Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 29 of 121
Found at i:5039504 original size:4 final size:4
Alignment explanation
Indices: 5039495--5039521 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5039485 TAAACACCAT
5039495 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
5039522 CTTTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:5041991 original size:14 final size:16
Alignment explanation
Indices: 5041972--5042007 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5041962 GAAGCTTTGC
5041972 AAAAACAA-A-AAAAA
1 AAAAACAAGATAAAAA
5041986 AAAAACAAGATAAAAA
1 AAAAACAAGATAAAAA
5042002 AAAAAC
1 AAAAAC
5042008 TCATTGCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 11 0.55
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAACAAGATAAAAA
Found at i:5042079 original size:21 final size:19
Alignment explanation
Indices: 5042037--5042079 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5042027 AAAACTTTCT
* *
5042037 ATCAAAAAAAAGAAAAAGA
1 ATCAAAAAAAAAAAAAACA
5042056 ATCAAACAAAAAAAAAACACA
1 ATCAAA-AAAAAAAAAA-ACA
5042077 ATC
1 ATC
5042080 CCTAGAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 9 0.45
21 5 0.25
ACGTcount: A:0.74, C:0.14, G:0.05, T:0.07
Consensus pattern (19 bp):
ATCAAAAAAAAAAAAAACA
Found at i:5043030 original size:3 final size:3
Alignment explanation
Indices: 5043024--5043053 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5043014 TTTTTTTGTT
5043024 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5043054 TAAATAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5044175 original size:130 final size:129
Alignment explanation
Indices: 5043959--5044211 Score: 418
Period size: 130 Copynumber: 1.9 Consensus size: 129
5043949 TAAATTAATT
*
5043959 GGAGTGGAAGTTTACTATAATTTGACTAAAGTGGAAAGTACAAGGTAGGATTCCAAGGTTTGGTT
1 GGAGTGGAAGTTTAATATAATTTGACTAAAGTGGAAAGTACAAGGTAGGATTCCAAGGTTTGGTT
5044024 GGTCTATTAAATACATATATTAATGATTTAATTAATAACAATCGGCAATTAATAAATTGTTATAA
66 GGTCTATTAAATA-ATATATTAATGATTTAATTAATAACAATCGGCAATTAATAAATTGTTATAA
* *
5044089 GGAGTGGAAGTTTAATATAATTTGACTAAAGTGGACAAAGTGCAAGGTGGGATTCCAAGGTTTGG
1 GGAGTGGAAGTTTAATATAATTTGACTAAAGTGG--AAAGTACAAGGTAGGATTCCAAGGTTTGG
* * *
5044154 TTGGTCTATTAAAT-ATATATTAATTATTTAATTAATAATAATTGGCAATTAATAAATT
64 TTGGTCTATTAAATAATATATTAATGATTTAATTAATAACAATCGGCAATTAATAAATT
5044212 ATAATTTATT
Statistics
Matches: 115, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
130 74 0.64
132 41 0.36
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (129 bp):
GGAGTGGAAGTTTAATATAATTTGACTAAAGTGGAAAGTACAAGGTAGGATTCCAAGGTTTGGTT
GGTCTATTAAATAATATATTAATGATTTAATTAATAACAATCGGCAATTAATAAATTGTTATAA
Found at i:5046226 original size:29 final size:29
Alignment explanation
Indices: 5046194--5046250 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
5046184 ATAAAATTAA
*
5046194 AATTTATTATATAATAAATTAATAAATAC
1 AATTGATTATATAATAAATTAATAAATAC
5046223 AATTGATTATATAATAAATTAATAAATA
1 AATTGATTATATAATAAATTAATAAATA
5046251 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
AATTGATTATATAATAAATTAATAAATAC
Found at i:5046738 original size:26 final size:26
Alignment explanation
Indices: 5046687--5046747 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
5046677 TATTAATATA
5046687 ATTATT-AAAATATTAAAAATTATTT
1 ATTATTAAAAATATTAAAAATTATTT
*
5046712 ATTATTAAAACATATT-GAAATTATTT
1 ATTATTAAAA-ATATTAAAAATTATTT
5046738 ATTATTAAAA
1 ATTATTAAAA
5046748 TTAATAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 6 0.18
26 22 0.67
27 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATTAAAAATATTAAAAATTATTT
Found at i:5046867 original size:15 final size:15
Alignment explanation
Indices: 5046866--5046986 Score: 106
Period size: 15 Copynumber: 8.0 Consensus size: 15
5046856 TTTATTAATA
5046866 TATTAATATATTATT
1 TATTAATATATTATT
5046881 TATTAATATATTATAT
1 TATTAATATATTAT-T
* *
5046897 TAATAGTATATTATT
1 TATTAATATATTATT
5046912 TATTAATATATTA-T
1 TATTAATATATTATT
5046926 TA-TAATAT-TTATT
1 TATTAATATATTATT
* * * *
5046939 AATTAAATTAAAAATACT
1 TATT-AA-T-ATATTATT
5046957 TATT-ATAATATTATT
1 TATTAAT-ATATTATT
*
5046972 TATTAATATAATATT
1 TATTAATATATTATT
5046987 ATTTATAAGT
Statistics
Matches: 85, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
12 3 0.04
13 8 0.09
14 4 0.05
15 46 0.54
16 17 0.20
17 1 0.01
18 6 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (15 bp):
TATTAATATATTATT
Found at i:5046875 original size:23 final size:23
Alignment explanation
Indices: 5046849--5046981 Score: 100
Period size: 23 Copynumber: 5.8 Consensus size: 23
5046839 TATTATTCTT
5046849 TATATTATTTATTAATATATTAA
1 TATATTATTTATTAATATATTAA
5046872 TATATTATTTATTAATATATT-A
1 TATATTATTTATTAATATATTAA
* * *
5046894 TATTAATAGTATATT-ATTTATTAA
1 TA-TATTA-TTTATTAATATATTAA
*
5046918 TATATTA-TTA-TAATAT-TTAT
1 TATATTATTTATTAATATATTAA
* **
5046938 TA-ATTAAATTAAAAATACTTATT-A
1 TATATT-ATTTATTAATA--TATTAA
5046962 TAATATTATTTATTAATATA
1 T-ATATTATTTATTAATATA
5046982 ATATTATTTA
Statistics
Matches: 86, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
19 3 0.03
20 7 0.08
21 8 0.09
22 7 0.08
23 37 0.43
24 10 0.12
25 11 0.13
26 3 0.03
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
TATATTATTTATTAATATATTAA
Found at i:5046932 original size:31 final size:29
Alignment explanation
Indices: 5046866--5046943 Score: 61
Period size: 31 Copynumber: 2.6 Consensus size: 29
5046856 TTTATTAATA
*
5046866 TATTAATATATTATTTATTAATATATTATAT
1 TATTAATATATTAATTA-TAATATATTAT-T
* * *
5046897 TAATAGTATATTATTTATTAATATATTA-T
1 TATTAATATATTAATTA-TAATATATTATT
5046926 TA-TAATATTTATTAATTA
1 TATTAATA--TATTAATTA
5046944 AATTAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.10
29 3 0.07
30 8 0.20
31 26 0.63
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
TATTAATATATTAATTATAATATATTATT
Found at i:5047138 original size:22 final size:22
Alignment explanation
Indices: 5047096--5047143 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5047086 AAATAATATC
**
5047096 ATTTTTCATTGATTAAAAAATT
1 ATTTTTCATTGACCAAAAAATT
*
5047118 ATTTTTCATTGACCAACAAATT
1 ATTTTTCATTGACCAAAAAATT
5047140 -TTTT
1 ATTTT
5047144 ACCAAATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTTTCATTGACCAAAAAATT
Found at i:5048931 original size:2 final size:2
Alignment explanation
Indices: 5048924--5048949 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5048914 TTGTCGTAAA
5048924 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
5048950 CGTACTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5049252 original size:3 final size:3
Alignment explanation
Indices: 5049244--5049293 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
5049234 ATGATGTAAC
5049244 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5049292 TA
1 TA
5049294 TTGTCGAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5049591 original size:17 final size:17
Alignment explanation
Indices: 5049571--5049605 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5049561 TAGTAATGTA
*
5049571 ATTATTAAAGTGATTTT
1 ATTATCAAAGTGATTTT
5049588 ATTATCAAAGTGATTTT
1 ATTATCAAAGTGATTTT
5049605 A
1 A
5049606 AAATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (17 bp):
ATTATCAAAGTGATTTT
Found at i:5055100 original size:11 final size:11
Alignment explanation
Indices: 5055068--5055100 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
5055058 TTACCCCAAT
*
5055068 CTTCCACAAGT
1 CTTCCACAAGC
5055079 CTTCCACAAGC
1 CTTCCACAAGC
5055090 CTTCCACAAGC
1 CTTCCACAAGC
5055101 TTTGAGTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.27, C:0.42, G:0.09, T:0.21
Consensus pattern (11 bp):
CTTCCACAAGC
Found at i:5058353 original size:60 final size:59
Alignment explanation
Indices: 5058070--5058489 Score: 523
Period size: 60 Copynumber: 7.0 Consensus size: 59
5058060 TAAAAATAAA
*
5058070 AAATTCCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-TAGAAAAT
* *
5058129 AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAAT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA-TTTTCCT---AG-AAAAT
* *
5058193 AAATTTCCAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTA-AAAAT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-TAGAAAAT
* * *
5058252 AAATTTC--CAAAAAATATTTTTGGGGAAGAGTTGAAAGTATCAATTTTCCTCAG-AAAT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT-AGAAAAT
*
5058309 AAATTTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 AAATTTC-AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAAT
* *
5058369 CAAAATTTC-AAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 --AAATTTCAAAAAAAAATA-TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAAT
* *
5058430 CGAAATTTTC--AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCCTACAAAA
1 --AAA-TTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA-TTTTCCTAGAAAA
5058490 AAAAATCATT
Statistics
Matches: 326, Mismatches: 17, Indels: 34
0.86 0.05 0.09
Matches are distributed among these distances:
56 1 0.00
57 50 0.15
59 57 0.17
60 86 0.26
61 65 0.20
62 13 0.04
63 5 0.02
64 49 0.15
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (59 bp):
AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAAT
Found at i:5058414 original size:121 final size:116
Alignment explanation
Indices: 5058070--5058479 Score: 558
Period size: 121 Copynumber: 3.4 Consensus size: 116
5058060 TAAAAATAAA
*
5058070 AAATTCCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AAATAAATTT
* *
5058135 CCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAAT
65 -CAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAA-TTTTCCT---AG-AAAAT
* *
5058193 AAATTTCCAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAATTT
* *
5058258 C-CAAAAAATATTTTTGGGGAAGAGTTGAAAGTATCAATTTTCCTCAG-AAAT
65 CAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT-AGAAAAT
5058309 AAATTTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAA
1 AAATTTC-AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT--AAA
*
5058374 TTTCAAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
62 TTTCAAAAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAAT
*
5058430 CGAAATTTTC--AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 --AAA-TTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
5058480 TCCTACAAAA
Statistics
Matches: 262, Mismatches: 15, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
116 11 0.04
117 49 0.19
118 2 0.01
119 7 0.03
120 15 0.06
121 109 0.42
122 1 0.00
123 63 0.24
124 5 0.02
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (116 bp):
AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAATTTC
AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAAT
Found at i:5058449 original size:181 final size:180
Alignment explanation
Indices: 5058079--5058479 Score: 621
Period size: 181 Copynumber: 2.2 Consensus size: 180
5058069 AAAATTCCAA
* * *
5058079 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAA
*
5058144 ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAATAAATTTCCAAAAAAAA
66 ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCAAAAAAAA
5058209 TATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC
131 TATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC
* *
5058259 CAAAAAATATTTTTGGGGAAGAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC-AAAAAAA
* **
5058324 AATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAA-AATCA-AAATTT-CAAAAAAA
65 AATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCAAAAAAA
* * *
5058385 ATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTTC
130 ATA-TTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAA-TTTC
5058440 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
5058480 TCCTACAAAA
Statistics
Matches: 202, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
177 11 0.05
178 44 0.22
179 3 0.01
180 58 0.29
181 86 0.43
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (180 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAA
ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCAAAAAAAA
TATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC
Found at i:5063587 original size:42 final size:42
Alignment explanation
Indices: 5063541--5064475 Score: 1354
Period size: 41 Copynumber: 23.0 Consensus size: 42
5063531 GTCTAGGAGT
*
5063541 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
5063583 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
* *
5063623 ATTTACTTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
5063665 ATTCAC-TTTCC-AAGTTCGT--TACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
* *
5063704 ATTTAC-TTTCC-AAGT-TTGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
5063743 ATTTAC-TTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
*
5063783 ATTTA-TTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
5063824 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
5063864 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
5063905 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
5063947 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
5063988 ATTTAC-TTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
5064029 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
5064069 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
5064110 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
5064152 ATTTAC-TTT-C-AAGT--TGTTGCCTCTATTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
5064189 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
5064231 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
*
5064271 ATTTACTTTTTC-AAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
*
5064311 ATTTACTTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
5064352 ATTTAC-TTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
5064394 ATTTACTTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
5064435 ATTTAC-TTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
1 ATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGC
5064476 TTTGGTAAAA
Statistics
Matches: 825, Mismatches: 28, Indels: 80
0.88 0.03 0.09
Matches are distributed among these distances:
37 26 0.03
38 4 0.00
39 91 0.11
40 214 0.26
41 256 0.31
42 231 0.28
43 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (42 bp):
ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:5063700 original size:81 final size:81
Alignment explanation
Indices: 5063541--5064475 Score: 1314
Period size: 81 Copynumber: 11.5 Consensus size: 81
5063531 GTCTAGGAGT
* *
5063541 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
1 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGTTGC
5063606 CTCTGTTTAGAGGAGCA
65 CTCTGTTTAGAGGAGCA
* * * *
5063623 ATTTACTTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTCAC-TTTCCAAGTTCGTTAC
1 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGTTGC
5063687 CTCTGTTTAGAGGAGCA
65 CTCTGTTTAGAGGAGCA
* *
5063704 ATTTACTTTCC-AAGT-TTGTTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAGTTCGTTGC
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCC-AAGTTCGTTGC
5063766 CTCTGTTTAGAGGAGCA
65 CTCTGTTTAGAGGAGCA
* * *
5063783 ATTTATTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCC
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGTTGCC
5063848 TCTGTTTAGAGGAGCA
66 TCTGTTTAGAGGAGCA
5063864 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAG-TCGTGGT
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCC-AAGTTCGT--T
*
5063928 ACCTCTGTTTAGAGGAGCA
63 GCCTCTGTTTAGAGGAGCA
5063947 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAG-TCGTGGT
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCC-AAGTTCGT--T
*
5064010 ACCTCTGTTTAGAGGAGCA
63 GCCTCTGTTTAGAGGAGCA
*
5064029 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAG-TCGTGG
1 ATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCC-AAGTTCGT--
5064090 TGCCTCTGTTTAGAGGAGCA
62 TGCCTCTGTTTAGAGGAGCA
*
5064110 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTAC-TTT-CAAGTT-GTTGC
1 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGTTGC
*
5064172 CTCTATTTAGAGGAGCA
65 CTCTGTTTAGAGGAGCA
* * *
5064189 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
1 ATTTA-CTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGTTGC
5064254 CTCTGTTTAGAGGAGCA
65 CTCTGTTTAGAGGAGCA
* *
5064271 ATTTACTTTTTC-AAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGG
1 ATTTAC-TTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGT--
*
5064332 TACCTCTGTTTAGAGGAGCA
62 TGCCTCTGTTTAGAGGAGCA
*
5064352 ATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGGT
1 ATTTACTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGT--T
*
5064416 ACCTCTGTTTAGAGGAGCA
63 GCCTCTGTTTAGAGGAGCA
5064435 ATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
1 ATTTACTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGC
5064476 TTTGGTAAAA
Statistics
Matches: 797, Mismatches: 32, Indels: 47
0.91 0.04 0.05
Matches are distributed among these distances:
78 31 0.04
79 110 0.14
80 49 0.06
81 258 0.32
82 149 0.19
83 200 0.25
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (81 bp):
ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGTTGCC
TCTGTTTAGAGGAGCA
Found at i:5064488 original size:1 final size:1
Alignment explanation
Indices: 5064482--5064552 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
5064472 GAGCTTTGGT
* * * * *** **
5064482 AAAAAAAACAAAAAAAAACAAAAAAAACAAAAAACAAAAATTTAAAAAAAAAAAAAATCAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
5064547 TAAAAA
1 AAAAAA
5064553 TGTTGAGTTG
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (1 bp):
A
Found at i:5064496 original size:9 final size:9
Alignment explanation
Indices: 5064482--5064546 Score: 60
Period size: 9 Copynumber: 6.7 Consensus size: 9
5064472 GAGCTTTGGT
5064482 AAAAAAAAC
1 AAAAAAAAC
5064491 AAAAAAAAAC
1 -AAAAAAAAC
5064501 AAAAAAAAC
1 AAAAAAAAC
5064510 AAAAAACAA-
1 AAAAAA-AAC
*
5064519 AAATTTAAAAAA
1 AAA---AAAAAC
5064531 AAAAAAAATC
1 AAAAAAAA-C
5064541 AAAAAA
1 AAAAAA
5064547 TAAAAATGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
9 23 0.48
10 17 0.35
11 2 0.04
12 6 0.12
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:5064513 original size:16 final size:16
Alignment explanation
Indices: 5064484--5064552 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
5064474 GCTTTGGTAA
*
5064484 AAAAAACAAAAAAAAAC
1 AAAAAA-AACAAAAAAC
5064501 AAAAAAAACAAAAAAC
1 AAAAAAAACAAAAAAC
**
5064517 AAAAATTTA-AAAAAA-
1 AAAAA-AAACAAAAAAC
* *
5064532 AAAAAAATCAAAAAAT
1 AAAAAAAACAAAAAAC
5064548 AAAAA
1 AAAAA
5064553 TGTTGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 11 0.26
16 25 0.58
17 7 0.16
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (16 bp):
AAAAAAAACAAAAAAC
Found at i:5064536 original size:31 final size:32
Alignment explanation
Indices: 5064493--5064553 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
5064483 AAAAAAACAA
5064493 AAAAAAACAAAAAAAACAAAAAACAAAAATTT
1 AAAAAAACAAAAAAAACAAAAAACAAAAATTT
* *
5064525 AAAAAAA-AAAAAAATCAAAAAATAAAAAT
1 AAAAAAACAAAAAAAACAAAAAACAAAAAT
5064554 GTTGAGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.84, C:0.07, G:0.00, T:0.10
Consensus pattern (32 bp):
AAAAAAACAAAAAAAACAAAAAACAAAAATTT
Found at i:5065399 original size:31 final size:31
Alignment explanation
Indices: 5065334--5065400 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
5065324 AATTTCCAGA
*
5065334 TTCCGGCGAAAATTCCGACGAAATTTAAATT
1 TTCCGGCGAAAATTCCGACGAAATTTAAAGT
* *
5065365 TTCCGGC-AACAATTCCGGCGAACA-TTGAAGT
1 TTCCGGCGAA-AATTCCGACGAA-ATTTAAAGT
5065396 TTCCG
1 TTCCG
5065401 ACGACCAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 2 0.06
31 28 0.90
32 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (31 bp):
TTCCGGCGAAAATTCCGACGAAATTTAAAGT
Found at i:5065470 original size:19 final size:20
Alignment explanation
Indices: 5065446--5065490 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
5065436 ACCGGCGATC
5065446 TTCCGGCG-AAATTTCCAGA
1 TTCCGGCGAAAATTTCCAGA
5065465 TTCCGGCGAAAATTTCCAGA
1 TTCCGGCGAAAATTTCCAGA
*
5065485 ATCCGG
1 TTCCGG
5065491 TACCGGTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (20 bp):
TTCCGGCGAAAATTTCCAGA
Found at i:5066150 original size:61 final size:59
Alignment explanation
Indices: 5065939--5066219 Score: 392
Period size: 60 Copynumber: 4.7 Consensus size: 59
5065929 AAAAATTCCA
* * *
5065939 AAAAAAAATA-TTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC
1 AAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTC
* * *
5065997 -CAAAAAATA-TTTTTGGGGAAGAGTTGAAAGTATCAATTTTCC-TCAGAAATAAATTTC
1 AAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATAAATTTC
* *
5066054 AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTC
1 AAAAAAAATAT-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAATTTC
5066116 AAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTC
1 AAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAATTTC
*
5066177 CAAAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
5066220 CTACAAAAAA
Statistics
Matches: 202, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.01
57 49 0.24
58 7 0.03
60 68 0.34
61 59 0.29
62 17 0.08
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (59 bp):
AAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTC
Found at i:5066183 original size:121 final size:116
Alignment explanation
Indices: 5065931--5066219 Score: 420
Period size: 121 Copynumber: 2.4 Consensus size: 116
5065921 TAAAAATAAA
* *
5065931 AAATTCCAAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
* *
5065996 CCAAAAAATATTTTTGGGGAAGAGTTGAAAGTATCAATTTTCCTCAGAAAT
66 CAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
*
5066047 AAATTTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAA
1 AAATTTC-AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAA
*
5066112 TTTCAAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT-TGAAAAT
63 TTTC-AAAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAAT
* *
5066168 CGAAATTTC-CAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 --AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
5066220 CTACAAAAAA
Statistics
Matches: 157, Mismatches: 8, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
116 6 0.04
117 50 0.32
119 7 0.04
120 9 0.06
121 78 0.50
123 7 0.04
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (116 bp):
AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
CAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
Found at i:5068138 original size:3 final size:3
Alignment explanation
Indices: 5068132--5068211 Score: 72
Period size: 3 Copynumber: 26.7 Consensus size: 3
5068122 AAGGAAAGAA
* * *
5068132 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAG AAA AAT -AT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * * * *
5068177 AGT AAT AGT AAA AAT AAT AAT AAT AGT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5068212 GCATTAATTG
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5068157 original size:18 final size:18
Alignment explanation
Indices: 5068134--5068211 Score: 90
Period size: 18 Copynumber: 4.5 Consensus size: 18
5068124 GGAAAGAAAA
5068134 TAATAATAATAATAATAG
1 TAATAATAATAATAATAG
* *
5068152 TAATAATAAGAAAAATA-
1 TAATAATAATAATAATAG
*
5068169 T-AT-ATAATAGTAATAG
1 TAATAATAATAATAATAG
*
5068185 TAAAAATAATAATAATAG
1 TAATAATAATAATAATAG
*
5068203 TAACAATAA
1 TAATAATAA
5068212 GCATTAATTG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
15 9 0.18
16 3 0.06
17 2 0.04
18 35 0.71
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.29
Consensus pattern (18 bp):
TAATAATAATAATAATAG
Found at i:5068747 original size:55 final size:55
Alignment explanation
Indices: 5068534--5068767 Score: 183
Period size: 55 Copynumber: 4.2 Consensus size: 55
5068524 ATTGAACTGT
* * * *
5068534 AAGTCTAGAAAATGATCTAGGTCGA-ATCGAGATCGAACAATC-GAGATTGAACCAT
1 AAGTCTAGAAAATGATCTAGATCGAGCT-GAGATCAAACAATCAG-GATTGAACCAC
* * * * * **
5068589 ATGTCTA-AAAAGTGATATAGATTGAGCTAAGATCGAAA-AGTCAGGATT-AAATAGC
1 AAGTCTAGAAAA-TGATCTAGATCGAGCTGAGATC-AAACAATCAGGATTGAACCA-C
* * * **
5068644 AAGTCT-GAAAAATCGACCTAGATCGAGTTGAGGTCAAACAATGGGGATTGAACCAC
1 AAGTCTAG-AAAAT-GATCTAGATCGAGCTGAGATCAAACAATCAGGATTGAACCAC
* *
5068700 AAGTCTAGAAAATGATCTGGATCGAGCTGAGATCAAACAATCAGGATTGAACCAT
1 AAGTCTAGAAAATGATCTAGATCGAGCTGAGATCAAACAATCAGGATTGAACCAC
**
5068755 AAGTAAAGAAAAT
1 AAGTCTAGAAAAT
5068768 TGTCCTGGAT
Statistics
Matches: 136, Mismatches: 32, Indels: 22
0.72 0.17 0.12
Matches are distributed among these distances:
54 7 0.05
55 83 0.61
56 42 0.31
57 4 0.03
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (55 bp):
AAGTCTAGAAAATGATCTAGATCGAGCTGAGATCAAACAATCAGGATTGAACCAC
Found at i:5080811 original size:45 final size:45
Alignment explanation
Indices: 5080762--5080847 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
5080752 TTAAAGTTCA
* *
5080762 AATAGAACCAATCTAGGTTTGAATCCTA-AGATTGGATTTTGCTTG
1 AATAGAACCAATCCAGGCTTGAATCCTAGA-ATTGGATTTTGCTTG
* *
5080807 AATAGAATCAATCCAGGCTTGAATCCTAGAATTTGATTTTG
1 AATAGAACCAATCCAGGCTTGAATCCTAGAATTGGATTTTG
5080848 TTCAACATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 35 0.97
46 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (45 bp):
AATAGAACCAATCCAGGCTTGAATCCTAGAATTGGATTTTGCTTG
Found at i:5081035 original size:18 final size:18
Alignment explanation
Indices: 5080996--5081035 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5080986 ATAATGATAC
* **
5080996 TAATAATAATAATAACTG
1 TAATAATAAAAATAACAA
5081014 TAATAATAAAAATAACAA
1 TAATAATAAAAATAACAA
5081032 TAAT
1 TAAT
5081036 GGTAACAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (18 bp):
TAATAATAAAAATAACAA
Found at i:5081498 original size:97 final size:97
Alignment explanation
Indices: 5081330--5081512 Score: 296
Period size: 97 Copynumber: 1.9 Consensus size: 97
5081320 AGGAAATAAA
*
5081330 CATTGAAGCCATTCCTCAAGCATTAACTCAAACTTATCAATATGAATAGGCTAAACTCACTTAGT
1 CATTGAAGCCATTCCTCAAGCATTAACTCAAACTTATCAATATGAATAGGCTAAACTCACTTAAT
5081395 GAACTCACCATTTGTCAAGAAAAAGTAAGAAC
66 GAACTCACCATTTGTCAAGAAAAAGTAAGAAC
* *
5081427 CATTGGAGCCATTCC-CTAAGCATTAACTCAAATTTATCAATATGAATAGGCTAAACTCACTTAA
1 CATTGAAGCCATTCCTC-AAGCATTAACTCAAACTTATCAATATGAATAGGCTAAACTCACTTAA
* * *
5081491 TGGACTCACCGTTTGTCGAGAA
65 TGAACTCACCATTTGTCAAGAA
5081513 TGCTAGCCTT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
96 1 0.01
97 78 0.99
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (97 bp):
CATTGAAGCCATTCCTCAAGCATTAACTCAAACTTATCAATATGAATAGGCTAAACTCACTTAAT
GAACTCACCATTTGTCAAGAAAAAGTAAGAAC
Found at i:5083892 original size:22 final size:21
Alignment explanation
Indices: 5083850--5083892 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5083840 AAATTTTTAG
*
5083850 AAAAAGAAAATTTTGATTTGA
1 AAAAAGAAAATTTTGAATTGA
5083871 AAAAAG-AAATTTGATGAATTGA
1 AAAAAGAAAATTT--TGAATTGA
5083893 TTAATGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 6 0.32
22 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.30
Consensus pattern (21 bp):
AAAAAGAAAATTTTGAATTGA
Found at i:5084417 original size:21 final size:22
Alignment explanation
Indices: 5084384--5084426 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5084374 TATATTCCCC
*
5084384 ATGCTTGTTGATAT-TATGTTTA
1 ATGCTTGTAGATATATAT-TTTA
5084406 ATGCTTG-AGATATATATTTTA
1 ATGCTTGTAGATATATATTTTA
5084427 GATATGCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.51
Consensus pattern (22 bp):
ATGCTTGTAGATATATATTTTA
Found at i:5087526 original size:16 final size:16
Alignment explanation
Indices: 5087507--5087541 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5087497 TGTGATAATA
*
5087507 TATCTTTAACAAGTGG
1 TATCCTTAACAAGTGG
*
5087523 TATCCTTAACAATTGG
1 TATCCTTAACAAGTGG
5087539 TAT
1 TAT
5087542 GAGCTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (16 bp):
TATCCTTAACAAGTGG
Found at i:5089105 original size:21 final size:21
Alignment explanation
Indices: 5089081--5089136 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
5089071 TGCATGAAAA
5089081 GGGATCAATCACCCTATGTAG
1 GGGATCAATCACCCTATGTAG
5089102 GGGATCAATCACCCTATGTAG
1 GGGATCAATCACCCTATGTAG
5089123 GGGATCAATCACCC
1 GGGATCAATCACCC
5089137 CTTAAACCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (21 bp):
GGGATCAATCACCCTATGTAG
Found at i:5091438 original size:20 final size:20
Alignment explanation
Indices: 5091397--5091439 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5091387 TATTTCATGC
**
5091397 AATCAAAAAATTTTAAAAAA
1 AATCAAAAAATTCAAAAAAA
5091417 AATCAAAAAA-TCAAAAATAA
1 AATCAAAAAATTCAAAAA-AA
5091437 AAT
1 AAT
5091440 TTCAAGTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (20 bp):
AATCAAAAAATTCAAAAAAA
Found at i:5094548 original size:2 final size:2
Alignment explanation
Indices: 5094543--5094567 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5094533 TGTGTGTGTG
5094543 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5094568 TTAAAAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5094756 original size:127 final size:129
Alignment explanation
Indices: 5094617--5094865 Score: 403
Period size: 130 Copynumber: 1.9 Consensus size: 129
5094607 AAATTAAATT
* * * *
5094617 GAGTGGAAGTTTACTATAATTTGACTAAAGTGG-AAAGTGCAAGGTTGGATT-CGAGGTTTGGTT
1 GAGTGGAAGTTTAATATAATTTGACTAAAGTGGAAAAATGCAAGGTTAGATTCCAAGGTTTGGTT
5094680 GGTCTATTAAATATATATTAATGATTTAATTAATAACAATCAGCAATTAATAAATTGGTATAAG
66 GGTCTATTAAATATATATTAATGATTTAATTAATAACAATCAGCAATTAATAAATTGGTATAAG
5094744 GAGTGGAAGTTTAATATAATTTGACTAAAGTGGAAAAAATGCAAGGTTAGATTCCAAGGTTTGGT
1 GAGTGGAAGTTTAATATAATTTGACTAAAGTGG-AAAAATGCAAGGTTAGATTCCAAGGTTTGGT
* * **
5094809 TGGTCTATTAAATATATATTAATTATTTAATTAATAATAATTGGCAATTAATAAATT
65 TGGTCTATTAAATATATATTAATGATTTAATTAATAACAATCAGCAATTAATAAATT
5094866 ATAATTTATT
Statistics
Matches: 111, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
127 32 0.29
129 16 0.14
130 63 0.57
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.37
Consensus pattern (129 bp):
GAGTGGAAGTTTAATATAATTTGACTAAAGTGGAAAAATGCAAGGTTAGATTCCAAGGTTTGGTT
GGTCTATTAAATATATATTAATGATTTAATTAATAACAATCAGCAATTAATAAATTGGTATAAG
Found at i:5095411 original size:12 final size:12
Alignment explanation
Indices: 5095394--5095418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5095384 ACGCACCAAA
5095394 TATGAAATATAC
1 TATGAAATATAC
5095406 TATGAAATATAC
1 TATGAAATATAC
5095418 T
1 T
5095419 TTTTTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TATGAAATATAC
Found at i:5103669 original size:16 final size:16
Alignment explanation
Indices: 5103650--5103683 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5103640 ACTTATATAT
*
5103650 AATAAAATATATAATA
1 AATAAAATATAAAATA
5103666 AATAAAATATAAAATA
1 AATAAAATATAAAATA
5103682 AA
1 AA
5103684 ATTTTAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAAATATAAAATA
Found at i:5104881 original size:19 final size:19
Alignment explanation
Indices: 5104857--5104893 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5104847 AAAATGATTA
5104857 AAAATAAAATGAAAAAAAT
1 AAAATAAAATGAAAAAAAT
5104876 AAAATAAAATGAAAAAAA
1 AAAATAAAATGAAAAAAA
5104894 AAACCTGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAATAAAATGAAAAAAAT
Found at i:5104893 original size:14 final size:14
Alignment explanation
Indices: 5104841--5104884 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5104831 CAAAAAACTT
*
5104841 AAAATAAAAATGATTA
1 AAAAT-AAAATGA-AA
5104857 AAAATAAAATGAAA
1 AAAATAAAATGAAA
5104871 AAAATAAAAT-AAA
1 AAAATAAAATGAAA
5104884 A
1 A
5104885 TGAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 11 0.41
15 7 0.26
16 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (14 bp):
AAAATAAAATGAAA
Found at i:5105694 original size:6 final size:6
Alignment explanation
Indices: 5105685--5105785 Score: 55
Period size: 6 Copynumber: 16.8 Consensus size: 6
5105675 AAAATAACAA
* * * * *
5105685 TAATAG TAATAG TAGCAGCAG TAATAG TAGTAG TAGTAG TAGTAG TAATAA
1 TAATAG TAATAG TA--A-TAG TAATAG TAATAG TAATAG TAATAG TAATAG
* * * * * *
5105736 TAATAA TAATA- TAATAA TAATAG -CATAA TAATAA TAATA- TAATAA
1 TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG
5105781 TAATA
1 TAATA
5105786 AATCAACATC
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
5 13 0.16
6 61 0.76
7 1 0.01
8 1 0.01
9 4 0.05
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (6 bp):
TAATAG
Found at i:5105695 original size:9 final size:9
Alignment explanation
Indices: 5105683--5105782 Score: 60
Period size: 9 Copynumber: 10.8 Consensus size: 9
5105673 AAAAAATAAC
5105683 AATAATAGT
1 AATAATAGT
* *
5105692 AATAGTAGC
1 AATAATAGT
5105701 AGCAGTAATAGT
1 A--A-TAATAGT
* *
5105713 AGTAGTAGT
1 AATAATAGT
* *
5105722 AGTAGTAGT
1 AATAATAGT
*
5105731 AATAATAAT
1 AATAATAGT
5105740 AATAATA-T
1 AATAATAGT
*
5105748 AATAATAAT
1 AATAATAGT
*
5105757 AGCATAATAAT
1 A--ATAATAGT
5105768 AATAATA-T
1 AATAATAGT
5105776 AATAATA
1 AATAATA
5105783 ATAAATCAAC
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
8 16 0.21
9 44 0.58
11 10 0.13
12 6 0.08
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.31
Consensus pattern (9 bp):
AATAATAGT
Found at i:5105715 original size:3 final size:3
Alignment explanation
Indices: 5105688--5105731 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
5105678 ATAACAATAA
* * * *
5105688 TAG TAA TAG TAG CAG CAG TAA TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
5105732 ATAATAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.30
Consensus pattern (3 bp):
TAG
Found at i:5105730 original size:15 final size:15
Alignment explanation
Indices: 5105688--5105731 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5105678 ATAACAATAA
*
5105688 TAGTAATAGTAGCAG
1 TAGTAATAGTAGTAG
*
5105703 CAGTAATAGTAGTAG
1 TAGTAATAGTAGTAG
*
5105718 TAGTAGTAGTAGTA
1 TAGTAATAGTAGTA
5105732 ATAATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.30
Consensus pattern (15 bp):
TAGTAATAGTAGTAG
Found at i:5105736 original size:3 final size:3
Alignment explanation
Indices: 5105730--5105786 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
5105720 GTAGTAGTAG
5105730 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAGCA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA--A TAA TAA TAA TAA TAA
5105775 TAA TAA TAA TAA
1 TAA TAA TAA TAA
5105787 ATCAACATCG
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 43 0.86
5 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5105751 original size:14 final size:14
Alignment explanation
Indices: 5105732--5105786 Score: 92
Period size: 14 Copynumber: 3.9 Consensus size: 14
5105722 AGTAGTAGTA
5105732 ATAATAATAATAAT
1 ATAATAATAATAAT
**
5105746 ATAATAATAATAGC
1 ATAATAATAATAAT
5105760 ATAATAATAATAAT
1 ATAATAATAATAAT
5105774 ATAATAATAATAA
1 ATAATAATAATAA
5105787 ATCAACATCG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:5105752 original size:17 final size:17
Alignment explanation
Indices: 5105730--5105786 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
5105720 GTAGTAGTAG
5105730 TAATAATAATAATAAT-A
1 TAATAATAAT-ATAATAA
**
5105747 TAATAATAATAGCATAA
1 TAATAATAATATAATAA
5105764 TAATAATAATATAATAA
1 TAATAATAATATAATAA
5105781 TAATAA
1 TAATAA
5105787 ATCAACATCG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 3 0.09
17 32 0.91
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
TAATAATAATATAATAA
Found at i:5111393 original size:19 final size:19
Alignment explanation
Indices: 5111369--5111407 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5111359 AAAAGTACAT
5111369 AGTCCAATTTGTATGGTTA
1 AGTCCAATTTGTATGGTTA
5111388 AGTCCAATTTGTATGGTTA
1 AGTCCAATTTGTATGGTTA
5111407 A
1 A
5111408 CTCAATGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (19 bp):
AGTCCAATTTGTATGGTTA
Found at i:5118521 original size:3 final size:3
Alignment explanation
Indices: 5118515--5118667 Score: 167
Period size: 3 Copynumber: 52.3 Consensus size: 3
5118505 AACAACAATT
5118515 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
5118563 AT- ATA A-C ATA AT- ATA ATA ATA GCATA ATA AT- ATA AT- ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA ATA
* * * * **
5118604 ATA ATA AT- ATA ATA CTA GTA ATA ATA ACA ATA ATG GCA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
5118649 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
5118668 AATCGACACC
Statistics
Matches: 127, Mismatches: 13, Indels: 20
0.79 0.08 0.12
Matches are distributed among these distances:
2 13 0.10
3 108 0.85
4 3 0.02
5 3 0.02
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5118923 original size:21 final size:21
Alignment explanation
Indices: 5118886--5118925 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5118876 AGGTGATTTT
*
5118886 TTTGTTTTTTCGGTTTGGTAG
1 TTTGTTTTTTCGATTTGGTAG
5118907 TTTGTGTTTTTC-ATTTGGT
1 TTTGT-TTTTTCGATTTGGT
5118926 TTATTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.05, C:0.05, G:0.25, T:0.65
Consensus pattern (21 bp):
TTTGTTTTTTCGATTTGGTAG
Found at i:5120107 original size:3 final size:3
Alignment explanation
Indices: 5120099--5120143 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
5120089 AAACAAAAAA
5120099 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5120144 ATTCTAAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5122755 original size:7 final size:7
Alignment explanation
Indices: 5122710--5122779 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
5122700 GGGATTGGTT
5122710 TTTAGGG
1 TTTAGGG
*
5122717 TTTGGGTTG
1 TTTAGG--G
*
5122726 TTTAGGA
1 TTTAGGG
5122733 TTTAGGG
1 TTTAGGG
*
5122740 TTTAAGG
1 TTTAGGG
5122747 TTTAGGG
1 TTTAGGG
*
5122754 TTTTAGAG
1 -TTTAGGG
**
5122762 TTTAAAAG
1 TTT-AGGG
5122770 TTTAGGG
1 TTTAGGG
5122777 TTT
1 TTT
5122780 CAAATTTAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
7 31 0.63
8 12 0.24
9 6 0.12
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:5124012 original size:22 final size:22
Alignment explanation
Indices: 5123984--5124028 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5123974 AAATCACATA
**
5123984 AGAGATTTATTTACGATTTGTT
1 AGAGATTTATTTAAAATTTGTT
5124006 AGAGATTTATTTAAAATTTGTT
1 AGAGATTTATTTAAAATTTGTT
5124028 A
1 A
5124029 AATATTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
AGAGATTTATTTAAAATTTGTT
Found at i:5124605 original size:31 final size:31
Alignment explanation
Indices: 5124567--5124743 Score: 139
Period size: 31 Copynumber: 5.7 Consensus size: 31
5124557 GGCTCTTTAG
5124567 CCTAACAAATGGTATCAGAGCTATAGTGATC
1 CCTAACAAATGGTATCAGAGCTATAGTGATC
* * * * *
5124598 CCTAACAAGTGATATCAAAGTTGTAGTGATC
1 CCTAACAAATGGTATCAGAGCTATAGTGATC
* * * *
5124629 CTTAACACATGGAATTAGAG-T-TAGGTGATC
1 CCTAACAAATGGTATCAGAGCTATA-GTGATC
* *
5124659 CCTAACAAGTGGTATTAGAGCTATAGTGATC
1 CCTAACAAATGGTATCAGAGCTATAGTGATC
* * * *
5124690 ACC-AACAAATGATATCAAAGCTGT-GATGATTT
1 -CCTAACAAATGGTATCAGAGCTATAG-TGA-TC
*
5124722 CC-AATAAATGGTATCAGAGCTA
1 CCTAACAAATGGTATCAGAGCTA
5124744 AAGGTTCAAG
Statistics
Matches: 114, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
29 2 0.02
30 24 0.21
31 83 0.73
32 5 0.04
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (31 bp):
CCTAACAAATGGTATCAGAGCTATAGTGATC
Found at i:5133373 original size:45 final size:44
Alignment explanation
Indices: 5133311--5133428 Score: 121
Period size: 45 Copynumber: 2.6 Consensus size: 44
5133301 GCATTACCAA
* *
5133311 TAACATCT-AAACTATCATTAAATTCATCCCTACCCACATCTTCAT
1 TAACACCTAAAAC-ATCATTAAATTCATCCCTA-CCACATCTTCAC
* * **
5133356 TAACACCTGAACCATCATTAAATTCATACTTTACCACATCTTCAC
1 TAACACCTAAAACATCATTAAATTCAT-CCCTACCACATCTTCAC
** *
5133401 TAATTCCTAAAACATCATTAAAGTCATC
1 TAACACCTAAAACATCATTAAATTCATC
5133429 AATTGCAACC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
44 1 0.02
45 54 0.89
46 6 0.10
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.32
Consensus pattern (44 bp):
TAACACCTAAAACATCATTAAATTCATCCCTACCACATCTTCAC
Found at i:5133952 original size:16 final size:16
Alignment explanation
Indices: 5133931--5133964 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5133921 ACTTATATAT
5133931 AATAAAATATAAAATA
1 AATAAAATATAAAATA
5133947 AATAAAATATAAAATA
1 AATAAAATATAAAATA
5133963 AA
1 AA
5133965 ATTTTAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAAAATATAAAATA
Found at i:5134020 original size:13 final size:14
Alignment explanation
Indices: 5133993--5134027 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5133983 CACCATAACA
5133993 AATTTATTATTATT
1 AATTTATTATTATT
5134007 AATTTATT-TTATT
1 AATTTATTATTATT
5134020 AA-TTATTA
1 AATTTATTA
5134028 AATTCAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 7 0.35
14 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTATTATTATT
Found at i:5135139 original size:15 final size:15
Alignment explanation
Indices: 5135121--5135162 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
5135111 AACAAAAAAC
*
5135121 TTAAAATCAAAATGA
1 TTAAAATCAAAATCA
5135136 TTAAAAATCAAAATCA
1 TT-AAAATCAAAATCA
5135152 -TAAAAT-AAAAT
1 TTAAAATCAAAAT
5135163 AAAATGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 5 0.20
14 5 0.20
15 3 0.12
16 12 0.48
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.26
Consensus pattern (15 bp):
TTAAAATCAAAATCA
Found at i:5135987 original size:15 final size:15
Alignment explanation
Indices: 5135969--5136006 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5135959 ATAACAATAA
5135969 CAGTAATAGTAGCAG
1 CAGTAATAGTAGCAG
*
5135984 CAGTAATAGTAGTAG
1 CAGTAATAGTAGCAG
*
5135999 TAGTAATA
1 CAGTAATA
5136007 ATAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (15 bp):
CAGTAATAGTAGCAG
Found at i:5136008 original size:3 final size:3
Alignment explanation
Indices: 5136002--5136074 Score: 121
Period size: 3 Copynumber: 24.0 Consensus size: 3
5135992 GTAGTAGTAG
5136002 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAGCA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA--A TAA TAA TAA TAA
5136049 TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
5136075 ATCAACATCG
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.03
3 62 0.93
5 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5136383 original size:55 final size:55
Alignment explanation
Indices: 5136245--5136384 Score: 147
Period size: 55 Copynumber: 2.5 Consensus size: 55
5136235 AGTTAGAAAG
* * * * * *
5136245 ATAATCTAGACTAAGCCAAGATCAAACAAACGGGATTGAATTGTAAATAAAAAAA
1 ATAATCTAGACTGAGCCAAGATCAAACGATCGGGATTAAATCGCAAATAAAAAAA
* * * * * * *
5136300 ATGATCTAGACTGAGTCGAGACCGAACGATCGGGATTAAATCGCAAGTCAAAAAA
1 ATAATCTAGACTGAGCCAAGATCAAACGATCGGGATTAAATCGCAAATAAAAAAA
5136355 ATAATCTAGA-TCGAGCCAAGATCAAACGAT
1 ATAATCTAGACT-GAGCCAAGATCAAACGAT
5136385 TGAGATTGAA
Statistics
Matches: 66, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
54 1 0.02
55 65 0.98
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (55 bp):
ATAATCTAGACTGAGCCAAGATCAAACGATCGGGATTAAATCGCAAATAAAAAAA
Found at i:5147013 original size:20 final size:18
Alignment explanation
Indices: 5146972--5147019 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
5146962 ATGAATAACT
*
5146972 AAAGAAAATATAAGCAAGG
1 AAAGAAAA-ATAAGCAAAG
*
5146991 AAAAGAAAAATAGAGGAAAG
1 -AAAGAAAAATA-AGCAAAG
5147011 AAAGAAAAA
1 AAAGAAAAA
5147020 AATCTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (18 bp):
AAAGAAAAATAAGCAAAG
Found at i:5148788 original size:3 final size:3
Alignment explanation
Indices: 5148782--5148904 Score: 107
Period size: 3 Copynumber: 42.3 Consensus size: 3
5148772 AACAACAATT
*
5148782 ATA ATA ATA ATA ATA ATA AT- ATA A-C ATA AT- ATA ATA ATA GCATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA
* * *
5148826 ATA AT- ATA AT- ATA AT- ATA AT- ATA ATA ATA CTA GTA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* **
5148870 ATA ATG GCA ATAA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA A
5148905 AATCGATACC
Statistics
Matches: 97, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
2 13 0.13
3 78 0.80
4 3 0.03
5 3 0.03
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5148810 original size:5 final size:5
Alignment explanation
Indices: 5148785--5148851 Score: 71
Period size: 5 Copynumber: 12.2 Consensus size: 5
5148775 AACAATTATA
*
5148785 ATAAT AATAAT AATAAT ATAAC ATAAT ATAAT AATAGCAT AATAAT ATAAT
1 ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT -ATA--AT -ATAAT ATAAT
5148836 ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT A
5148852 ATACTAGTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
5 34 0.61
6 16 0.29
8 6 0.11
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:5148827 original size:29 final size:27
Alignment explanation
Indices: 5148785--5148854 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 27
5148775 AACAATTATA
5148785 ATAATAATAATAATAATATAACATAAT
1 ATAATAATAATAATAATATAACATAAT
*
5148812 ATAATAATAGCATAATAATATAATATAAT
1 ATAATAATA--ATAATAATATAACATAAT
5148841 ATAAT-ATAATAATA
1 ATAATAATAATAATA
5148855 CTAGTAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 6 0.15
27 9 0.22
28 3 0.08
29 22 0.55
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (27 bp):
ATAATAATAATAATAATATAACATAAT
Found at i:5148874 original size:34 final size:33
Alignment explanation
Indices: 5148782--5148907 Score: 130
Period size: 34 Copynumber: 3.7 Consensus size: 33
5148772 AACAACAATT
* *
5148782 ATAATAATAATAATAATAATATAACATAATATA
1 ATAATAATAATAATAATAAAATAATATAATATA
*
5148815 ATAATAGCATAATAAT-ATAATATAATATAATATA
1 ATAATA--ATAATAATAATAAAATAATATAATATA
* *
5148849 ATAATACTAGTAATAATAACAATAATGGCAATAA-ATA
1 ATAATAATAATAATAATAA-AATAAT----ATAATATA
5148886 ATAATAATAATAATAATAAAAT
1 ATAATAATAATAATAATAAAAT
5148908 CGATACCAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
32 6 0.08
33 10 0.13
34 28 0.35
35 8 0.10
36 3 0.04
37 20 0.25
38 4 0.05
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (33 bp):
ATAATAATAATAATAATAAAATAATATAATATA
Found at i:5149710 original size:21 final size:20
Alignment explanation
Indices: 5149656--5149717 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 20
5149646 GCCTAAATTC
*
5149656 TAATT-TTTAAAATAAAAAA
1 TAATTATTTAAAATAAAAAT
*
5149675 TAA--ATTTATAATAAAAAT
1 TAATTATTTAAAATAAAAAT
*
5149693 TAATTATTGTAAAATAAATAT
1 TAATTATT-TAAAATAAAAAT
5149714 TAAT
1 TAAT
5149718 CAACAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 15 0.43
19 3 0.09
20 3 0.09
21 14 0.40
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TAATTATTTAAAATAAAAAT
Found at i:5150376 original size:3 final size:3
Alignment explanation
Indices: 5150370--5150447 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
5150360 ACAAAAAAAA
*
5150370 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5150418 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5150448 ATTCTAAACA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5153063 original size:26 final size:23
Alignment explanation
Indices: 5153011--5153069 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 23
5153001 GGGATTGGTC
*
5153011 TTTAGGGTTTGGGTTGTTTAGGA
1 TTTAGGGTTTAGGTTGTTTAGGA
5153034 TTTAGGGTTTAAGGTTAAGTTTAAGG-
1 TTTAGGGTTT-AGGTT--GTTT-AGGA
5153060 TTTAGGGTTT
1 TTTAGGGTTT
5153070 TAGAGTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 10 0.32
24 4 0.13
26 14 0.45
27 3 0.10
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (23 bp):
TTTAGGGTTTAGGTTGTTTAGGA
Found at i:5153079 original size:22 final size:21
Alignment explanation
Indices: 5153034--5153106 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 21
5153024 TTGTTTAGGA
* *
5153034 TTTAGGGTTTAAGG-TT-AAG
1 TTTAAGGTTTAGGGTTTCAAG
*
5153053 TTTAAGGTTTAGGGTTTTAGAG
1 TTTAAGGTTTAGGGTTTCA-AG
* *
5153075 TTTAAAAGTTTAGGGTTTCAAA
1 TTT-AAGGTTTAGGGTTTCAAG
5153097 TTTAAGGTTT
1 TTTAAGGTTT
5153107 CATAGAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.27
20 2 0.05
21 7 0.16
22 9 0.20
23 14 0.32
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.45
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTTCAAG
Found at i:5154125 original size:12 final size:12
Alignment explanation
Indices: 5154098--5154136 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5154088 TTTTCCAAGC
5154098 TTTCTCTATCTTTT
1 TTTCTCT-T-TTTT
5154112 TTTC-CTTTTTT
1 TTTCTCTTTTTT
5154123 TTTCTCTTTTTT
1 TTTCTCTTTTTT
5154135 TT
1 TT
5154137 CACATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 10 0.42
13 2 0.08
14 4 0.17
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTCTTTTTT
Found at i:5154951 original size:31 final size:31
Alignment explanation
Indices: 5154913--5155055 Score: 128
Period size: 31 Copynumber: 4.6 Consensus size: 31
5154903 GGCTCTTTAG
5154913 CCTAACAAATGGTATCAAAGTTATAGTGATC
1 CCTAACAAATGGTATCAAAGTTATAGTGATC
* * *
5154944 CCTAACAAGTGATATCAAAGTTGTAGTGATC
1 CCTAACAAATGGTATCAAAGTTATAGTGATC
* ** * * **
5154975 CCTAACACATGAAATTAGAGTT-GGGTGATC
1 CCTAACAAATGGTATCAAAGTTATAGTGATC
* * * * *
5155005 CCTAACAAGTGGTATTAGAGCTATGGTGATC
1 CCTAACAAATGGTATCAAAGTTATAGTGATC
5155036 ACC-AACAAATGGTATCAAAG
1 -CCTAACAAATGGTATCAAAG
5155056 CTGTGATGAT
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
30 23 0.25
31 66 0.73
32 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (31 bp):
CCTAACAAATGGTATCAAAGTTATAGTGATC
Found at i:5155390 original size:11 final size:11
Alignment explanation
Indices: 5155374--5155414 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5155364 AATCCCATAA
*
5155374 GAGATTTATTT
1 GAGATTTGTTT
*
5155385 GAGATTTGTTA
1 GAGATTTGTTT
5155396 GAGATTTGTTT
1 GAGATTTGTTT
*
5155407 GGGATTTG
1 GAGATTTG
5155415 ATAGATATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:5155401 original size:22 final size:22
Alignment explanation
Indices: 5155373--5155419 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5155363 AAATCCCATA
*
5155373 AGAGATTTATTTGAGATTTGTT
1 AGAGATTTATTTGAGATTTGAT
* *
5155395 AGAGATTTGTTTGGGATTTGAT
1 AGAGATTTATTTGAGATTTGAT
5155417 AGA
1 AGA
5155420 TATTGCTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (22 bp):
AGAGATTTATTTGAGATTTGAT
Found at i:5156344 original size:194 final size:194
Alignment explanation
Indices: 5156015--5156398 Score: 734
Period size: 194 Copynumber: 2.0 Consensus size: 194
5156005 CCATCTCTCA
5156015 CCATTAGATTTAGCTCCCTAGAATGATCATATCATCAAGGATGCTCACTGCCAAAAGTTGAATTT
1 CCATTAGATTTAGCTCCCTAGAATGATCATATCATCAAGGATGCTCACTGCCAAAAGTTGAATTT
5156080 TTAATAATGTTAGAACCAAGTGAAAAGACCATTTTGCCCCCCATTAAAAAATTTTCGATTTCTAG
66 TTAATAATGTTAGAACCAAGTGAAAAGACCATTTTGCCCCCCATTAAAAAATTTTCGATTTCTAG
*
5156145 GATATTTTCTTAGAAAACAATGCTTCCTTATTCATTTTGTAGTTTTAAAACACCAAAAATGATC
131 GATATTTTCTTAGAAAACAATGCTTCCTTATTCATTTTGTAATTTTAAAACACCAAAAATGATC
*
5156209 CCATTAGATTTAGCTCCCTAGAATGATCATATCATCAAGGATGCTCACTGTCAAAAGTTGAATTT
1 CCATTAGATTTAGCTCCCTAGAATGATCATATCATCAAGGATGCTCACTGCCAAAAGTTGAATTT
5156274 TTAATAATGTTAGAACCAAGTGAAAAGACCATTTTGCCCCCCATTAAAAAATTTTC-AGTTTCTA
66 TTAATAATGTTAGAACCAAGTGAAAAGACCATTTTGCCCCCCATTAAAAAATTTTCGA-TTTCTA
5156338 GGATATTTTCTTAGAAAACAATGCTTCCTTATTCATTTTGTAATTTTAAAACACCAAAAAT
130 GGATATTTTCTTAGAAAACAATGCTTCCTTATTCATTTTGTAATTTTAAAACACCAAAAAT
5156399 CATGAAATAA
Statistics
Matches: 187, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
193 1 0.01
194 186 0.99
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (194 bp):
CCATTAGATTTAGCTCCCTAGAATGATCATATCATCAAGGATGCTCACTGCCAAAAGTTGAATTT
TTAATAATGTTAGAACCAAGTGAAAAGACCATTTTGCCCCCCATTAAAAAATTTTCGATTTCTAG
GATATTTTCTTAGAAAACAATGCTTCCTTATTCATTTTGTAATTTTAAAACACCAAAAATGATC
Found at i:5158569 original size:263 final size:259
Alignment explanation
Indices: 5158089--5158609 Score: 604
Period size: 264 Copynumber: 2.0 Consensus size: 259
5158079 TAGTGTAATT
* *
5158089 GTAGAGAGATAACGACATACAACAACCTCTTGATTGTTTTTCAGTAGCTTATTCACAGTTTCAAG
1 GTAGAGAGATAACAACATACAACAACCTCTTGACTGTTTTTCAGTAGCTTATTCACAGTTTCAAG
* * * * * *
5158154 TGATAAGCACCGACTGGTAGTTACAAGTAAATTTCAAACTACAAATACAAACCCATCAAATTAAT
66 AGATAAGCACAGACTGGCAGCTACAAATAAATTTCAAACTAAAAATACAAACCCATCAAATTAA-
* * * * ** * *
5158219 GATTAATTTAGCATTGAAGTTGAAATTTATTTTTGTGTTAAAAAATGGCTTTTATTTCAATTTTA
130 GACTAACTTAGCATTGAAGTTGAAATTTATTTTTGTATCAAAAAATACCTTTTAATTCAATATTA
**** *
5158284 ATGTTAAATTATTTTTAAAAAA-TGACTTTAT-AATTTAAAATTTTGATTTGAAAACCCAAACAA
195 ATGTTAAATTATAAAAAAAAAATTGACTTT-TCAATTTAAAATTTTCATTTGAAAACCCAAACAA
5158347 A
259 A
* *
5158348 GTAGAGAGATAATAACATACAACAACCTACCTCTTGACTGTTTTTTAGTAGCTTATTCACAGTTT
1 GTAGAGAGATAACAACATACAAC-A---ACCTCTTGACTGTTTTTCAGTAGCTTATTCACAGTTT
* * * * * *
5158413 CAAGAGGTAAAGCACAGACTGGCAGCTGCAAATACATTTCAAACTAAAAATGCGAATCCATCAAA
62 CAAGAGAT-AAGCACAGACTGGCAGCTACAAATAAATTTCAAACTAAAAATACAAACCCATCAAA
* *
5158478 TTAA-ACTAGCTTAGCATTGAAGTTGAAAATTT-TTTTT-TATCAAAAACTACCTTTTAATTCAA
126 TTAAGACTAACTTAGCATTGAAGTTG-AAATTTATTTTTGTATCAAAAAATACCTTTTAATTCAA
* *
5158540 TATTAAT-TCTAAATTATAAAAAAAAAAAATTGGCTTTTCAATTTAAAATTTTCATTTGAAAATC
190 TATTAATGT-TAAATTAT--AAAAAAAAAATTGACTTTTCAATTTAAAATTTTCATTTGAAAACC
5158604 CAAACA
252 CAAACA
5158610 GAAAGTTGGC
Statistics
Matches: 218, Mismatches: 33, Indels: 17
0.81 0.12 0.06
Matches are distributed among these distances:
259 21 0.10
260 2 0.01
261 33 0.15
262 23 0.11
263 54 0.25
264 85 0.39
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (259 bp):
GTAGAGAGATAACAACATACAACAACCTCTTGACTGTTTTTCAGTAGCTTATTCACAGTTTCAAG
AGATAAGCACAGACTGGCAGCTACAAATAAATTTCAAACTAAAAATACAAACCCATCAAATTAAG
ACTAACTTAGCATTGAAGTTGAAATTTATTTTTGTATCAAAAAATACCTTTTAATTCAATATTAA
TGTTAAATTATAAAAAAAAAATTGACTTTTCAATTTAAAATTTTCATTTGAAAACCCAAACAAA
Found at i:5168500 original size:14 final size:13
Alignment explanation
Indices: 5168475--5168511 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
5168465 AGTCTCAAAT
*
5168475 AGAAAGAAAAAAA
1 AGAAAAAAAAAAA
5168488 AGTAAAAAAAAAAA
1 AG-AAAAAAAAAAA
5168502 AGAAAAAAAA
1 AGAAAAAAAA
5168512 TGAATGCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:5168900 original size:18 final size:18
Alignment explanation
Indices: 5168874--5168914 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5168864 AATGGATGGG
*
5168874 AAAATATGAAAAAAGGAA
1 AAAAAATGAAAAAAGGAA
* *
5168892 AAAAAATGAAAAGATGAA
1 AAAAAATGAAAAAAGGAA
5168910 AAAAA
1 AAAAA
5168915 TCAAAAGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAAATGAAAAAAGGAA
Found at i:5170163 original size:25 final size:25
Alignment explanation
Indices: 5170128--5170451 Score: 225
Period size: 25 Copynumber: 13.6 Consensus size: 25
5170118 TTTGAGCCTT
**
5170128 AAATGAGAATCTTTAAGATGTTTTC
1 AAATGAGAATCTTTAAGACATTTTC
* *
5170153 AAATGAAAATCTTTAAGACGTTTTC
1 AAATGAGAATCTTTAAGACATTTTC
* *
5170178 AAATGAGAATATTTAAG---TCTT-
1 AAATGAGAATCTTTAAGACATTTTC
* * *
5170199 ATATGAAAATCTTTAAGGCATTTTC
1 AAATGAGAATCTTTAAGACATTTTC
* * *
5170224 AAATTAGAATCTTT--GA-GTCTT-
1 AAATGAGAATCTTTAAGACATTTTC
* * *
5170245 AAATAAGAATCTTTAAGATATTTTT
1 AAATGAGAATCTTTAAGACATTTTC
* * *
5170270 AAATGAGAACCTTT--GA-GTCTT-
1 AAATGAGAATCTTTAAGACATTTTC
* * *
5170291 AAATGAAAATCTTTAAAACATCTTC
1 AAATGAGAATCTTTAAGACATTTTC
*
5170316 AAATTAGAATCTTT--GACATTTTC
1 AAATGAGAATCTTTAAGACATTTTC
*
5170339 AAATGAGAATCTTTAAGACATTATC
1 AAATGAGAATCTTTAAGACATTTTC
* * *
5170364 AAATGAGAATATTTGAGTCA---T-
1 AAATGAGAATCTTTAAGACATTTTC
*
5170385 AAATGAGAATCTTTAAGATATTTTC
1 AAATGAGAATCTTTAAGACATTTTC
* * *
5170410 AAATGAGAATCTTTGAGTTTAGAATTTC
1 AAATGAGAATCTTTAAG---ACATTTTC
5170438 AAATGAGAATCTTT
1 AAATGAGAATCTTT
5170452 GAGGTGTGAA
Statistics
Matches: 236, Mismatches: 42, Indels: 39
0.74 0.13 0.12
Matches are distributed among these distances:
21 55 0.23
22 10 0.04
23 26 0.11
24 11 0.05
25 114 0.48
28 20 0.08
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (25 bp):
AAATGAGAATCTTTAAGACATTTTC
Found at i:5170206 original size:46 final size:46
Alignment explanation
Indices: 5170128--5170427 Score: 341
Period size: 46 Copynumber: 6.4 Consensus size: 46
5170118 TTTGAGCCTT
* *
5170128 AAATGAGAATCTTTAAGATGTTTTCAAATGAAAATCTTTAAGACGTTTTC
1 AAATGAGAATCTTT--GA-GTCTT-AAATGAAAATCTTTAAGACATTTTC
* * * *
5170178 AAATGAGAATATTTAAGTCTTATATGAAAATCTTTAAGGCATTTTC
1 AAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTAAGACATTTTC
* * *
5170224 AAATTAGAATCTTTGAGTCTTAAAT-AAGAATCTTTAAGATATTTTT
1 AAATGAGAATCTTTGAGTCTTAAATGAA-AATCTTTAAGACATTTTC
* * *
5170270 AAATGAGAACCTTTGAGTCTTAAATGAAAATCTTTAAAACATCTTC
1 AAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTAAGACATTTTC
* * * * *
5170316 AAATTAGAATCTTTGACATTTTCAAATGAGAATCTTTAAGACATTATC
1 AAATGAGAATCTTTGA-GTCTT-AAATGAAAATCTTTAAGACATTTTC
* * * *
5170364 AAATGAGAATATTTGAGTCATAAATGAGAATCTTTAAGATATTTTC
1 AAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTAAGACATTTTC
5170410 AAATGAGAATCTTTGAGT
1 AAATGAGAATCTTTGAGT
5170428 TTAGAATTTC
Statistics
Matches: 211, Mismatches: 35, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
45 2 0.01
46 149 0.71
47 11 0.05
48 36 0.17
50 13 0.06
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (46 bp):
AAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTAAGACATTTTC
Found at i:5170223 original size:71 final size:71
Alignment explanation
Indices: 5170105--5170261 Score: 169
Period size: 71 Copynumber: 2.3 Consensus size: 71
5170095 TCTTGAATCC
* * * **
5170105 TCAAATAAGAATCTTTGAGCCTTAAATGAGAATCTTTAAGATGTTTTCAAATGAAAATCTTTAAG
1 TCAAATAAGAATATTTAAGCCTTAAATGAAAATCTTTAAGACATTTTCAAATGAAAATCTTTAAG
5170170 ACGTTT
66 ACGTTT
* * * * * *
5170176 TCAAATGAGAATATTTAAGTCTTATATGAAAATCTTTAAGGCATTTTCAAATTAGAATCTTT--G
1 TCAAATAAGAATATTTAAGCCTTAAATGAAAATCTTTAAGACATTTTCAAATGAAAATCTTTAAG
*
5170239 A-GTCT
66 ACGTTT
*
5170244 T-AAATAAGAATCTTTAAG
1 TCAAATAAGAATATTTAAG
5170262 ATATTTTTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
67 15 0.21
68 4 0.06
69 2 0.03
71 51 0.71
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (71 bp):
TCAAATAAGAATATTTAAGCCTTAAATGAAAATCTTTAAGACATTTTCAAATGAAAATCTTTAAG
ACGTTT
Found at i:5170468 original size:28 final size:28
Alignment explanation
Indices: 5170409--5170468 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
5170399 AAGATATTTT
* ***
5170409 CAAATGAGAATCTTTGAGTTTAGAATTT
1 CAAATGAGAATCTTTGAGTGTAGAAACC
5170437 CAAATGAGAATCTTTGAGGTGT-GAAACC
1 CAAATGAGAATCTTTGA-GTGTAGAAACC
5170465 CAAA
1 CAAA
5170469 ATTTGTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (28 bp):
CAAATGAGAATCTTTGAGTGTAGAAACC
Found at i:5171082 original size:41 final size:41
Alignment explanation
Indices: 5171031--5171206 Score: 190
Period size: 41 Copynumber: 4.3 Consensus size: 41
5171021 AGCCTTCTAT
* *
5171031 TTTTTCAAAGTTATGGTGCCTTTATTTAGACGAGCATTTTA
1 TTTTTCAAAGTTATGGTGCCTCTATTTAGAAGAGCATTTTA
* * *
5171072 TTTTTCAAAGTTGTGGTGCTTCTATTTAGATGAGCATTTTA
1 TTTTTCAAAGTTATGGTGCCTCTATTTAGAAGAGCATTTTA
* * * * *
5171113 GTTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCATTTTA
1 TTTTTCAAAGTTATGGTGCCTCTATTTAGAAGAGCATTTTA
* * * * * *
5171154 TTCTTCAAAAGTTATGGCGTCGCTGTTTAGAAGAGCATTGTA
1 TTTTTC-AAAGTTATGGTGCCTCTATTTAGAAGAGCATTTTA
*
5171196 TTTCTCAAAGT
1 TTTTTCAAAGT
5171207 CATTAAACCC
Statistics
Matches: 114, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
41 82 0.72
42 32 0.28
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (41 bp):
TTTTTCAAAGTTATGGTGCCTCTATTTAGAAGAGCATTTTA
Found at i:5171412 original size:7 final size:8
Alignment explanation
Indices: 5171395--5171421 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5171385 AATAAATGAT
5171395 AAATGGAA
1 AAATGGAA
5171403 AAATGGAA
1 AAATGGAA
5171411 AAATGGAA
1 AAATGGAA
5171419 AAA
1 AAA
5171422 AGAAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (8 bp):
AAATGGAA
Found at i:5173306 original size:57 final size:57
Alignment explanation
Indices: 5173216--5173323 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
5173206 TTTCCAAAAA
* * * *
5173216 AAAAAAAGAGAGAATTTCTAAATATGCCTAAATGGTGAAAAATTTAGAAATTCTCTC
1 AAAAAAAGAGAAAATTTCTAAATATGCCAAAATGATGAAAAATTTAAAAATTCTCTC
5173273 AAAAAAAGA-AAATATTTCTAAAT-TGACCAAAATGATGAAAAATTTAAAAAT
1 AAAAAAAGAGAAA-ATTTCTAAATATG-CCAAAATGATGAAAAATTTAAAAAT
5173324 AAAAAAAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
56 4 0.09
57 41 0.91
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (57 bp):
AAAAAAAGAGAAAATTTCTAAATATGCCAAAATGATGAAAAATTTAAAAATTCTCTC
Found at i:5173317 original size:28 final size:27
Alignment explanation
Indices: 5173228--5173317 Score: 65
Period size: 28 Copynumber: 3.2 Consensus size: 27
5173218 AAAAAGAGAG
* *
5173228 AATTTCTAAATATGCCTAAATGGTGAAA
1 AATTTCTAAAT-TGCCAAAATGATGAAA
** * * *
5173256 AATTTAGAAATTCTCTCAAAA-AAAGAAA
1 AATTTCTAAATT-GC-CAAAATGATGAAA
5173284 ATATTTCTAAATTGACCAAAATGATGAAA
1 A-ATTTCTAAATTG-CCAAAATGATGAAA
5173313 AATTT
1 AATTT
5173318 AAAAATAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
27 1 0.02
28 24 0.53
29 20 0.44
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (27 bp):
AATTTCTAAATTGCCAAAATGATGAAA
Found at i:5175766 original size:18 final size:17
Alignment explanation
Indices: 5175745--5175789 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
5175735 TAATTTTTTA
5175745 ATATATTTTAATTACTT-T
1 ATATATTTTAA-TA-TTAT
5175763 ATATATATTTAATATTAT
1 ATATAT-TTTAATATTAT
5175781 ATATATTTT
1 ATATATTTT
5175790 TACCATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATATTTTAATATTAT
Found at i:5175840 original size:12 final size:12
Alignment explanation
Indices: 5175823--5175859 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
5175813 AAATCCATCC
5175823 ATGGCGATGGCA
1 ATGGCGATGGCA
5175835 ATGGCGATGGCA
1 ATGGCGATGGCA
5175847 ATGGCGATGGCA
1 ATGGCGATGGCA
5175859 A
1 A
5175860 ATGGGGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.41, T:0.16
Consensus pattern (12 bp):
ATGGCGATGGCA
Found at i:5175850 original size:18 final size:18
Alignment explanation
Indices: 5175823--5175857 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5175813 AAATCCATCC
*
5175823 ATGGCGATGGCAATGGCG
1 ATGGCAATGGCAATGGCG
*
5175841 ATGGCAATGGCGATGGC
1 ATGGCAATGGCAATGGC
5175858 AAATGGGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.43, T:0.17
Consensus pattern (18 bp):
ATGGCAATGGCAATGGCG
Found at i:5177517 original size:13 final size:14
Alignment explanation
Indices: 5177500--5177550 Score: 63
Period size: 13 Copynumber: 3.7 Consensus size: 14
5177490 AAATAATTAT
5177500 TATTAATATTTTTA
1 TATTAATATTTTTA
5177514 -ATTATATTATTTTTA
1 TATTA-A-TATTTTTA
5177529 TATTAAT-TTTTTA
1 TATTAATATTTTTA
5177542 TATT-ATATT
1 TATTAATATT
5177551 ATCATTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.06
13 16 0.48
14 2 0.06
15 9 0.27
16 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTAATATTTTTA
Found at i:5184832 original size:5 final size:6
Alignment explanation
Indices: 5184814--5184839 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5184804 ATTTAAATTA
5184814 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
5184840 TGAACAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:5191652 original size:18 final size:18
Alignment explanation
Indices: 5191619--5191653 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5191609 TATTTTTTAA
* *
5191619 ATATAAATATATAATTAT
1 ATATAAATAAAAAATTAT
5191637 ATATAAATAAAAAATTA
1 ATATAAATAAAAAATTA
5191654 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATAAATAAAAAATTAT
Found at i:5195004 original size:12 final size:12
Alignment explanation
Indices: 5194987--5195011 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5194977 TTGGAAGATT
5194987 TTTTATTTTTTC
1 TTTTATTTTTTC
5194999 TTTTATTTTTTC
1 TTTTATTTTTTC
5195011 T
1 T
5195012 GTATTTTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTTTC
Found at i:5199562 original size:14 final size:15
Alignment explanation
Indices: 5199543--5199574 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5199533 TAATATAATA
5199543 AATTTATT-TTTTTG
1 AATTTATTATTTTTG
5199557 AATTTATTATTTTTG
1 AATTTATTATTTTTG
5199572 AAT
1 AAT
5199575 GGTGAGACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
AATTTATTATTTTTG
Found at i:5200996 original size:29 final size:29
Alignment explanation
Indices: 5200938--5200996 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
5200928 ATTTTATATT
* * *
5200938 TTTTATATCAATACAAATTTTAACATAAA
1 TTTTATATCAAAACAAATATTAACACAAA
*
5200967 TTTTATAT-AAAACATAATATTAATACAAA
1 TTTTATATCAAAACA-AATATTAACACAAA
5200996 T
1 T
5200997 ATTTTATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (29 bp):
TTTTATATCAAAACAAATATTAACACAAA
Found at i:5200996 original size:41 final size:38
Alignment explanation
Indices: 5200942--5201024 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 38
5200932 TATATTTTTT
5200942 ATATCAATACAAAT-TTTAACATAAATTTTATATAAAACATA
1 ATATCAATACAAATATTT--CAT-AATTTTATATAAAACA-A
* * *
5200983 ATATTAATACAAATATTTTATTATTTTATATAAAACAA
1 ATATCAATACAAATATTTCATAATTTTATATAAAACAA
5201021 ATAT
1 ATAT
5201025 ATAAATTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
38 5 0.13
39 15 0.39
40 2 0.05
41 13 0.34
42 3 0.08
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (38 bp):
ATATCAATACAAATATTTCATAATTTTATATAAAACAA
Found at i:5201730 original size:19 final size:19
Alignment explanation
Indices: 5201690--5201736 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
5201680 TTTTTTTTCC
5201690 TTTATAAATATTTAATAAATT
1 TTTA-AAATATTT-ATAAATT
5201711 TTTAAAATATTT-TAACATT
1 TTTAAAATATTTATAA-ATT
5201730 TTTAAAA
1 TTTAAAA
5201737 GTATGGAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.12
19 10 0.40
20 8 0.32
21 4 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAAAATATTTATAAATT
Found at i:5202912 original size:40 final size:38
Alignment explanation
Indices: 5202863--5202953 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 38
5202853 GCGATTTTAG
* *
5202863 AATTTTTTATTATATCTTG-AGTATATATATGATTATTTTT
1 AATTATTTATTATATCTTGTA-TATATATAT-ATTA-TATT
* * * *
5202903 AATTGTTTATTTTATTTTGTATTTATATATATTATATT
1 AATTATTTATTATATCTTGTATATATATATATTATATT
5202941 AATTATTTATTAT
1 AATTATTTATTAT
5202954 TTAATATCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 14 0.33
39 4 0.09
40 24 0.56
41 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (38 bp):
AATTATTTATTATATCTTGTATATATATATATTATATT
Found at i:5203222 original size:10 final size:10
Alignment explanation
Indices: 5203203--5203248 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
5203193 AAACACTCAT
*
5203203 TATATATATA
1 TATATGTATA
5203213 TATATGTATA
1 TATATGTATA
5203223 TATATGTATA
1 TATATGTATA
5203233 TGTATATGTAT-
1 --TATATGTATA
5203244 TATAT
1 TATAT
5203249 TAATAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
9 5 0.15
10 19 0.58
12 9 0.27
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (10 bp):
TATATGTATA
Found at i:5203669 original size:21 final size:21
Alignment explanation
Indices: 5203645--5203684 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5203635 ACAAAATTTC
5203645 AAAAAAATTTTAAAAAAATCT
1 AAAAAAATTTTAAAAAAATCT
* *
5203666 AAAAAATTTTTTAAAAAAT
1 AAAAAAATTTTAAAAAAAT
5203685 ATGAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAAAATTTTAAAAAAATCT
Found at i:5203695 original size:21 final size:21
Alignment explanation
Indices: 5203645--5203695 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5203635 ACAAAATTTC
* *
5203645 AAAAAAATTTTAAAAAAATCT
1 AAAAAATTTTTAAAAAAATAT
*
5203666 AAAAAATTTTTTAAAAAATAT
1 AAAAAATTTTTAAAAAAATAT
* *
5203687 GAAATATTT
1 AAAAAATTT
5203696 AAAATTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAAATTTTTAAAAAAATAT
Found at i:5203775 original size:18 final size:17
Alignment explanation
Indices: 5203732--5203768 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5203722 CCTAAATATT
**
5203732 TTTAAAAATTAAAAAAA
1 TTTAAAAAACAAAAAAA
5203749 TTTAAAAAACAAAAAAA
1 TTTAAAAAACAAAAAAA
5203766 TTT
1 TTT
5203769 TGAAAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TTTAAAAAACAAAAAAA
Found at i:5203925 original size:21 final size:21
Alignment explanation
Indices: 5203887--5203926 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5203877 AATTGAAAAC
**
5203887 AAAAAATCTAAATTTTTTATA
1 AAAAAATCTAAAAATTTTATA
5203908 AAAAAATCTAAAAATTTTA
1 AAAAAATCTAAAAATTTTA
5203927 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAATCTAAAAATTTTATA
Found at i:5204019 original size:8 final size:9
Alignment explanation
Indices: 5204000--5204029 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5203990 ATTTTATGCA
5204000 TTTTTCATT
1 TTTTTCATT
5204009 TTTTTCATT
1 TTTTTCATT
*
5204018 TTTTTAATT
1 TTTTTCATT
5204027 TTT
1 TTT
5204030 ATTAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCATT
Found at i:5205706 original size:12 final size:12
Alignment explanation
Indices: 5205682--5205752 Score: 74
Period size: 12 Copynumber: 5.8 Consensus size: 12
5205672 TTTATATAAA
5205682 AATTAATTT-TTT
1 AATT-ATTTATTT
5205694 AATTATTTATTT
1 AATTATTTATTT
5205706 AATT-TTTATTT
1 AATTATTTATTT
*
5205717 ATATATATTTATAT
1 A-AT-TATTTATTT
*
5205731 AATTATATATTT
1 AATTATTTATTT
*
5205743 AAATATTTAT
1 AATTATTTAT
5205753 ATTTAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
11 12 0.24
12 28 0.56
13 3 0.06
14 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTATTTATTT
Found at i:5205731 original size:8 final size:8
Alignment explanation
Indices: 5205718--5205754 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
5205708 TTTTTATTTA
5205718 TATATATT
1 TATATATT
*
5205726 TATATAAT
1 TATATATT
5205734 TATATATT
1 TATATATT
*
5205742 TAAATATT
1 TATATATT
5205750 TATAT
1 TATAT
5205755 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:5205758 original size:14 final size:16
Alignment explanation
Indices: 5205718--5205772 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
5205708 TTTTTATTTA
*
5205718 TATATATTTATATAAT
1 TATATATTTAAATAAT
5205734 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
*
5205749 T-TATATTTAAAAAAT
1 TATATATTTAAATAAT
*
5205764 AATAT-TTTA
1 TATATATTTA
5205773 TTAATTTCGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:5210768 original size:12 final size:12
Alignment explanation
Indices: 5210750--5210783 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5210740 AAATTTTTAG
5210750 GTTTTCATATCT
1 GTTTTCATATCT
*
5210762 TTTTTCATAT-T
1 GTTTTCATATCT
5210773 GTTTTCATATC
1 GTTTTCATATC
5210784 AAGTCATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.62
Consensus pattern (12 bp):
GTTTTCATATCT
Found at i:5212777 original size:3 final size:3
Alignment explanation
Indices: 5212769--5212806 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5212759 AGAGTGGCTT
5212769 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
5212807 ACAGGTAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.32, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:5223111 original size:22 final size:25
Alignment explanation
Indices: 5223083--5223142 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 25
5223073 GATATTTATT
5223083 ATTTATAAAAAT-ATTTATT-TT-A
1 ATTTATAAAAATAATTTATTATTAA
* *
5223105 ATTTATAAATATAATTTTTTATTAA
1 ATTTATAAAAATAATTTATTATTAA
5223130 ATTTAATAAAAAT
1 ATTT-ATAAAAAT
5223143 CAAATATCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 11 0.35
23 6 0.19
24 2 0.06
25 5 0.16
26 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTATAAAAATAATTTATTATTAA
Found at i:5223688 original size:22 final size:21
Alignment explanation
Indices: 5223663--5223732 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
5223653 AATTTAAACT
5223663 TTTAATAATTATTATATATAAA
1 TTTAATAATTATTATATA-AAA
* *
5223685 TTTAATATTTTTTATATAAAA
1 TTTAATAATTATTATATAAAA
* * * *
5223706 TATAATAA-AAATATATAAAT
1 TTTAATAATTATTATATAAAA
5223726 TTTAATA
1 TTTAATA
5223733 TTTTAGTTCG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 14 0.36
21 9 0.23
22 16 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAATAATTATTATATAAAA
Found at i:5224396 original size:18 final size:18
Alignment explanation
Indices: 5224360--5224393 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5224350 AAAAAGTATA
*
5224360 TATTTAAAATTATTTAAT
1 TATTCAAAATTATTTAAT
5224378 TATTCAAAATT-TTTAA
1 TATTCAAAATTATTTAA
5224394 ATTTAACTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTCAAAATTATTTAAT
Found at i:5224521 original size:38 final size:38
Alignment explanation
Indices: 5224474--5224590 Score: 96
Period size: 38 Copynumber: 3.1 Consensus size: 38
5224464 TAAAAAATGT
*
5224474 ATTTCAAAATAATATAAATATATATTTTTTAATTTAAA
1 ATTTTAAAATAATATAAATATATATTTTTTAATTTAAA
* * * ** *
5224512 ATTTTAAAAT-ATAGT-GATATATTATCTTATAAAAT-AG
1 ATTTTAAAATAATA-TAAATATA-TATTTTTTAATTTAAA
**
5224549 ATTTTCTAATAATATAAATATATATCTTTTTAAATTTAAA
1 ATTTTAAAATAATATAAATATATAT-TTTTT-AATTTAAA
5224589 AT
1 AT
5224591 CTCAAATATA
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
37 21 0.37
38 30 0.53
39 3 0.05
40 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (38 bp):
ATTTTAAAATAATATAAATATATATTTTTTAATTTAAA
Found at i:5224536 original size:75 final size:76
Alignment explanation
Indices: 5224453--5224607 Score: 201
Period size: 75 Copynumber: 2.1 Consensus size: 76
5224443 TTTAATTTAA
*
5224453 ATATATTATTTTAAAAAAT-G-TATTTCAAAATAATATAAATATATAT-TTTTT-AATTTAAAAT
1 ATATATTATCTTAAAAAATAGAT-TTTC-AAATAATATAAATATATATCTTTTTAAATTTAAAA-
* *
5224514 TTTAAAATATAGTG
63 TCTAAAATATAATG
* *
5224528 ATATATTATCTTATAAAATAGATTTTCTAATAATATAAATATATATCTTTTTAAATTTAAAATCT
1 ATATATTATCTTAAAAAATAGATTTTCAAATAATATAAATATATATCTTTTTAAATTTAAAATCT
*
5224593 CAAATATAATG
66 AAAATATAATG
5224604 ATAT
1 ATAT
5224608 TATAAAATAC
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
75 35 0.50
76 25 0.36
77 10 0.14
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (76 bp):
ATATATTATCTTAAAAAATAGATTTTCAAATAATATAAATATATATCTTTTTAAATTTAAAATCT
AAAATATAATG
Found at i:5224646 original size:20 final size:20
Alignment explanation
Indices: 5224621--5224669 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
5224611 AAAATACATT
5224621 TTTTTAAAATATAACTTTCA
1 TTTTTAAAATATAACTTTCA
* *
5224641 TTTTT-AAGTATAACTTTTA
1 TTTTTAAAATATAACTTTCA
5224660 TTTTTAAAAT
1 TTTTTAAAAT
5224670 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTAAAATATAACTTTCA
Done.