGATAGACTCTTAGGCCCCAAGATATT
1 CCTTGGATAGGCTTTTAGGCCCCAAG-TATT
266940 CCATTAGATT
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
30 1 0.01
31 25 0.23
32 81 0.74
33 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.31
Consensus pattern (31 bp):
CCTTGGATAGGCTTTTAGGCCCCAAGTATTT
Found at i:268297 original size:24 final size:20
Alignment explanation
Indices: 268250--268325 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
268240 AATGCAATTA
*
268250 ATGCATCGATGCAT--AAGG
1 ATGCATCGATGCATGGTAGG
*
268268 AGTGCATCGATGCATACGTTAAGGG
1 A-TGCATCGATGCAT--GGT-A-GG
*
268293 ATGCATCGATACATGGTAGG
1 ATGCATCGATGCATGGTAGG
268313 ATGCATCGATGCA
1 ATGCATCGATGCA
268326 CTTCAAAGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
18 1 0.02
19 13 0.28
20 14 0.30
21 1 0.02
22 2 0.04
24 13 0.28
25 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (20 bp):
ATGCATCGATGCATGGTAGG
Found at i:269909 original size:23 final size:23
Alignment explanation
Indices: 269841--269901 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
269831 ACATTTTATA
269841 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
269864 CGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
269887 TGGCACTTAGGTGCA
1 TGGCACTTCGGTGCA
269902 TTTATACGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:276841 original size:21 final size:21
Alignment explanation
Indices: 276815--276870 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
276805 ATCCTTGAAT
*
276815 GGGTACCAATACCCCCTATGA
1 GGGTACCGATACCCCCTATGA
276836 GGGTACCGATACCCCCTATGA
1 GGGTACCGATACCCCCTATGA
276857 GGGTACCGATACCC
1 GGGTACCGATACCC
276871 TTCACGGGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.18
Consensus pattern (21 bp):
GGGTACCGATACCCCCTATGA
Found at i:277348 original size:14 final size:13
Alignment explanation
Indices: 277331--277371 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
277321 TGAAAACTAC
277331 ACATTGATTTTCAA
1 ACATTG-TTTTCAA
*
277345 ACATTTTTTTCAA
1 ACATTGTTTTCAA
*
277358 ACATAGTTTTCAA
1 ACATTGTTTTCAA
277371 A
1 A
277372 ATTTGTCCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (13 bp):
ACATTGTTTTCAA
Found at i:277356 original size:13 final size:13
Alignment explanation
Indices: 277338--277375 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
277328 TACACATTGA
277338 TTTTCAAACATTT
1 TTTTCAAACATTT
**
277351 TTTTCAAACATAG
1 TTTTCAAACATTT
277364 TTTTCAAA-ATTT
1 TTTTCAAACATTT
277376 GTCCATTAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 2 0.10
13 19 0.90
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (13 bp):
TTTTCAAACATTT
Found at i:279690 original size:17 final size:17
Alignment explanation
Indices: 279623--279691 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
279613 TTCGGTTTGT
*
279623 AAAAAACCGGA-TTTAA
1 AAAAAACCGGATTTTTA
*
279639 AAAAAAACGGATTTTTTGA
1 AAAAAACCGGA-TTTTT-A
** *
279658 TAAAAATTCGGTTTTTTA
1 -AAAAAACCGGATTTTTA
279676 AAAAAACCGGATTTTT
1 AAAAAACCGGATTTTT
279692 TTTCGGATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
16 10 0.24
17 13 0.32
18 4 0.10
19 6 0.15
20 8 0.20
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (17 bp):
AAAAAACCGGATTTTTA
Found at i:281207 original size:26 final size:24
Alignment explanation
Indices: 281178--281236 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 24
281168 AGTAAAATGA
281178 TTCGGTTTGGATTTACCTTTAAACGG
1 TTCGG-TTGG-TTTACCTTTAAACGG
281204 TTC-G--GGTTTACCTTTAAACGG
1 TTCGGTTGGTTTACCTTTAAACGG
281225 TTCGGTTCGGTT
1 TTCGGTT-GGTT
281237 CGGGTTTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
21 18 0.62
22 3 0.10
25 5 0.17
26 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (24 bp):
TTCGGTTGGTTTACCTTTAAACGG
Found at i:281213 original size:21 final size:21
Alignment explanation
Indices: 281180--281229 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
281170 TAAAATGATT
*
281180 CGGTTTGGATTTACCTTTAAA
1 CGGTTCGGATTTACCTTTAAA
*
281201 CGGTTCGGGTTTACCTTTAAA
1 CGGTTCGGATTTACCTTTAAA
281222 CGGTTCGG
1 CGGTTCGG
281230 TTCGGTTCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (21 bp):
CGGTTCGGATTTACCTTTAAA
Found at i:281256 original size:26 final size:27
Alignment explanation
Indices: 281201--281257 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 27
281191 TACCTTTAAA
281201 CGGTTCGGGTTTACCTTTAAACGGTTCGGTT
1 CGGTTCGGGTTTACCTTTAAA--G--CGGTT
281232 CGGTTCGGGTTTACCTTTAAA-CGGTT
1 CGGTTCGGGTTTACCTTTAAAGCGGTT
281258 TGATTTCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 5 0.19
31 21 0.81
ACGTcount: A:0.14, C:0.19, G:0.28, T:0.39
Consensus pattern (27 bp):
CGGTTCGGGTTTACCTTTAAAGCGGTT
Found at i:284788 original size:19 final size:19
Alignment explanation
Indices: 284764--284809 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
284754 TGAATAGTGA
284764 TGAACAGTATTGTTAACAG
1 TGAACAGTATTGTTAACAG
284783 TGAACAGTATTGTTAACAG
1 TGAACAGTATTGTTAACAG
284802 TGAACAGT
1 TGAACAGT
284810 GCATCGATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (19 bp):
TGAACAGTATTGTTAACAG
Found at i:284916 original size:30 final size:30
Alignment explanation
Indices: 284876--284936 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
284866 ATTAATATTA
284876 TGCATAGATACGCTAAAGTAACTGCTACAG
1 TGCATAGATACGCTAAAGTAACTGCTACAG
* * *
284906 TGCATCGATACGCTACATTAACTGCTACAG
1 TGCATAGATACGCTAAAGTAACTGCTACAG
284936 T
1 T
284937 AACTTCCGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (30 bp):
TGCATAGATACGCTAAAGTAACTGCTACAG
Found at i:285410 original size:47 final size:47
Alignment explanation
Indices: 285322--285574 Score: 433
Period size: 47 Copynumber: 5.4 Consensus size: 47
285312 TTTTTTTTCT
* *
285322 CATAAGCTCGTAAGCTTATTTTTACCAAAATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTA-TTTTATCAATATACTTACCATTTAAATTC
285370 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
285417 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
285464 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
285511 CATAAGCTCGTAAGCTTATTTTATCAATATACTTGCCA-TT--ATT-
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
285554 CATAAGCTCATAAGCTTATTT
1 CATAAGCTCGTAAGCTTATTT
285575 GCATACTTAC
Statistics
Matches: 201, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
43 20 0.10
44 3 0.01
46 2 0.01
47 158 0.79
48 18 0.09
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (47 bp):
CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
Found at i:293800 original size:72 final size:73
Alignment explanation
Indices: 293682--293821 Score: 201
Period size: 72 Copynumber: 1.9 Consensus size: 73
293672 TCACTCTACA
* *
293682 TTATATTAGGTAGTGTTTCCCTTTGCTTTGAAACACTGAGATGTTAACAATTTCAGTTTAAAATT
1 TTATATTAGGTAGTGTTTCCCTTTGCTTTGAAACACTAAGATGTTAACAATTTCACTTTAAAATT
293747 TTTGAACC
66 TTTGAACC
* * ** * *
293755 TTATATTAGGTGGTG-TTCCCTTTGGTTTGAAACGTTAAGATGTTAACAATTTGACTTTAAATTT
1 TTATATTAGGTAGTGTTTCCCTTTGCTTTGAAACACTAAGATGTTAACAATTTCACTTTAAAATT
293819 TTT
66 TTT
293822 TATAAGAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 45 0.76
73 14 0.24
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.45
Consensus pattern (73 bp):
TTATATTAGGTAGTGTTTCCCTTTGCTTTGAAACACTAAGATGTTAACAATTTCACTTTAAAATT
TTTGAACC
Found at i:303147 original size:43 final size:43
Alignment explanation
Indices: 303048--303149 Score: 195
Period size: 43 Copynumber: 2.4 Consensus size: 43
303038 TTGCTTTATC
*
303048 TTTAGTATCGATACTAAATGGCACATTGGAATCTTATGAATCG
1 TTTAGTATCGATATTAAATGGCACATTGGAATCTTATGAATCG
303091 TTTAGTATCGATATTAAATGGCACATTGGAATCTTATGAATCG
1 TTTAGTATCGATATTAAATGGCACATTGGAATCTTATGAATCG
303134 TTTAGTATCGATATTA
1 TTTAGTATCGATATTA
303150 TCTAAGGGGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (43 bp):
TTTAGTATCGATATTAAATGGCACATTGGAATCTTATGAATCG
Found at i:304477 original size:19 final size:19
Alignment explanation
Indices: 304453--304502 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
304443 CAATCAAAAC
304453 AATATTATTTTATGTA-TTT
1 AATATTATTTTAT-TATTTT
* *
304472 AATATTAATATATTATTTT
1 AATATTATTTTATTATTTT
304491 AATATTATTTTA
1 AATATTATTTTA
304503 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AATATTATTTTATTATTTT
Found at i:304495 original size:11 final size:11
Alignment explanation
Indices: 304481--304505 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
304471 TAATATTAAT
304481 ATATTATTTTA
1 ATATTATTTTA
304492 ATATTATTTTA
1 ATATTATTTTA
304503 ATA
1 ATA
304506 AAAATATTAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTATTTTA
Found at i:304565 original size:22 final size:23
Alignment explanation
Indices: 304531--304575 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
304521 AACATATATT
*
304531 TATTAATAATTTTACTAATATAA
1 TATTAATAATTTTAATAATATAA
* *
304554 TATT-ATATTTTTAATATTATAA
1 TATTAATAATTTTAATAATATAA
304576 CAATATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATAATTTTAATAATATAA
Found at i:304583 original size:30 final size:32
Alignment explanation
Indices: 304490--304584 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 32
304480 TATATTATTT
* *
304490 TAATATTAT-TTTAATAAAAATATTAACT-AT-
1 TAATATTATATTTATTAATAAT-TTAACTAATA
* *
304520 TAACA-TATATTTATTAATAATTTTACTAATA
1 TAATATTATATTTATTAATAATTTAACTAATA
304551 TAATATTATATTT-TTAAT-ATTATAAC-AATA
1 TAATATTATATTTATTAATAATT-TAACTAATA
304581 TAAT
1 TAAT
304585 TTGATTATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
29 8 0.15
30 27 0.50
31 12 0.22
32 7 0.13
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.48
Consensus pattern (32 bp):
TAATATTATATTTATTAATAATTTAACTAATA
Found at i:304746 original size:29 final size:29
Alignment explanation
Indices: 304701--304769 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
304691 GTAATATTCC
* *
304701 TAATATTTTATTTATAAAATT-AGAAAAA
1 TAATATTTTAATAATAAAATTAAGAAAAA
* *
304729 TTAATATTTTAATAATAATATTAAGATAAA
1 -TAATATTTTAATAATAAAATTAAGAAAAA
*
304759 TAATATATTAA
1 TAATATTTTAA
304770 ATAAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 28 0.82
30 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
TAATATTTTAATAATAAAATTAAGAAAAA
Found at i:306593 original size:2 final size:2
Alignment explanation
Indices: 306581--306618 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
306571 TTCTTTAACC
306581 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
306619 CACATACACG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:307039 original size:2 final size:2
Alignment explanation
Indices: 307032--307073 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
307022 TTGAAAGTAC
307032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
307074 CTACAATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:307876 original size:31 final size:32
Alignment explanation
Indices: 307820--307880 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
307810 TTTAATAGGG
**
307820 AATTTATGTATTTAGTCATTTAATTACTTTTAT
1 AATTTATGTATTTAGTCATCAAATTA-TTTTAT
307853 AATTT-TGT-TTTAGTCATCAAATTATTTT
1 AATTTATGTATTTAGTCATCAAATTATTTT
307881 GGTCCGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 14 0.54
32 3 0.12
33 5 0.19
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (32 bp):
AATTTATGTATTTAGTCATCAAATTATTTTAT
Found at i:312804 original size:209 final size:203
Alignment explanation
Indices: 312464--312872 Score: 509
Period size: 209 Copynumber: 2.0 Consensus size: 203
312454 CTCTAAGGGC
* * **
312464 TAACTATATGATTGATCACTTATGTTTGTGTTTTGTTTATTTTTCCTCACTTATTTCAAAAAAAT
1 TAACTACATGATTGATCACTTATGTTTGTGTTTTATCCATTTTTCCTCACTTATTTCAAAAAAAT
* * * *
312529 AACATATAGTTACTTTCGTTTTTATTTAATTAAGATGTGGCCATCAATAGTTGACTGTCGTTAGA
66 AACATATAGTCACTTTCGTTTTTATTTAATTAAGATGTGGCCACCAAGAGTTAACTGTCGTTAGA
* * *
312594 CCATTAACGATTTACTGAGCT-ATCATGGTAATTAAATAAAATAGAAAATACATCATTTCCACGT
131 CCATTAACGATTTACTGAGCTGA-CACGATAATGAAATAAAATAGAAAATACATCATTTCCACGT
312658 GGATTATGT
195 GGATTATGT
*
312667 TAACTACATGATTGATCACTTATGTTTTTGTTTTATCCATTTTTCCTCA-TTGATTTTTCAAAAA
1 TAACTACATGATTGATCACTTATGTTTGTGTTTTATCCATTTTTCCTCACTT-A--TTTC-AAAA
* * * * *
312731 AACATAATATATATTGTCACTTTTGTTTTTATTTAATTAAGATGT-GCTCACCACGGGTTAATTG
62 AA-ATAACATATA--GTCACTTTCGTTTTTATTTAATTAAGATGTGGC-CACCAAGAGTTAACTG
* * * * * *
312795 TCTTTAGACCATTAACGATTTACTGAGTTGACACGATAATGAAGTAAAATATAAAATACCTCTTT
123 TCGTTAGACCATTAACGATTTACTGAGCTGACACGATAATGAAATAAAATAGAAAATACATCATT
312860 TCCACGTGGATTA
188 TCCACGTGGATTA
312873 CATGTGGATT
Statistics
Matches: 174, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
202 2 0.01
203 45 0.26
205 4 0.02
206 6 0.03
207 9 0.05
208 2 0.01
209 105 0.60
210 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.42
Consensus pattern (203 bp):
TAACTACATGATTGATCACTTATGTTTGTGTTTTATCCATTTTTCCTCACTTATTTCAAAAAAAT
AACATATAGTCACTTTCGTTTTTATTTAATTAAGATGTGGCCACCAAGAGTTAACTGTCGTTAGA
CCATTAACGATTTACTGAGCTGACACGATAATGAAATAAAATAGAAAATACATCATTTCCACGTG
GATTATGT
Found at i:313742 original size:36 final size:33
Alignment explanation
Indices: 313697--313990 Score: 116
Period size: 37 Copynumber: 8.6 Consensus size: 33
313687 GGTTTTCAAA
*
313697 AAAACATATAATATA-ATTTTTAAAAATCGATTTTCG
1 AAAA-ATATAATATATAGTTTTAAAAA-C-ATTTT-G
*
313733 AAAATATATAATATATAGTTTTGAAAACATTTTG
1 AAAA-ATATAATATATAGTTTTAAAAACATTTTG
* * *
313767 -AAAA-AT-ATA-GT--TTTTGAAAACGGGTTTTGG
1 AAAAATATAATATATAGTTTTAAAAAC--ATTTT-G
* *
313797 AAATATATATTATATAGTTTTTGAAAAACATTTT-
1 AAAAATATAATATATAG-TTTT-AAAAACATTTTG
*
313831 ---AA-AT-ATA-GT--TTTTAAAAAGCATTTTG
1 AAAAATATAATATATAGTTTTAAAAA-CATTTTG
* *
313857 AAAAAATATATAATATATAATTTTTAAAACATTTTTG
1 --AAAA-ATATAATATATAGTTTTAAAAACA-TTTTG
*
313894 AAAAAATATATATATTATATAGTTTTTAAAACATTGTTG
1 --AAAA-ATATA-A-TATATAGTTTTAAAAACATT-TTG
* * * *
313933 AAAATATATATTATATAAATTTTAAAAATATTTTT
1 AAAA-ATATAATATAT-AGTTTTAAAAACATTTTG
313968 AAAAATATATATTATATAGTTTT
1 AAAAATATA-A-TATATAGTTTT
313991 TAATTTTTTA
Statistics
Matches: 203, Mismatches: 23, Indels: 65
0.70 0.08 0.22
Matches are distributed among these distances:
24 5 0.02
25 10 0.05
27 10 0.05
28 1 0.00
29 7 0.03
30 6 0.03
31 7 0.03
32 4 0.02
33 7 0.03
34 10 0.05
35 22 0.11
36 38 0.19
37 48 0.24
38 8 0.04
39 20 0.10
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (33 bp):
AAAAATATAATATATAGTTTTAAAAACATTTTG
Found at i:313811 original size:63 final size:63
Alignment explanation
Indices: 313706--313903 Score: 208
Period size: 63 Copynumber: 3.1 Consensus size: 63
313696 AAAAACATAT
* *
313706 AATATAATTTTTAAAAATCGATTTTCG-AAAATATATAATATATAGTTTTGAAAACATTTTGAAA
1 AATATAGTTTTTAAAAAGC-ATTTT-GAAAAATATATAATATATAGTTTTGAAAACATTTTGAAA
* ** * *
313770 AATATAGTTTTTGAAAACGGGTTTTG-GAAATATATATTATATAGTTTTTGAAAAACATTTT---
1 AATATAGTTTTT-AAAAAGCATTTTGAAAAATATATAATATATAG-TTTTG-AAAACATTTTGAA
313831 A
63 A
* *
313832 AATATAGTTTTTAAAAAGCATTTTGAAAAAATATATAATATATAATTTTTAAAACATTTTTGAAA
1 AATATAGTTTTTAAAAAGCATTTTG-AAAAATATATAATATATAGTTTTGAAAACA-TTTTG-AA
313897 A
63 A
313898 AATATA
1 AATATA
313904 TATATTATAT
Statistics
Matches: 110, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
61 16 0.15
62 21 0.19
63 32 0.29
64 20 0.18
65 14 0.13
66 7 0.06
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (63 bp):
AATATAGTTTTTAAAAAGCATTTTGAAAAATATATAATATATAGTTTTGAAAACATTTTGAAA
Found at i:313840 original size:25 final size:25
Alignment explanation
Indices: 313808--313855 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
313798 AATATATATT
313808 ATATAGTTTTTGAAAAA-CATTTTAA
1 ATATAGTTTTT-AAAAAGCATTTTAA
313833 ATATAGTTTTTAAAAAGCATTTT
1 ATATAGTTTTTAAAAAGCATTTT
313856 GAAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (25 bp):
ATATAGTTTTTAAAAAGCATTTTAA
Found at i:313856 original size:37 final size:35
Alignment explanation
Indices: 313815--313993 Score: 141
Period size: 37 Copynumber: 4.9 Consensus size: 35
313805 ATTATATAGT
313815 TTTTGAAAAACAT-TTTAAATATAGTTTTTAAAAAGCA
1 TTTTGAAAAA-ATATTTAAATATAGTTTTT-AAAA-CA
* *
313852 TTTTGAAAAAATATATAATATATAATTTTTAAAACA
1 TTTTGAAAAAATATTTAA-ATATAGTTTTTAAAACA
*
313888 TTTTTGAAAAAATATATATATTATATAGTTTTTAAAACA
1 -TTTTGAAAAAATAT-T-TA-AATATAGTTTTTAAAACA
* * * * *
313927 TTGTTGAAAATATATATTATATA-AATTTTAAAAATA
1 TT-TTGAAAAAATAT-TTAAATATAGTTTTTAAAACA
*
313963 TTTTTAAAAATATATATT--ATATAGTTTTTAA
1 TTTTGAAAAA-ATAT-TTAAATATAGTTTTTAA
313994 TTTTTTATAT
Statistics
Matches: 120, Mismatches: 13, Indels: 20
0.78 0.08 0.13
Matches are distributed among these distances:
34 3 0.03
35 13 0.11
36 23 0.19
37 36 0.30
38 14 0.12
39 31 0.26
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (35 bp):
TTTTGAAAAAATATTTAAATATAGTTTTTAAAACA
Found at i:313992 original size:36 final size:37
Alignment explanation
Indices: 313833--313993 Score: 188
Period size: 36 Copynumber: 4.4 Consensus size: 37
313823 AACATTTTAA
*
313833 ATATAGTTTTTAAAAAGCATTTTGAAAAAATATATAAT
1 ATATAGTTTTTAAAAA-CATTTTGAAAAAATATATATT
*
313871 ATATAATTTTT-AAAACATTTTTGAAAAAATATATATATT
1 ATATAGTTTTTAAAAACA-TTTTG-AAAAA-ATATATATT
313910 ATATAGTTTTT-AAAACATTGTTG--AAAATATATATT
1 ATATAGTTTTTAAAAACATT-TTGAAAAAATATATATT
** * *
313945 ATATAAATTTTAAAAATATTTT-TAAAAATATATATT
1 ATATAGTTTTTAAAAACATTTTGAAAAAATATATATT
313981 ATATAGTTTTTAA
1 ATATAGTTTTTAA
313994 TTTTTTATAT
Statistics
Matches: 108, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
35 20 0.19
36 35 0.32
37 9 0.08
38 17 0.16
39 27 0.25
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATAGTTTTTAAAAACATTTTGAAAAAATATATATT
Found at i:320527 original size:169 final size:169
Alignment explanation
Indices: 320248--320962 Score: 986
Period size: 169 Copynumber: 4.2 Consensus size: 169
320238 AAAAACACAT
* * * *
320248 TCAACCAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAA
1 TCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTGCAGCATAGCTCAA
320313 GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
66 GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
320378 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
131 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * * *
320417 TCAACCAAAACCTTTGAGTTCGATTACACTCAGCTCAAAGGCTCATCAATTGCAGTATAACTCAA
1 TCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTGCAGCATAGCTCAA
* *
320482 GGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACGCTCAGCTCAAAGGCACAT
66 GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* * * *
320547 CCCATTTACAACATAACTTAAGGTGAGAAGGGTTATCTG
131 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* *
320586 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 TCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTGCAGCATAGCTCAA
* * *
320651 GGCGAGAAGGGATATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAATGTACAT
66 GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* * * * *
320716 CCAATTTACTGCATAGCTCAAGGTGAGAAAGGCTATCTG
131 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * * * *
320755 TCAA-CAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATATCCAATTTACAGTATAGCT
1 TCAACCAAA-ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CAA-TTGCAGCATAGCT
** ** * *
320819 CAAGGCGAGAAGGGTTATCTATCGTC-AAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCA
63 CAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
** ** *
320883 TGTAAAATTTACAGTATAACTCAAGGCGAGAAGGGTTATCTG
128 CATCCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * *
320925 TC-ATCAAAGACCTTTGAGTTCGATTACATTCAGCTCAA
1 TCAACCAAA-ACCTTCGAGTTCGATTACACTCAGCTCAA
320963 GGGAATGCCA
Statistics
Matches: 483, Mismatches: 59, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
168 3 0.01
169 346 0.72
170 102 0.21
171 32 0.07
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (169 bp):
TCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTGCAGCATAGCTCAA
GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
Found at i:320988 original size:85 final size:85
Alignment explanation
Indices: 320248--320962 Score: 922
Period size: 85 Copynumber: 8.4 Consensus size: 85
320238 AAAAACACAT
* * * * *
320248 TCAACCAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCAGCATAGCTT
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
320311 AAGGCGAGAAGGGTTATCTG
66 AAGGCGAGAAGGGTTATCTG
*
320331 CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
320396 CAAGGCGAGAAGGGTTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * * *
320417 TCAACCAAA-ACCTTTGAGTTCGATTACACTCAGCTCAAAGGCTCAT-CAA-TTGCAGTATAACT
1 TCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
*
320479 CAAGGCGAGAAGGGCTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * * *
320500 CCAACAAAAGACCTTCGAGTTCGATTACGCTCAGCTCAAAGGCACATCCCATTTACAACATAACT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
* *
320565 TAAGGTGAGAAGGGTTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * *
320586 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCAGCATAGCTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
*
320649 AAGGCGAGAAGGGATATCTG
66 AAGGCGAGAAGGGTTATCTG
* * * * *
320669 CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAATGTACATCCAATTTACTGCATAGCT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
* * *
320734 CAAGGTGAGAAAGGCTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * * * *
320755 TCAACAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATATCCAATTTACAGTATAGCTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
*
320820 AAGGCGAGAAGGGTTATCTA
66 AAGGCGAGAAGGGTTATCTG
** * * ** ** *
320840 TCGTCAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCATGTAAAATTTACAGTATAACTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
320905 AAGGCGAGAAGGGTTATCTG
66 AAGGCGAGAAGGGTTATCTG
* * *
320925 TCATCAAAGACCTTTGAGTTCGATTACATTCAGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAA
320963 GGGAATGCCA
Statistics
Matches: 558, Mismatches: 63, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
82 1 0.00
83 75 0.13
84 115 0.21
85 260 0.47
86 106 0.19
87 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (85 bp):
TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
AAGGCGAGAAGGGTTATCTG
Found at i:321008 original size:85 final size:85
Alignment explanation
Indices: 320254--321045 Score: 505
Period size: 85 Copynumber: 9.4 Consensus size: 85
320244 ACATTCAACC
* * * * * * *
320254 AAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACAT--C--ATTTGCAGCATAGCTTAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * ** *
320315 CGAGAAGGGTTATCTGCCAACAA
64 CGAGAAAGGCTATCTATCATC-A
* * *
320338 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CC-AATTTACAGCATAACTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * * *
320401 CGAGAAGGGTTATCTGTCAACCA
64 CGAGAAAGGCTATCTATC-ATCA
* * * * *
320424 AA-ACCTTTGAGTTCGATTACACTCAGCTCAAAGG-CT--CATCAA-TTGCAGTATAACTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATGCCA--AATTTACAGTATAACTCAAGG
* ** *
320484 CGAGAAGGGCTATCTGCCAACAA
64 CGAGAAAGGCTATCTATCATC-A
** * * ** *
320507 AAGACCTTCGAGTTCGATTACGCTCAGCTCAAAGGCACAT-CC-CATTTACAACATAACTTAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * * * * *
320570 TGAGAAGGGTTATCTGTCAACC
64 CGAGAAAGGCTATCTATCATCA
* * * * *
320592 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT--C--ATTTGCAGCATAGCTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * ** *
320653 CGAGAAGGGATATCTGCCAACAA
64 CGAGAAAGGCTATCTATCATC-A
* * * * * *
320676 AAGACCTTCGAGTTCGATTACACTCAGCTCAAATGTACAT-CC-AATTTACTGCATAGCTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * *
320739 TGAGAAAGGCTATCTGTCAACA
64 CGAGAAAGGCTATCTATCATCA
* * *
320761 AAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATAT-CC-AATTTACAGTATAGCTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * *
320824 CGAGAAGGGTTATCTATCGTCA
64 CGAGAAAGGCTATCTATCATCA
* * * **
320846 AAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCATGTAAAATTTACAGTATAACTCAAGGCG
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATGCCAAATTTACAGTATAACTCAAGGCG
* * *
320911 AGAAGGGTTATCTGTCATCA
66 AGAAAGGCTATCTATCATCA
* * * * *
320931 AAGACCTTTGAGTTCGATTACATTCAGCTCAAGGGAATGCCAAATTCACAGTATAACTTAAGTCA
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATGCCAAATTTACAGTATAACTCAAGGCG
*
320996 AGAAAAGCTATCTATCAAT-A
66 AGAAAGGCTATCTATC-ATCA
* *
321016 AA-AACTGTCGAGTTCGATTCCATTCAGCTC
1 AAGACCT-TCGAGTTCGATTACATTCAGCTC
321046 GATGATACAT
Statistics
Matches: 604, Mismatches: 84, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
81 1 0.00
82 3 0.00
83 71 0.12
84 114 0.19
85 305 0.50
86 106 0.18
87 3 0.00
88 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (85 bp):
AAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATGCCAAATTTACAGTATAACTCAAGGCG
AGAAAGGCTATCTATCATCA
Found at i:321871 original size:36 final size:36
Alignment explanation
Indices: 321831--321901 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
321821 TTTGAAAATA
*
321831 TTTTTTAAAA-CGGTTTTCGAAAAACATATAATATAC
1 TTTTTAAAAATCGGTTTTCG-AAAACATATAATATAC
*
321867 TTTTTAAAAATCGGTTTTCGAAAATATATAATATA
1 TTTTTAAAAATCGGTTTTCGAAAACATATAATATA
321902 TAGTTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 23 0.72
37 9 0.28
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (36 bp):
TTTTTAAAAATCGGTTTTCGAAAACATATAATATAC
Found at i:321886 original size:37 final size:35
Alignment explanation
Indices: 321831--321930 Score: 107
Period size: 36 Copynumber: 2.8 Consensus size: 35
321821 TTTGAAAATA
*
321831 TTTTTTAAAACGGTTTTCGAAAAACATATAATATAC
1 TTTTTAAAAACGGTTTTCG-AAAACATATAATATAC
*
321867 TTTTTAAAAATCGGTTTTCGAAAATATATAATATA-
1 TTTTTAAAAA-CGGTTTTCGAAAACATATAATATAC
* *
321902 TAGTTTTGAAAAC-ATTTT-GAAAACATATA
1 T--TTTTAAAAACGGTTTTCGAAAACATATA
321931 GTTTTTGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
34 10 0.18
35 5 0.09
36 24 0.43
37 17 0.30
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (35 bp):
TTTTTAAAAACGGTTTTCGAAAACATATAATATAC
Found at i:321930 original size:36 final size:36
Alignment explanation
Indices: 321890--322155 Score: 222
Period size: 36 Copynumber: 7.5 Consensus size: 36
321880 GTTTTCGAAA
321890 ATATATAATATATAGTTTTGAAAACATTTTG--AA-
1 ATATATAATATATAGTTTTGAAAACATTTTGAAAAT
* * * *
321923 A-ACAT-ATA-GT--TTTTGAAAACGGTTTTTGGAAAT
1 ATATATAATATATAGTTTTGAAAAC--ATTTTGAAAAT
321956 ATATAT--TATATAGTTTTTGAAAAACATTTTGAAAAT
1 ATATATAATATATAG-TTTTG-AAAACATTTTGAAAAT
*
321992 ATATATAATATATAGTTTTTAAAAAACATTTTGAAAAT
1 ATATATAATATATAG-TTTT-GAAAACATTTTGAAAAT
* * *
322030 ATATATAATATATAATTTT-AAAATATTTTTGAATAT
1 ATATATAATATATAGTTTTGAAAACA-TTTTGAAAAT
*
322066 ATATAT-ATATTATAGTTTTTAAAACATTGTTGAAAAT
1 ATATATAATA-TATAGTTTTGAAAACATT-TTGAAAAT
* *
322103 ATATAT--TATATAATTTTTAAAGACATTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAA-ACA-TTTTGAAAAT
322139 ATATAT--TATATAGTTTT
1 ATATATAATATATAGTTTT
322156 TAATTTTTTT
Statistics
Matches: 197, Mismatches: 16, Indels: 37
0.79 0.06 0.15
Matches are distributed among these distances:
28 10 0.05
30 6 0.03
31 3 0.02
32 5 0.03
33 4 0.02
34 4 0.02
35 20 0.10
36 69 0.35
37 29 0.15
38 47 0.24
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (36 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAAAT
Found at i:321956 original size:64 final size:67
Alignment explanation
Indices: 321861--321996 Score: 197
Period size: 64 Copynumber: 2.1 Consensus size: 67
321851 AAAACATATA
321861 ATATACTTTTTAAAAATCGGTTTTCGAAAATATATAATATATAG-TTTTG-AAAACATTTTGAAA
1 ATATACTTTTTAAAAATCGGTTTTCGAAAATATATAATATATAGTTTTTGAAAAACATTTTGAAA
321924 AC
66 AC
* * * * *
321926 ATATAGTTTTTGAAAA-CGGTTTTTGGAAATATATATTATATAGTTTTTGAAAAACATTTTGAAA
1 ATATACTTTTTAAAAATCGGTTTTCGAAAATATATAATATATAGTTTTTGAAAAACATTTTGAAA
*
321990 AT
66 AC
321992 ATATA
1 ATATA
321997 TAATATATAG
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 24 0.38
65 19 0.30
66 20 0.32
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (67 bp):
ATATACTTTTTAAAAATCGGTTTTCGAAAATATATAATATATAGTTTTTGAAAAACATTTTGAAA
AC
Found at i:322156 original size:36 final size:36
Alignment explanation
Indices: 321926--322158 Score: 271
Period size: 36 Copynumber: 6.4 Consensus size: 36
321916 TTTTGAAAAC
* *
321926 ATATAGTTTTTGAAAACGGTTTTTGGAAATATATAT-T
1 ATATAGTTTTT-AAAAC-ATTTTTGAAAATATATATAT
321963 ATATAGTTTTTGAAAAACA-TTTTGAAAATATATATAAT
1 ATATAGTTTTT--AAAACATTTTTGAAAATATATAT-AT
322001 ATATAGTTTTTAAAAAACA-TTTTGAAAATATATATAAT
1 ATATAGTTTTT--AAAACATTTTTGAAAATATATAT-AT
* * *
322039 ATATA-ATTTTAAAATATTTTTGAATATATATATAT
1 ATATAGTTTTTAAAACATTTTTGAAAATATATATAT
*
322074 ATTATAGTTTTTAAAACATTGTTGAAAATATATAT-T
1 A-TATAGTTTTTAAAACATTTTTGAAAATATATATAT
*
322110 ATATAATTTTTAAAGACATTTTTGAAAATATATAT-T
1 ATATAGTTTTTAAA-ACATTTTTGAAAATATATATAT
322146 ATATAGTTTTTAA
1 ATATAGTTTTTAA
322159 TTTTTTTATA
Statistics
Matches: 175, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
35 20 0.11
36 68 0.39
37 39 0.22
38 48 0.27
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (36 bp):
ATATAGTTTTTAAAACATTTTTGAAAATATATATAT
Found at i:323434 original size:20 final size:18
Alignment explanation
Indices: 323397--323440 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
323387 TTTTCTTAAC
323397 ATTTTTATTTATTTATTT
1 ATTTTTATTTATTTATTT
*
323415 ATTTTTAGTTTTTCTTATTT
1 ATTTTTA-TTTAT-TTATTT
323435 ATTTTT
1 ATTTTT
323441 CTTATTCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 4 0.17
20 12 0.52
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
ATTTTTATTTATTTATTT
Found at i:323441 original size:13 final size:14
Alignment explanation
Indices: 323418--323446 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
323408 TTTATTTATT
323418 TTTAGTTTTTCTTA
1 TTTAGTTTTTCTTA
323432 TTTA-TTTTTCTTA
1 TTTAGTTTTTCTTA
323445 TT
1 TT
323447 CTTCTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTAGTTTTTCTTA
Found at i:323454 original size:28 final size:28
Alignment explanation
Indices: 323401--323473 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 28
323391 CTTAACATTT
* *
323401 TTATTTATTTATTTATTTTTAGTTTTTC
1 TTATTTATTTATTTATTCTTACTTTTTC
*
323429 TTATTTATTTTTCTTATTCTT-CTTTTTAC
1 TTATTTATTTAT-TTATTCTTACTTTTT-C
*
323458 TAAGTTTTATTTATTT
1 TTA--TTTATTTATTT
323474 TTACTTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
28 16 0.44
29 10 0.28
30 2 0.06
31 8 0.22
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.73
Consensus pattern (28 bp):
TTATTTATTTATTTATTCTTACTTTTTC
Found at i:330723 original size:26 final size:26
Alignment explanation
Indices: 330694--330746 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
330684 TTTTCAGATC
330694 TAGGGTATTTCAATCATTTCATTCCG
1 TAGGGTATTTCAATCATTTCATTCCG
330720 TAGGGTATTTCAATCATTTCATTCCG
1 TAGGGTATTTCAATCATTTCATTCCG
330746 T
1 T
330747 CTGGTCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (26 bp):
TAGGGTATTTCAATCATTTCATTCCG
Found at i:340241 original size:24 final size:24
Alignment explanation
Indices: 340138--340243 Score: 90
Period size: 24 Copynumber: 4.4 Consensus size: 24
340128 CGGAGATATT
*
340138 AGAAATCA-AAGCAAAATTCAGATC
1 AGAAATCAGAA-CAGAATTCAGATC
** *
340162 AGTTATCAGAACAGAATCCAGATC
1 AGAAATCAGAACAGAATTCAGATC
* * *
340186 AGAAATCAGAACA-AAATCTAGGTT
1 AGAAATCAGAACAGAATTC-AGATC
** *
340210 AGGTATCAGAACAGAATTCAAATC
1 AGAAATCAGAACAGAATTCAGATC
340234 AGAAATCAGA
1 AGAAATCAGA
340244 TAAAACATTC
Statistics
Matches: 61, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
23 3 0.05
24 52 0.85
25 6 0.10
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (24 bp):
AGAAATCAGAACAGAATTCAGATC
Found at i:341341 original size:26 final size:26
Alignment explanation
Indices: 341310--341384 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
341300 TGTTTTTTCC
*
341310 ATTCATTTCAAAGCTTGAG-GATATA-T
1 ATTCATTCCAAAGCTTG-GTGATA-ACT
*
341336 ATTCATTCCTAAGCTTGGTGATAACT
1 ATTCATTCCAAAGCTTGGTGATAACT
***
341362 ATTCATTCTTGAGCTTGGTGATA
1 ATTCATTCCAAAGCTTGGTGATA
341385 TTCTTGAGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.05
26 41 0.95
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (26 bp):
ATTCATTCCAAAGCTTGGTGATAACT
Found at i:341422 original size:26 final size:28
Alignment explanation
Indices: 341383--341442 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
341373 AGCTTGGTGA
341383 TATTCTTGAGTCATTTT-CAT-TATAGGGG
1 TATT-TTGAGTCATTTTACATATATA-GGG
*
341411 TATTTTG-GTCATTTTACATATCTAGGG
1 TATTTTGAGTCATTTTACATATATAGGG
341438 TATTT
1 TATTT
341443 CAATCCTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 8 0.28
27 14 0.48
28 7 0.24
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.50
Consensus pattern (28 bp):
TATTTTGAGTCATTTTACATATATAGGG
Found at i:342718 original size:22 final size:22
Alignment explanation
Indices: 342693--342763 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
342683 CAATGCCTGT
342693 TCAACGTCGGTCAAAGGTCCGG
1 TCAACGTCGGTCAAAGGTCCGG
* * *
342715 TCAACGGTCAGTC-AATG-CCTAG
1 TCAAC-GTCGGTCAAAGGTCC-GG
*
342737 TCAACGTTGGTCAAAGGT-CGG
1 TCAACGTCGGTCAAAGGTCCGG
342758 TCAACG
1 TCAACG
342764 GTCAATAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
21 14 0.37
22 18 0.47
23 6 0.16
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.21
Consensus pattern (22 bp):
TCAACGTCGGTCAAAGGTCCGG
Found at i:342734 original size:44 final size:43
Alignment explanation
Indices: 342671--342767 Score: 160
Period size: 44 Copynumber: 2.2 Consensus size: 43
342661 CCGAAAAAAA
342671 TCAACGGTCAGTCAATGCCT-GTTCAACGTCGGTCAAAGGTCCGG
1 TCAACGGTCAGTCAATGCCTAG-TCAACGTCGGTCAAAGGT-CGG
*
342715 TCAACGGTCAGTCAATGCCTAGTCAACGTTGGTCAAAGGTCGG
1 TCAACGGTCAGTCAATGCCTAGTCAACGTCGGTCAAAGGTCGG
342758 TCAACGGTCA
1 TCAACGGTCA
342768 ATAGTAAACG
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
43 13 0.25
44 37 0.73
45 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.23
Consensus pattern (43 bp):
TCAACGGTCAGTCAATGCCTAGTCAACGTCGGTCAAAGGTCGG
Found at i:351422 original size:21 final size:22
Alignment explanation
Indices: 351379--351440 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
351369 TTTTGGTGCA
*
351379 GAGGGAATCGA-TCCCCCACTT
1 GAGGGAACCGATTCCCCCACTT
*
351400 GAGGGAACCGATTCCCCC-TTT
1 GAGGGAACCGATTCCCCCACTT
351421 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
351441 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.36
22 7 0.19
23 16 0.44
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.18
Consensus pattern (22 bp):
GAGGGAACCGATTCCCCCACTT
Found at i:354052 original size:22 final size:23
Alignment explanation
Indices: 354027--354070 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
354017 AATTAAGTTT
354027 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
354049 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
354071 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:360951 original size:3 final size:3
Alignment explanation
Indices: 360945--361007 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
360935 GGAAGAAGAA
* * * * *
360945 GAT GAT GAT GAT GAT GAT GAA GAA GAA GAT GAT GAT GAT GAT GAA GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
360993 GAA GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT
361008 CATAAACTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (3 bp):
GAT
Found at i:360974 original size:27 final size:27
Alignment explanation
Indices: 360936--361007 Score: 135
Period size: 27 Copynumber: 2.7 Consensus size: 27
360926 TAAACACCAG
*
360936 GAAGAAGAAGATGATGATGATGATGAT
1 GAAGAAGAAGATGATGATGATGATGAA
360963 GAAGAAGAAGATGATGATGATGATGAA
1 GAAGAAGAAGATGATGATGATGATGAA
360990 GAAGAAGAAGATGATGAT
1 GAAGAAGAAGATGATGAT
361008 CATAAACTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.19
Consensus pattern (27 bp):
GAAGAAGAAGATGATGATGATGATGAA
Found at i:360975 original size:24 final size:24
Alignment explanation
Indices: 360939--361007 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
360929 ACACCAGGAA
*
360939 GAAGAAGATGATGATGATGATGAT
1 GAAGAAGAAGATGATGATGATGAT
360963 GAAGAAGAAGATGATGATGATGAT
1 GAAGAAGAAGATGATGATGATGAT
*
360987 GAAGAAGAAGAAGATGATGAT
1 GAAGAAGAAGATGATGATGAT
361008 CATAAACTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.20
Consensus pattern (24 bp):
GAAGAAGAAGATGATGATGATGAT
Found at i:362676 original size:17 final size:18
Alignment explanation
Indices: 362650--362683 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
362640 CCAGTGCTCA
362650 GAATTAATTA-TAAAATG
1 GAATTAATTATTAAAATG
*
362667 GAATTTATTATTAAAAT
1 GAATTAATTATTAAAAT
362684 ATCACGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
GAATTAATTATTAAAATG
Found at i:364885 original size:29 final size:29
Alignment explanation
Indices: 364852--365291 Score: 229
Period size: 29 Copynumber: 15.2 Consensus size: 29
364842 TGTAAAATAT
*
364852 ATTAATTATTAGAATATCCAGCGATCAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * *** *
364881 ATTAATGATTAGGATATCCAGTTTTTAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * *
364910 ATTAATTAGTAAAATATCCA-AGTTTAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* *
364938 ATTAATCATTAAAATATCCAGAGATCAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
** ** * * *
364967 ATTAACGATTAGTCTATCCAGTGTTTAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * * * *
364996 AATAATTAGTAAAATATCC-TAGTTTAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* *
365024 ATTAATTATTAGCATATCCAAAGATCAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * *** *
365053 ATTAATGATTAGGATATCCAGTTTTTAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * ** *
365082 AATAATTAGTAAAATATCCACATTTCAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* *
365111 ATTACTTATTAGAATATCCAGAGATCATA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * *** *
365140 ATTAATGATTAGGATATCCAGTTTTTAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * ** *
365169 AATAATTAGTAAAATATCCACATTTCAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * *
365198 ATTAATTATTAGAATATCCAAAAATCAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * ** *
365227 ATCAATTATTAGGATACCCTCG-TTTTAGA
1 ATTAATTATTAGAATATCC-AGAGATCAGA
*
365256 ATTAATTATTAGAATATCCAGAGATAAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
365285 ATTAATT
1 ATTAATT
365292 GGATATCAGT
Statistics
Matches: 300, Mismatches: 107, Indels: 8
0.72 0.26 0.02
Matches are distributed among these distances:
28 45 0.15
29 255 0.85
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (29 bp):
ATTAATTATTAGAATATCCAGAGATCAGA
Found at i:364965 original size:86 final size:87
Alignment explanation
Indices: 364852--365275 Score: 579
Period size: 87 Copynumber: 4.9 Consensus size: 87
364842 TGTAAAATAT
* *
364852 ATTAATTATTAGAATATCCAGCGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAATTAATT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
364917 AGTAAAATATCCA-AGTTT-AAA
66 AGTAAAATATCCACA-TTTCAAA
* * * ** *
364938 ATTAATCATTAAAATATCCAGAGATCAGAATTAACGATTAGTCTATCCAGTGTTTAGAAATAATT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
*
365003 AGTAAAATATCCTA-GTTT-AAA
66 AGTAAAATATCC-ACATTTCAAA
* *
365024 ATTAATTATTAGCATATCCAAAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
365089 AGTAAAATATCCACATTTCAAA
66 AGTAAAATATCCACATTTCAAA
* *
365111 ATTACTTATTAGAATATCCAGAGATCATAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
365176 AGTAAAATATCCACATTTCAAA
66 AGTAAAATATCCACATTTCAAA
* * * * * * * *
365198 ATTAATTATTAGAATATCCAAAAATCAAAATCAATTATTAGGATACCCTCG-TTTTAGAATTAAT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCC-AGTTTTTAGAAATAAT
* *
365262 TATTAGAATATCCA
65 TAGTAAAATATCCA
365276 GAGATAAGAA
Statistics
Matches: 301, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
85 1 0.00
86 147 0.49
87 152 0.50
88 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (87 bp):
ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
AGTAAAATATCCACATTTCAAA
Found at i:366249 original size:70 final size:71
Alignment explanation
Indices: 366100--366259 Score: 218
Period size: 70 Copynumber: 2.3 Consensus size: 71
366090 TGGGGTAAAG
* * *
366100 ATCGAAATTTACGTGAATCGGAACTTAAAGCCCTTAGTCTACCTCGGATCCTCGAGAGGTCGAGG
1 ATCGAAATTTACGTGCATCAGAACTTAAAGCCCTTAGTCTACCTCAGATCCTCGAGAGGTCGAGG
366165 TGAGGT
66 TGAGGT
* * * *
366171 AT-GGAATTTATGTGCATCAGAACTTAAAGCCCTTAGTCTACCTCATATCCTTGAGAGGTC-AGG
1 ATCGAAATTTACGTGCATCAGAACTTAAAGCCCTTAGTCTACCTCAGATCCTCGAGAGGTCGA-G
366234 GTGAGGT
65 GTGAGGT
*
366241 -TCGAAATTTACATGCATCA
1 ATCGAAATTTACGTGCATCA
366260 AAAACTCACA
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
69 2 0.03
70 73 0.95
71 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (71 bp):
ATCGAAATTTACGTGCATCAGAACTTAAAGCCCTTAGTCTACCTCAGATCCTCGAGAGGTCGAGG
TGAGGT
Found at i:366692 original size:20 final size:19
Alignment explanation
Indices: 366663--366718 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
366653 TTTTGAAAAA
366663 TACT-TGGGTATCGATACTC
1 TACTCTGGGTATCGATAC-C
366682 TACTCTGGGTATCGATACC
1 TACTCTGGGTATCGATACC
* *
366701 CAC-CTGAGTATCGATACC
1 TACTCTGGGTATCGATACC
366719 AGTTTTCGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 14 0.41
19 7 0.21
20 13 0.38
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (19 bp):
TACTCTGGGTATCGATACC
Found at i:382624 original size:31 final size:30
Alignment explanation
Indices: 382588--382685 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 30
382578 CATACCTAAT
*
382588 ATTTACTTTTTGTTTCATTTTAGTACCCGGA
1 ATTTACTTTTTGTTTCATTTTAGTACCC-AA
* * * *
382619 GTTTACTTTTTATTTAATTTTATTACCCAA
1 ATTTACTTTTTGTTTCATTTTAGTACCCAA
*
382649 ATATTAACTTTTTTGTTTCATTTTAGTACCTAA
1 AT-TT-AC-TTTTTGTTTCATTTTAGTACCCAA
382682 ATTT
1 ATTT
382686 TTAACAGAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
30 2 0.04
31 26 0.48
32 4 0.07
33 22 0.41
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.55
Consensus pattern (30 bp):
ATTTACTTTTTGTTTCATTTTAGTACCCAA
Found at i:382774 original size:31 final size:31
Alignment explanation
Indices: 382739--382825 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 31
382729 TATGGTTTTA
382739 AAAAGCTGAAAGTTT-AGAAACTAAACAGAAT
1 AAAAGCTGAAAGTTTAAG-AACTAAACAGAAT
** * *
382770 AAAAG-TGATTGTTTAAGTACTAAACATAAT
1 AAAAGCTGAAAGTTTAAGAACTAAACAGAAT
** *
382800 AAAA-CTGATTGTTTAAGTACTAAACA
1 AAAAGCTGAAAGTTTAAGAACTAAACA
382826 TGTAATTTAC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
30 43 0.86
31 7 0.14
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (31 bp):
AAAAGCTGAAAGTTTAAGAACTAAACAGAAT
Found at i:382826 original size:30 final size:30
Alignment explanation
Indices: 382758--382826 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
382748 AAGTTTAGAA
* *
382758 ACTAAACAGAATAAAAGTGATTGTTTAAGT
1 ACTAAACATAATAAAACTGATTGTTTAAGT
382788 ACTAAACATAATAAAACTGATTGTTTAAGT
1 ACTAAACATAATAAAACTGATTGTTTAAGT
382818 ACTAAACAT
1 ACTAAACAT
382827 GTAATTTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (30 bp):
ACTAAACATAATAAAACTGATTGTTTAAGT
Found at i:383567 original size:17 final size:17
Alignment explanation
Indices: 383545--383587 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
383535 TATTTAAATA
383545 TTTTTATTTAATCTAAT
1 TTTTTATTTAATCTAAT
*
383562 TTTTTATTT-ATTTAAT
1 TTTTTATTTAATCTAAT
383578 TTTTTATTTA
1 TTTTTATTTA
383588 CCTCGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTTAATCTAAT
Found at i:392829 original size:16 final size:16
Alignment explanation
Indices: 392784--392830 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
392774 ACATTTTTAC
*
392784 AAAAAAATAAAATAATT
1 AAAAATATAAAAT-ATT
*
392801 AAATATACT-AAATATT
1 AAAAATA-TAAAATATT
392817 AAAAATATAAAATA
1 AAAAATATAAAATA
392831 ATTTTAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 14 0.56
17 9 0.36
18 1 0.04
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATATAAAATATT
Found at i:393301 original size:35 final size:35
Alignment explanation
Indices: 393262--393329 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
393252 TGTATTACCT
393262 TGTTTGGTTTGCTTAGCAAGAATGCAAGATTACAG
1 TGTTTGGTTTGCTTAGCAAGAATGCAAGATTACAG
* * *
393297 TGTTTGGTTTGTTTAGCAGGAATGTAAGATTAC
1 TGTTTGGTTTGCTTAGCAAGAATGCAAGATTAC
393330 TTAGATGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (35 bp):
TGTTTGGTTTGCTTAGCAAGAATGCAAGATTACAG
Found at i:393615 original size:16 final size:17
Alignment explanation
Indices: 393596--393632 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
393586 TAAAATATTA
393596 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
393612 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
393629 TTTT
1 TTTT
393633 TTCATCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:395413 original size:20 final size:20
Alignment explanation
Indices: 395388--395425 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
395378 TTTCCTATAA
395388 AGAAAAATATTAAATTTAAT
1 AGAAAAATATTAAATTTAAT
*
395408 AGAAAAATATTTAATTTA
1 AGAAAAATATTAAATTTA
395426 TTTTTATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
AGAAAAATATTAAATTTAAT
Found at i:404186 original size:26 final size:26
Alignment explanation
Indices: 404149--404207 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 26
404139 GGACAAATTT
*
404149 AATACTTGGTTCAAAATGTTTTCTATA
1 AATA-TTGGTTCAAAACGTTTTCTATA
404176 AATATTGGTTCAAAACGTTTTCTATA
1 AATATTGGTTCAAAACGTTTTCTATA
404202 AATATT
1 AATATT
404208 TGGGTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (26 bp):
AATATTGGTTCAAAACGTTTTCTATA
Found at i:405139 original size:28 final size:28
Alignment explanation
Indices: 405108--405162 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
405098 ATGATGATTT
405108 AATA-AAATAATAATAATTTAATT-ATAAC
1 AATAGAAA-AATAATAA-TTAATTGATAAC
*
405136 AATAGAAAATTAATAATTAATTGATAA
1 AATAGAAAAATAATAATTAATTGATAA
405163 ATAATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 15 0.62
29 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (28 bp):
AATAGAAAAATAATAATTAATTGATAAC
Found at i:407434 original size:49 final size:49
Alignment explanation
Indices: 407381--407531 Score: 109
Period size: 49 Copynumber: 3.1 Consensus size: 49
407371 AACCGATCTA
407381 ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
1 ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
* * * * * * ** * *
407430 ATCAGGA-A---ACAG--GGTCCTATTGGAGAGAATCGATTATTAACCGATCT-A
1 ATCA-GACATTTAAAGTTGATACT-TT--AGA-ATTCCACTATTATTC-ATGTGC
407478 ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
1 ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
407527 ATCAG
1 ATCAG
407532 GAAAGCGTTC
Statistics
Matches: 69, Mismatches: 20, Indels: 26
0.60 0.17 0.23
Matches are distributed among these distances:
44 4 0.06
45 2 0.03
46 3 0.04
47 5 0.07
48 18 0.26
49 23 0.33
50 5 0.07
51 3 0.04
52 2 0.03
53 4 0.06
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (49 bp):
ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
Found at i:407506 original size:97 final size:97
Alignment explanation
Indices: 407340--407535 Score: 392
Period size: 97 Copynumber: 2.0 Consensus size: 97
407330 GGATTCTAAG
407340 AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
1 AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
407405 TAGAATTCCACTATTATTCATGTGCATCAGGA
66 TAGAATTCCACTATTATTCATGTGCATCAGGA
407437 AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
1 AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
407502 TAGAATTCCACTATTATTCATGTGCATCAGGA
66 TAGAATTCCACTATTATTCATGTGCATCAGGA
407534 AA
1 AA
407536 GCGTTCAGGA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (97 bp):
AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
TAGAATTCCACTATTATTCATGTGCATCAGGA
Found at i:419069 original size:29 final size:29
Alignment explanation
Indices: 419012--419080 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
419002 ATTTAAGTTA
419012 CTCAACTTTTAAAACTTGCAATACAGTCC
1 CTCAACTTTTAAAACTTGCAATACAGTCC
*
419041 CTCAACTTTTAAAACTTGCAATATAGTCC
1 CTCAACTTTTAAAACTTGCAATACAGTCC
* *
419070 CCCAACATTTA
1 CTCAACTTTTA
419081 GTTTGTTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.32
Consensus pattern (29 bp):
CTCAACTTTTAAAACTTGCAATACAGTCC
Found at i:419160 original size:31 final size:31
Alignment explanation
Indices: 419117--419193 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
419107 AGTTACGTCG
* *
419117 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGATCATATTGCAAACAGACTAAATGTTGA
*
419148 GGGATCATATTGCAAACAGACTAAATGTTGG
1 GGGATCATATTGCAAACAGACTAAATGTTGA
*
419179 GGGATTATATTGCAA
1 GGGATCATATTGCAA
419194 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (31 bp):
GGGATCATATTGCAAACAGACTAAATGTTGA
Found at i:429295 original size:18 final size:18
Alignment explanation
Indices: 429272--429318 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
429262 CGTAGGACCA
429272 CGTAGAA-CACATATGTCC
1 CGTAGAACCAC-TATGTCC
429290 CGTAGAACCACTATGTCC
1 CGTAGAACCACTATGTCC
*
429308 CGTAGGACCAC
1 CGTAGAACCAC
429319 GTAGAACCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (18 bp):
CGTAGAACCACTATGTCC
Found at i:438894 original size:10 final size:10
Alignment explanation
Indices: 438858--438886 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
438848 TCCTTTACCA
438858 TTTATTTATT
1 TTTATTTATT
438868 TTTATTTATT
1 TTTATTTATT
438878 TTTATTTAT
1 TTTATTTAT
438887 CTCTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:449217 original size:105 final size:105
Alignment explanation
Indices: 449035--449790 Score: 1386
Period size: 105 Copynumber: 7.2 Consensus size: 105
449025 AGGTTTTACC
449035 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
449100 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
449140 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
449205 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTTAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
449245 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
449310 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
449350 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
449415 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
449455 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
449520 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
**
449560 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
449625 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
449665 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
449730 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
*
449771 CGGAGCCAATTTCAACTTCA
1 CAGAGCCAATTTCAACTTCA
449791 TAGCGAAACA
Statistics
Matches: 629, Mismatches: 21, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
105 600 0.95
106 29 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:451753 original size:16 final size:15
Alignment explanation
Indices: 451716--451744 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
451706 TTCATTTACT
451716 TATTTTTTTTTTGTC
1 TATTTTTTTTTTGTC
451731 TATTTTTTTTTTGT
1 TATTTTTTTTTTGT
451745 TCCTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (15 bp):
TATTTTTTTTTTGTC
Found at i:455056 original size:26 final size:27
Alignment explanation
Indices: 454999--455056 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
454989 TATGTAATTT
454999 ATTTTATTTTTCTATAAAATTCTTTAA
1 ATTTTATTTTTCTATAAAATTCTTTAA
*
455026 A-TTTA-TTTTCTCTAAAATT-TTATAA
1 ATTTTATTTTTCTATAAAATTCTT-TAA
455051 ATTTTA
1 ATTTTA
455057 AATTAAGCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.07
25 17 0.61
26 8 0.29
27 1 0.04
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTTTATTTTTCTATAAAATTCTTTAA
Found at i:456974 original size:2 final size:2
Alignment explanation
Indices: 456967--457016 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
456957 ACTGATTTTA
456967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
457009 AT AT AT AT
1 AT AT AT AT
457017 TCTTAATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:464717 original size:167 final size:167
Alignment explanation
Indices: 464419--464751 Score: 567
Period size: 167 Copynumber: 2.0 Consensus size: 167
464409 GTTTATCTTG
* * *
464419 GACCCGAAACTTGACTTAAATTTGAATTAAATTTGATAATGTAATAATCGATCCCGAGTTGCATC
1 GACCCGAAACTTGACCTAAATCTGAATTAAATTTAATAATGTAATAATCGATCCCGAGTTGCATC
464484 CACCTAATGCGAAACTCAACCCGAGATTAATCTAGTAAATAATTAATATAACCCAACTTAAAGCG
66 CACCTAATGCGAAACTCAACCCGAGATTAATCTAGTAAATAATTAATATAACCCAACTTAAAGCG
* * * *
464549 ATCCGATATCTGATTTTAGTGAACTTATAATTGACGA
131 ATACGAAATCTAATTTTAGCGAACTTATAATTGACGA
* *
464586 GACCTGAAATTTGACCTAAATCTGAATTAAATTTAATAATGTAATAATCGATCCCGAGTTGCATC
1 GACCCGAAACTTGACCTAAATCTGAATTAAATTTAATAATGTAATAATCGATCCCGAGTTGCATC
*
464651 CACCTAATGCGAAACTCAACCCGAGATTAATCTAGTAAATAATTAATATAACCCAACTTGAAGCG
66 CACCTAATGCGAAACTCAACCCGAGATTAATCTAGTAAATAATTAATATAACCCAACTTAAAGCG
*
464716 ATATGAAATCTAATTTTAGCGAACTTATAATTGACG
131 ATACGAAATCTAATTTTAGCGAACTTATAATTGACG
464752 CAACCTATTA
Statistics
Matches: 155, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
167 155 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (167 bp):
GACCCGAAACTTGACCTAAATCTGAATTAAATTTAATAATGTAATAATCGATCCCGAGTTGCATC
CACCTAATGCGAAACTCAACCCGAGATTAATCTAGTAAATAATTAATATAACCCAACTTAAAGCG
ATACGAAATCTAATTTTAGCGAACTTATAATTGACGA
Found at i:466140 original size:30 final size:30
Alignment explanation
Indices: 466104--466169 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
466094 ACAGCACCGG
** *
466104 CGGTTCACATCAGTTTTGTCGGTTTTCAGC
1 CGGTTCACATCAGTTTTACCGGTTTTCAGA
*
466134 CGGTTCACATCGGTTTTACCGGTTTTCAGA
1 CGGTTCACATCAGTTTTACCGGTTTTCAGA
466164 CGGTTC
1 CGGTTC
466170 TACTGGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.38
Consensus pattern (30 bp):
CGGTTCACATCAGTTTTACCGGTTTTCAGA
Found at i:466189 original size:20 final size:20
Alignment explanation
Indices: 466144--466181 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
466134 CGGTTCACAT
*
466144 CGGTTTTACCGGTTTTCAGA
1 CGGTTCTACCGGTTTTCAGA
*
466164 CGGTTCTACTGGTTTTCA
1 CGGTTCTACCGGTTTTCA
466182 ACCGGTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.42
Consensus pattern (20 bp):
CGGTTCTACCGGTTTTCAGA
Found at i:467077 original size:13 final size:15
Alignment explanation
Indices: 467059--467091 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
467049 AATTTATTTA
467059 AATTTCA-GTTTGT-
1 AATTTCATGTTTGTC
467072 AATTTCATGTTTGTC
1 AATTTCATGTTTGTC
467087 AATTT
1 AATTT
467092 AATCCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (15 bp):
AATTTCATGTTTGTC
Found at i:467194 original size:28 final size:28
Alignment explanation
Indices: 467152--467222 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
467142 TTTTGTGATT
* *
467152 TCTCAAAATCCTATAAA-TAATATCATAA
1 TCTCCAAACCCTATAAATTAA-ATCATAA
* *
467180 TCTCCAAACCTTATAAATTAAATCGTAA
1 TCTCCAAACCCTATAAATTAAATCATAA
*
467208 TCTTCAAACCCTATA
1 TCTCCAAACCCTATA
467223 CACTTTTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 33 0.92
29 3 0.08
ACGTcount: A:0.44, C:0.23, G:0.01, T:0.32
Consensus pattern (28 bp):
TCTCCAAACCCTATAAATTAAATCATAA
Found at i:468989 original size:13 final size:13
Alignment explanation
Indices: 468958--468991 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
468948 AACGTTCTAG
*
468958 TAATTTTAAAAAT
1 TAATTTTAAAAAA
*
468971 TTATTTTAAAAAA
1 TAATTTTAAAAAA
468984 TAATTTTA
1 TAATTTTA
468992 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTTTAAAAAA
Done.