Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 5 of 185
Found at i:1465373 original size:20 final size:19
Alignment explanation
Indices: 1465329--1465373 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1465319 TGAGAAAACA
1465329 ATAAAAACTAAAATAATAT
1 ATAAAAACTAAAATAATAT
* *
1465348 ACAAAAACTAAAA-AATGT
1 ATAAAAACTAAAATAATAT
1465366 ATATAAAA
1 ATA-AAAA
1465374 TTAACTGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAACTAAAATAATAT
Found at i:1479124 original size:5 final size:5
Alignment explanation
Indices: 1479116--1479145 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1479106 AATCAAATCA
1479116 AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT
1479146 CATGCAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:1482416 original size:5 final size:5
Alignment explanation
Indices: 1482406--1482438 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
1482396 GCTGTAACCC
1482406 TCCTA TCCTA TCCTA TCCTA TCCTA TCCTA TCC
1 TCCTA TCCTA TCCTA TCCTA TCCTA TCCTA TCC
1482439 CTTCCTCTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.39
Consensus pattern (5 bp):
TCCTA
Found at i:1482793 original size:45 final size:44
Alignment explanation
Indices: 1482724--1482814 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 44
1482714 AGATTAGAGG
* *
1482724 TGTATTGGAATAGAGATGTAATAGTAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGACGTAATAGT-AATC-ATGTGTTTGGTTGAA
* *
1482769 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGACGTAATAGTAATCATGTGTTTGGTTGAA
1482813 TG
1 TG
1482815 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.44
45 22 0.54
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.37
Consensus pattern (44 bp):
TGTAATGGAATAGAGACGTAATAGTAATCATGTGTTTGGTTGAA
Found at i:1482996 original size:16 final size:16
Alignment explanation
Indices: 1482959--1483000 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1482949 TTAATCATAT
*
1482959 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
1482975 TT-AAATATATTATAA
1 TTAAAATATATTATAA
1482990 TTAAAATATAT
1 TTAAAATATAT
1483001 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:1483007 original size:14 final size:15
Alignment explanation
Indices: 1482968--1483009 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1482958 TTTAAACATA
*
1482968 ATTATTATTAAATAT
1 ATTATAATTAAATAT
1482983 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
1482997 A-TATAATTTAATA
1 ATTATAATTAAATA
1483010 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:1483126 original size:14 final size:15
Alignment explanation
Indices: 1483077--1483128 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1483067 TATAAATATA
1483077 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
1483092 TATTAAATATATTAT
1 AATTAAATATATTAT
1483107 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
1483120 AATTTAATA
1 AATTAAATA
1483129 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:1483173 original size:119 final size:119
Alignment explanation
Indices: 1482962--1483190 Score: 458
Period size: 119 Copynumber: 1.9 Consensus size: 119
1482952 ATCATATTTA
1482962 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1483027 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATATAAATT
1483081 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1483146 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
1483191 TTTACTCAAA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 110 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (119 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATATAAATT
Found at i:1487038 original size:4 final size:4
Alignment explanation
Indices: 1487029--1487123 Score: 176
Period size: 4 Copynumber: 24.2 Consensus size: 4
1487019 TTTTTTAAAA
1487029 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1487075 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1487123 A
1 A
1487124 TCACACGTTA
Statistics
Matches: 89, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.02
4 87 0.98
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1488450 original size:17 final size:17
Alignment explanation
Indices: 1488425--1488474 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
1488415 TATCAGATTT
1488425 TGATACTCATATCTTTC
1 TGATACTCATATCTTTC
*
1488442 TGATGCTCATATCTTTC
1 TGATACTCATATCTTTC
1488459 TGATACTCATATCTTT
1 TGATACTCATATCTTT
1488475 GACTTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.48
Consensus pattern (17 bp):
TGATACTCATATCTTTC
Found at i:1494275 original size:48 final size:48
Alignment explanation
Indices: 1494217--1494311 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
1494207 AGAAGCCGAG
1494217 GCAACGAGGAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGTC
1 GCAACGAGGAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGTC
1494265 GCAACGAGGAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGT
1 GCAACGAGGAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGT
1494312 TGCGAGAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (48 bp):
GCAACGAGGAAGTTTCAAGGTGAATCAAGTCAGTGTCATCCAGAAGTC
Found at i:1495409 original size:3 final size:3
Alignment explanation
Indices: 1495401--1495425 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1495391 ATAAGTGATA
1495401 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1495426 AAAGGTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1495648 original size:31 final size:31
Alignment explanation
Indices: 1495613--1495707 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 31
1495603 AGGTAATTGC
1495613 TTATTTGACTTTTTAATTTTACAAAAAATAA
1 TTATTTGACTTTTTAATTTTACAAAAAATAA
* * *** **
1495644 TTATTTTA-GTTTT--TTTT--AGGTAATGGC
1 TTATTTGACTTTTTAATTTTACAAAAAAT-AA
1495671 TTATTTGACTTTTTAATTTTACAAAAAATAA
1 TTATTTGACTTTTTAATTTTACAAAAAATAA
1495702 TTATTT
1 TTATTT
1495708 TAGTTTTATA
Statistics
Matches: 44, Mismatches: 14, Indels: 12
0.63 0.20 0.17
Matches are distributed among these distances:
26 4 0.09
27 7 0.16
28 8 0.18
30 8 0.18
31 13 0.30
32 4 0.09
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (31 bp):
TTATTTGACTTTTTAATTTTACAAAAAATAA
Found at i:1495657 original size:58 final size:58
Alignment explanation
Indices: 1495593--1495714 Score: 235
Period size: 58 Copynumber: 2.1 Consensus size: 58
1495583 CTTAAAAGAG
*
1495593 AGTTTTTTTTAGGTAATTGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
1 AGTTTTTTTTAGGTAATGGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
1495651 AGTTTTTTTTAGGTAATGGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
1 AGTTTTTTTTAGGTAATGGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
1495709 AGTTTT
1 AGTTTT
1495715 ATATTTAATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (58 bp):
AGTTTTTTTTAGGTAATGGCTTATTTGACTTTTTAATTTTACAAAAAATAATTATTTT
Found at i:1497201 original size:6 final size:6
Alignment explanation
Indices: 1497190--1497214 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1497180 TTTAGTTACC
1497190 TAGTGA TAGTGA TAGTGA TAGTGA T
1 TAGTGA TAGTGA TAGTGA TAGTGA T
1497215 TGTGTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TAGTGA
Found at i:1497724 original size:31 final size:31
Alignment explanation
Indices: 1497686--1497745 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1497676 TTGGTCACTG
*
1497686 AACTATTCGAAAGTTTTCATTTAAATCACAT
1 AACTATTCAAAAGTTTTCATTTAAATCACAT
* *
1497717 AACTATTCAAAAGTTTTTATTTAAGTCAC
1 AACTATTCAAAAGTTTTCATTTAAATCAC
1497746 TAAGTTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAATCACAT
Found at i:1507104 original size:8 final size:8
Alignment explanation
Indices: 1507093--1507146 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
1507083 ATGTTTTAAA
1507093 TATATTAT
1 TATATTAT
1507101 TATATTAT
1 TATATTAT
*
1507109 TTTATTAT
1 TATATTAT
* *
1507117 AAAATATAT
1 TATAT-TAT
1507126 TATATTATAT
1 TATA-T-TAT
1507136 TATATTAT
1 TATATTAT
1507144 TAT
1 TAT
1507147 GTAAAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
8 23 0.61
9 6 0.16
10 9 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATTAT
Found at i:1507108 original size:5 final size:5
Alignment explanation
Indices: 1507098--1507143 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
1507088 TTAAATATAT
*
1507098 TATTA TATTA T-TT- TATTA TAAAATA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA T--ATTA TATTA TATTA TATTA TATTA T
1507144 TATGTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 26 0.74
7 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:1507132 original size:30 final size:28
Alignment explanation
Indices: 1507090--1507146 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
1507080 TTTATGTTTT
*
1507090 AAATATATTATTATATTATTTTATTATA
1 AAATATATTATTATATTATATTATTATA
1507118 AAATATATTATATTATATTATATTATTAT
1 AAATATA-T-TATTATATTATATTATTAT
1507147 GTAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.27
29 1 0.04
30 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AAATATATTATTATATTATATTATTATA
Found at i:1508430 original size:39 final size:38
Alignment explanation
Indices: 1508377--1508517 Score: 228
Period size: 39 Copynumber: 3.6 Consensus size: 38
1508367 CAGGCACTTA
* *
1508377 TGTGCCGACTACTGTTACTGTTACCGATTCAGCACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGATTC-GCACTTTG
1508416 TGTGTCGAATACTGTTACTGTTACCGATTCGGCACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGATTC-GCACTTTG
1508455 TGTGTCGAATACTGTTACTGTTACCGATTCGACACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGATTCG-CACTTTG
*
1508494 TGTGTCGAATACTGTTACCGTTAC
1 TGTGTCGAATACTGTTACTGTTAC
1508518 TAATTACTGT
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
38 1 0.01
39 96 0.99
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (38 bp):
TGTGTCGAATACTGTTACTGTTACCGATTCGCACTTTG
Found at i:1511349 original size:25 final size:23
Alignment explanation
Indices: 1511290--1511365 Score: 61
Period size: 25 Copynumber: 3.3 Consensus size: 23
1511280 AAATAAATGA
*
1511290 AAGAAAAA-GA-ATAGAA-AAAG
1 AAGAAAAAGGAGAAAGAACAAAG
* *
1511310 AAGAACAAAGTAGAACGAAACAAAG
1 AAGAA-AAAGGAGAAAG-AACAAAG
*
1511335 AAGAAAAAGAGAGAAAGAAGAAAG
1 AAGAAAAAG-GAGAAAGAACAAAG
1511359 -AGAAAAA
1 AAGAAAAA
1511366 AATTAGGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 5 0.11
21 3 0.07
22 1 0.02
23 9 0.20
24 12 0.27
25 14 0.32
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.03
Consensus pattern (23 bp):
AAGAAAAAGGAGAAAGAACAAAG
Found at i:1512028 original size:41 final size:37
Alignment explanation
Indices: 1511983--1512072 Score: 101
Period size: 41 Copynumber: 2.3 Consensus size: 37
1511973 CTTCAAGTCA
*
1511983 ATGAGACACTGGGTG-TCAATTTACTACTTCGGATTAATTCG
1 ATGAGACACTGGGTGCT-AA-TT--TACTTCGGATTAACT-G
* *
1512024 ATGAGATACTGGGTGCTAATTTACTTCGGTTTAACTG
1 ATGAGACACTGGGTGCTAATTTACTTCGGATTAACTG
1512061 ATGAGACACTGG
1 ATGAGACACTGG
1512073 AAATCAACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
37 12 0.27
38 13 0.30
40 2 0.05
41 16 0.36
42 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (37 bp):
ATGAGACACTGGGTGCTAATTTACTTCGGATTAACTG
Found at i:1514053 original size:19 final size:20
Alignment explanation
Indices: 1514002--1514053 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1513992 CCAATTACAT
1514002 TATATAACCAATTTTCATATCA
1 TATATAACCAA--TTCATATCA
* *
1514024 T-TATTATCAATTCATAT-A
1 TATATAACCAATTCATATCA
1514042 TATATAACCAAT
1 TATATAACCAAT
1514054 ACCACATAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 2 0.08
19 15 0.60
21 7 0.28
22 1 0.04
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATAACCAATTCATATCA
Found at i:1515314 original size:6 final size:6
Alignment explanation
Indices: 1515282--1515311 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1515272 TAACCGAACC
*
1515282 TGGCAA TGGCAA TGGCAA TGGCAA AGGCAA
1 TGGCAA TGGCAA TGGCAA TGGCAA TGGCAA
1515312 AGGAAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.33, T:0.13
Consensus pattern (6 bp):
TGGCAA
Found at i:1524697 original size:6 final size:6
Alignment explanation
Indices: 1524680--1524715 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
1524670 AACTTAATCT
1524680 TCTGCTC TCTGCC TCTGCC TCTGCC TCTGCC TCTGC
1 TCTGC-C TCTGCC TCTGCC TCTGCC TCTGCC TCTGC
1524716 GTCTCATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.00, C:0.47, G:0.17, T:0.36
Consensus pattern (6 bp):
TCTGCC
Found at i:1527934 original size:18 final size:18
Alignment explanation
Indices: 1527911--1527954 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1527901 ATTACTTCTC
*
1527911 AAAAGTATTTTTGGGACA
1 AAAAGTATTTTTGAGACA
* *
1527929 AAAAGTACTTTTGAGATA
1 AAAAGTATTTTTGAGACA
1527947 AAAA-TATT
1 AAAAGTATT
1527955 GCTAAACAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (18 bp):
AAAAGTATTTTTGAGACA
Found at i:1540127 original size:19 final size:19
Alignment explanation
Indices: 1540105--1540144 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1540095 ATTTTTTTTG
*
1540105 AACAATATTAA-TATTAATA
1 AACAATAATAATTA-TAATA
1540124 AACAATAATAATTATAATA
1 AACAATAATAATTATAATA
1540143 AA
1 AA
1540145 TAAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AACAATAATAATTATAATA
Found at i:1541593 original size:7 final size:7
Alignment explanation
Indices: 1541581--1541622 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
1541571 CACCCCACTT
*
1541581 CCATATA
1 CCATAGA
*
1541588 CCATATA
1 CCATAGA
1541595 CCATAGA
1 CCATAGA
1541602 CCATAGA
1 CCATAGA
1541609 CCATAGA
1 CCATAGA
1541616 CCATAGA
1 CCATAGA
1541623 TCCACCTTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.43, C:0.29, G:0.10, T:0.19
Consensus pattern (7 bp):
CCATAGA
Found at i:1553143 original size:11 final size:11
Alignment explanation
Indices: 1553127--1553151 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1553117 CTCCAAAATT
1553127 ATTATTTTAAA
1 ATTATTTTAAA
1553138 ATTATTTTAAA
1 ATTATTTTAAA
1553149 ATT
1 ATT
1553152 TTAACTTTAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTTTAAA
Found at i:1553172 original size:21 final size:20
Alignment explanation
Indices: 1553142--1553191 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1553132 TTTAAAATTA
1553142 TTTTAAAA-TTTTAACTTTATT
1 TTTTAAAATTTTTAA-TTT-TT
*
1553163 TTTTAGAATTTTTAATTTTT
1 TTTTAAAATTTTTAATTTTT
1553183 TTTTAAAAT
1 TTTTAAAAT
1553192 ATATATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 10 0.38
21 10 0.38
22 6 0.23
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTAAAATTTTTAATTTTT
Found at i:1553186 original size:22 final size:21
Alignment explanation
Indices: 1553142--1553191 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1553132 TTTAAAATTA
1553142 TTTTAAAATTTTAACTTTATT
1 TTTTAAAATTTTAACTTTATT
*
1553163 TTTTAGAATTTTTAA-TTT-TT
1 TTTTA-AAATTTTAACTTTATT
1553183 TTTTAAAAT
1 TTTTAAAAT
1553192 ATATATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 3 0.12
20 7 0.27
21 8 0.31
22 8 0.31
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTAAAATTTTAACTTTATT
Found at i:1553206 original size:18 final size:18
Alignment explanation
Indices: 1553183--1553219 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1553173 TTTAATTTTT
1553183 TTTTAAAATATATATAAA
1 TTTTAAAATATATATAAA
* *
1553201 TTTTAAAATTTTTATAAA
1 TTTTAAAATATATATAAA
1553219 T
1 T
1553220 ATTTTGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAATATATATAAA
Found at i:1553216 original size:20 final size:19
Alignment explanation
Indices: 1553195--1553233 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1553185 TTAAAATATA
*
1553195 TATAAAT-TTTAAAATTTT
1 TATAAATATTTTAAATTTT
*
1553213 TATAAATATTTTGAATTTT
1 TATAAATATTTTAAATTTT
1553232 TA
1 TA
1553234 AAGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:1556709 original size:22 final size:22
Alignment explanation
Indices: 1556679--1556721 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1556669 ACACCAAAAC
* *
1556679 AGGCATTTAGTGGCGCTTTTTT
1 AGGCATTTAGCGGCACTTTTTT
*
1556701 AGGCCTTTAGCGGCACTTTTT
1 AGGCATTTAGCGGCACTTTTT
1556722 AGCGCCACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCATTTAGCGGCACTTTTTT
Found at i:1556859 original size:43 final size:43
Alignment explanation
Indices: 1556810--1557020 Score: 257
Period size: 43 Copynumber: 4.9 Consensus size: 43
1556800 TAAAGACCCT
1556810 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAC
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAC
* * *
1556853 GACCTTTAACGGTGCTTTTTCCACAAACGCCGCTAAAGACCAC
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAC
* * * *
1556896 GACCTTTAACGGCGCTTTTCCCTACAAACGCCGCTAAAGACCGC
1 GACCTTTAGCGGCGCTTTTTCC-ACAAACGCCGCTAAAAACCAC
1556940 GACCTTTAGCGGCG-TTTTTCCACAAACGCCGCTAAAGAA-CA-
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA-AACCAC
* * * ** * *
1556981 AACCTTTAGCGACGCTTCTGGCAAAAACGCCACTAAAAAC
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAAC
1557021 ATAATCTTTA
Statistics
Matches: 147, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
41 14 0.10
42 33 0.22
43 67 0.46
44 33 0.22
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (43 bp):
GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAC
Found at i:1556943 original size:44 final size:43
Alignment explanation
Indices: 1556798--1556977 Score: 274
Period size: 43 Copynumber: 4.2 Consensus size: 43
1556788 GCTAACTTTA
*
1556798 GCTAAAGACC-CTGACCTTTAGCGGCGCTTTTTCCACAAACGCC
1 GCTAAAGACCAC-GACCTTTAACGGCGCTTTTTCCACAAACGCC
* *
1556841 GCTAAAAACCACGACCTTTAACGGTGCTTTTTCCACAAACGCC
1 GCTAAAGACCACGACCTTTAACGGCGCTTTTTCCACAAACGCC
*
1556884 GCTAAAGACCACGACCTTTAACGGCGCTTTTCCCTACAAACGCC
1 GCTAAAGACCACGACCTTTAACGGCGCTTTTTCC-ACAAACGCC
* *
1556928 GCTAAAGACCGCGACCTTTAGCGGCG-TTTTTCCACAAACGCC
1 GCTAAAGACCACGACCTTTAACGGCGCTTTTTCCACAAACGCC
1556970 GCTAAAGA
1 GCTAAAGA
1556978 ACAAACCTTT
Statistics
Matches: 126, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
42 17 0.13
43 75 0.60
44 34 0.27
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (43 bp):
GCTAAAGACCACGACCTTTAACGGCGCTTTTTCCACAAACGCC
Found at i:1561605 original size:20 final size:21
Alignment explanation
Indices: 1561580--1561620 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1561570 AACTCTTAAC
*
1561580 CTCT-AACCCCCAACCCCTAA
1 CTCTAAACCCCAAACCCCTAA
1561600 CTCTAAACCCCAAACCCCTAA
1 CTCTAAACCCCAAACCCCTAA
1561621 ACCTTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.34, C:0.51, G:0.00, T:0.15
Consensus pattern (21 bp):
CTCTAAACCCCAAACCCCTAA
Found at i:1562323 original size:39 final size:39
Alignment explanation
Indices: 1562227--1562363 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 39
1562217 TGGGTTTATG
* * * *
1562227 TTTTTAGCGGCGTTTTTCGAAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGCTTTTAG-AAAAGCGCCGCTAATGTTCA
* * *
1562267 TTTTTGGCTGCGCTTTTAGGAAAGCGCCGCTAATGTTCA
1 TTTTTAGCGGCGCTTTTAGAAAAGCGCCGCTAATGTTCA
* ** * *
1562306 GTCTTTAGCGGCG-TTTTATTTAAAGCGCCGCTAATACTTGA
1 -TTTTTAGCGGCGCTTTTA-GAAAAGCGCCGCTAAT-GTTCA
*
1562347 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGCTTTT
1562364 TGTCCAAACG
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
39 22 0.28
40 49 0.63
41 7 0.09
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGCTTTTAGAAAAGCGCCGCTAATGTTCA
Found at i:1570730 original size:21 final size:21
Alignment explanation
Indices: 1570689--1570731 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1570679 AATAAAGTAG
*
1570689 ATTATATACTATTTTTATAGT
1 ATTATATACTATATTTATAGT
*
1570710 ATTATATATTATGATTT-TAGT
1 ATTATATACTAT-ATTTATAGT
1570731 A
1 A
1570732 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTATATACTATATTTATAGT
Found at i:1571067 original size:16 final size:16
Alignment explanation
Indices: 1571043--1571096 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1571033 TAAATTACTG
*
1571043 ATTATAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
1571059 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
1571075 ATTACA-CTCCTATTCC
1 ATTACAGCT-CTATTCC
1571091 ATTACA
1 ATTACA
1571097 ATGAAACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 2 0.06
16 32 0.94
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:1572496 original size:31 final size:32
Alignment explanation
Indices: 1572418--1572497 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
1572408 ACAAGTTTCA
1572418 AAAT-TATGCAT-AAACTTTGATTCAATGCTC
1 AAATATATGCATGAAACTTTGATTCAATGCTC
* * *
1572448 AATTATATACATG-AACTTTGA-TC-GTGGCTC
1 AAATATATGCATGAAACTTTGATTCAAT-GCTC
1572478 AAATATATGCATGAAACTTT
1 AAATATATGCATGAAACTTT
1572498 TATTTTGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
29 1 0.02
30 20 0.49
31 20 0.49
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (32 bp):
AAATATATGCATGAAACTTTGATTCAATGCTC
Found at i:1575841 original size:34 final size:35
Alignment explanation
Indices: 1575783--1575849 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
1575773 CAAACACCAG
1575783 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1575818 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
1575850 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1576287 original size:19 final size:20
Alignment explanation
Indices: 1576246--1576284 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1576236 TTTAATCCTT
1576246 TTAAAATGATAAAAATATAA
1 TTAAAATGATAAAAATATAA
*
1576266 TTAAAATGATAAAATTATA
1 TTAAAATGATAAAAATATA
1576285 TTATTACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
TTAAAATGATAAAAATATAA
Found at i:1582162 original size:9 final size:9
Alignment explanation
Indices: 1582131--1582273 Score: 57
Period size: 9 Copynumber: 15.6 Consensus size: 9
1582121 TATAAAAAAA
1582131 TTATAATTT
1 TTATAATTT
*
1582140 CTTA-GATTT
1 -TTATAATTT
1582149 ATTATAATTT
1 -TTATAATTT
*
1582159 TTATAAGTTA
1 TTATAA-TTT
*
1582169 ATATCAATTT
1 TTAT-AATTT
*
1582179 TCAT-A-TT
1 TTATAATTT
*
1582186 TT-TAATAT
1 TTATAATTT
1582194 TTA-ATATTT
1 TTATA-ATTT
1582203 TTAT--TTT
1 TTATAATTT
1582210 TTAATAATTT
1 TT-ATAATTT
* *
1582220 TTTTGATTT
1 TTATAATTT
*
1582229 TTCATAAATT
1 TT-ATAATTT
*
1582239 TTATGATTT
1 TTATAATTT
1582248 TTATAACATTT
1 TTAT-A-ATTT
*
1582259 TTAATCATTT
1 TT-ATAATTT
1582269 TTATA
1 TTATA
1582274 GGAAAAGTAT
Statistics
Matches: 97, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
6 1 0.01
7 9 0.09
8 7 0.07
9 37 0.38
10 33 0.34
11 8 0.08
12 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (9 bp):
TTATAATTT
Found at i:1582202 original size:16 final size:16
Alignment explanation
Indices: 1582181--1582221 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1582171 ATCAATTTTC
1582181 ATATTTTTAATATTTA
1 ATATTTTTAATATTTA
* *
1582197 ATATTTTTATTTTTTA
1 ATATTTTTAATATTTA
1582213 ATAATTTTT
1 AT-ATTTTT
1582222 TTGATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATTTTTAATATTTA
Found at i:1582228 original size:20 final size:20
Alignment explanation
Indices: 1582195--1582249 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
1582185 TTTTAATATT
*
1582195 TAATATTTTT-ATTTTTTAA
1 TAATTTTTTTGATTTTTTAA
*
1582214 TAATTTTTTTGA-TTTTTCA
1 TAATTTTTTTGATTTTTTAA
* *
1582233 TAAATTTTATGATTTTT
1 TAATTTTTTTGATTTTT
1582250 ATAACATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TAATTTTTTTGATTTTTTAA
Found at i:1582235 original size:19 final size:18
Alignment explanation
Indices: 1582207--1582273 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
1582197 ATATTTTTAT
* *
1582207 TTTTTAATAATTTTTTTGA
1 TTTTT-ATAAATTTTATGA
1582226 TTTTTCATAAATTTTATGA
1 TTTTT-ATAAATTTTATGA
*
1582245 TTTTTATAACATTTTTAATCA
1 TTTTTATAA-A-TTTT-ATGA
1582266 TTTTTATA
1 TTTTTATA
1582274 GGAAAAGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.10
19 22 0.54
20 4 0.10
21 11 0.27
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTTATAAATTTTATGA
Found at i:1584508 original size:34 final size:34
Alignment explanation
Indices: 1584442--1584524 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
1584432 ATAAATGTGC
*
1584442 AAATATATGTATATAAAAATTATAGAATATAAAA
1 AAATATATGTATATAAAAATTATAGAAAATAAAA
* * *
1584476 AAATATATGTATGTATATATTCAT-GAAAATAAAA
1 AAATATATGTATATAAAAATT-ATAGAAAATAAAA
* * *
1584510 ATATGTATATATATA
1 AAATATATGTATATA
1584525 GATATAGATA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 38 0.95
35 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (34 bp):
AAATATATGTATATAAAAATTATAGAAAATAAAA
Found at i:1584752 original size:15 final size:16
Alignment explanation
Indices: 1584722--1584770 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1584712 AAAATAATAG
*
1584722 TAATAATATTTAAAAA
1 TAATAATATGTAAAAA
1584738 TAATAATA-GTAAAAA
1 TAATAATATGTAAAAA
* *
1584753 TAATGATAATGTTAAAA
1 TAATAAT-ATGTAAAAA
1584770 T
1 T
1584771 TAATTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 12 0.43
16 9 0.32
17 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TAATAATATGTAAAAA
Found at i:1589971 original size:14 final size:14
Alignment explanation
Indices: 1589940--1589977 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1589930 TTATTTACTA
*
1589940 TTATT-TTACTATT
1 TTATTGTTATTATT
*
1589953 ATATTGTTATTATT
1 TTATTGTTATTATT
1589967 TTATTGTTATT
1 TTATTGTTATT
1589978 GTCTAGATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (14 bp):
TTATTGTTATTATT
Found at i:1592817 original size:18 final size:18
Alignment explanation
Indices: 1592794--1592833 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1592784 ATGACTTTTA
*
1592794 AATAATTTTTTATTAAGT
1 AATAATATTTTATTAAGT
*
1592812 AATAATATTTTATTAATT
1 AATAATATTTTATTAAGT
1592830 AATA
1 AATA
1592834 TTATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AATAATATTTTATTAAGT
Found at i:1610353 original size:34 final size:34
Alignment explanation
Indices: 1610314--1610383 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1610304 AAAAAAACTC
1610314 CTAATTATTTTAATATGGAAATTCGGCCAAGGGT
1 CTAATTATTTTAATATGGAAATTCGGCCAAGGGT
1610348 CTAATTATTTTAATATGGAAATTCGGCCAAGGGT
1 CTAATTATTTTAATATGGAAATTCGGCCAAGGGT
1610382 CT
1 CT
1610384 TTTATTTGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (34 bp):
CTAATTATTTTAATATGGAAATTCGGCCAAGGGT
Found at i:1614693 original size:13 final size:13
Alignment explanation
Indices: 1614675--1614708 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1614665 TCAAAATTTG
*
1614675 AAAATAATAATAA
1 AAAATAAAAATAA
1614688 AAAATAAAAATAA
1 AAAATAAAAATAA
*
1614701 AAAGTAAA
1 AAAATAAA
1614709 TAGTGATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:1615023 original size:12 final size:12
Alignment explanation
Indices: 1615008--1615092 Score: 89
Period size: 12 Copynumber: 6.8 Consensus size: 12
1614998 AGGTATAAAT
*
1615008 ATAATGATAGTA
1 ATAATAATAGTA
1615020 ATAATAATAGTA
1 ATAATAATAGTA
* *
1615032 GTAATAATACTA
1 ATAATAATAGTA
*
1615044 ACAATAATAGTAAA
1 ATAATAATAGT--A
1615058 GATAATAATAGTAA
1 -ATAATAATAGT-A
*
1615072 ATAATAATAATA
1 ATAATAATAGTA
1615084 ATAATAATA
1 ATAATAATA
1615093 AAATAAACAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
12 39 0.63
13 10 0.16
14 3 0.05
15 10 0.16
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:1615110 original size:3 final size:3
Alignment explanation
Indices: 1615008--1615098 Score: 78
Period size: 3 Copynumber: 30.3 Consensus size: 3
1614998 AGGTATAAAT
* * * * * * *
1615008 ATA ATG ATA GTA ATA ATA ATA GTA GTA ATA ATA CTA ACA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1615056 A-A GATA ATA ATA GTAA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA -ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1615099 ACAAAATAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
2 3 0.04
3 64 0.91
4 3 0.04
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1616990 original size:44 final size:43
Alignment explanation
Indices: 1616941--1617139 Score: 166
Period size: 44 Copynumber: 4.5 Consensus size: 43
1616931 ATCTACTCTG
* * * *
1616941 CTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTT-CTTCAATCTGCTCCA
* * ** * * *
1616985 CTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
* **
1617028 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATC-CTTTCTTCAATCTGCTCCA
*** *
1617072 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTTGGTCTGTTCCA
1 CTGTAACCTCAGGGAGATAAGATCCT----TTCTTCAATCTGCTCCA
*
1617118 CTGTAATCTCAGGGAGATAAGA
1 CTGTAACCTCAGGGAGATAAGA
1617140 CCTGTATAAT
Statistics
Matches: 123, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
42 2 0.02
43 30 0.24
44 59 0.48
46 32 0.26
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
Found at i:1617045 original size:87 final size:87
Alignment explanation
Indices: 1616929--1617139 Score: 219
Period size: 87 Copynumber: 2.4 Consensus size: 87
1616919 AGACTTGATG
* * * * * * * *
1616929 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC-TGACTTCAATCCGCTCCACTGTAACC
* *
1616993 TCAGGGAGATAGGATAGTG-TCTT
65 TCAGGGAGATAAGAT-CTGATCTT
* *
1617016 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
1617081 CAGGGAGATAAGATCTGAAATTCTT
66 CAGGGAGATAAGATCTG--A-TCTT
* * * *
1617106 TGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1617140 CCTGTATAAT
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
86 2 0.02
87 66 0.64
88 1 0.01
90 34 0.33
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (87 bp):
CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAAGATCTGATCTT
Found at i:1638430 original size:12 final size:13
Alignment explanation
Indices: 1638413--1638441 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1638403 ATCATGAATA
1638413 AATTTTAAAAAT-
1 AATTTTAAAAATC
1638425 AATTTTAAAAATC
1 AATTTTAAAAATC
1638438 AATT
1 AATT
1638442 AAATTATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTTTAAAAATC
Found at i:1643714 original size:11 final size:11
Alignment explanation
Indices: 1643698--1643723 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1643688 AAAAAAATAA
1643698 AAAAGTATTTT
1 AAAAGTATTTT
1643709 AAAAGTATTTT
1 AAAAGTATTTT
1643720 AAAA
1 AAAA
1643724 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:1643858 original size:13 final size:13
Alignment explanation
Indices: 1643840--1643864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1643830 TTTTTGCTCA
1643840 AGCCTATATTTTG
1 AGCCTATATTTTG
1643853 AGCCTATATTTT
1 AGCCTATATTTT
1643865 TACCCGAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
AGCCTATATTTTG
Found at i:1644545 original size:29 final size:31
Alignment explanation
Indices: 1644512--1644569 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
1644502 CCTTTTTACT
1644512 TTTCCCT-CAAAACTTTTACTCCT-TCCCAC
1 TTTCCCTCCAAAACTTTTACTCCTCTCCCAC
1644541 TTTCCCTCCAAAACTTTTACTCCTCTCCC
1 TTTCCCTCCAAAACTTTTACTCCTCTCCC
1644570 CTCCCAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 7 0.26
30 16 0.59
31 4 0.15
ACGTcount: A:0.19, C:0.43, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTCCCTCCAAAACTTTTACTCCTCTCCCAC
Found at i:1653219 original size:19 final size:20
Alignment explanation
Indices: 1653186--1653229 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
1653176 TAATGTTTAT
1653186 TAAAAATTAGAAAAAGATTA
1 TAAAAATTAGAAAAAGATTA
*
1653206 TAAAAATT-GTAAAAGATTA
1 TAAAAATTAGAAAAAGATTA
1653225 TAAAA
1 TAAAA
1653230 TTTTATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (20 bp):
TAAAAATTAGAAAAAGATTA
Found at i:1653228 original size:10 final size:10
Alignment explanation
Indices: 1653197--1653239 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
1653187 AAAAATTAGA
1653197 AAAAGATTAT
1 AAAAGATTAT
*
1653207 AAAA-ATTGT
1 AAAAGATTAT
1653216 AAAAGATTAT
1 AAAAGATTAT
**
1653226 AAAATTTTAT
1 AAAAGATTAT
1653236 AAAA
1 AAAA
1653240 TATATAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (10 bp):
AAAAGATTAT
Found at i:1653520 original size:19 final size:19
Alignment explanation
Indices: 1653487--1653538 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1653477 TAAAGGATGT
1653487 TTTTTTATGCA-TTTTATAA
1 TTTTTTATG-ATTTTTATAA
*
1653506 TTTTTTATGATTTTTTTAA
1 TTTTTTATGATTTTTATAA
**
1653525 AATTTTAT-ATTTTT
1 TTTTTTATGATTTTT
1653539 TATTAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTTTATGATTTTTATAA
Found at i:1653544 original size:20 final size:20
Alignment explanation
Indices: 1653515--1653562 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1653505 ATTTTTTATG
*
1653515 ATTTTT-TTAAAATTTTATA
1 ATTTTTATTAAAATTTAATA
* *
1653534 TTTTTTATTAAAGTTTAATA
1 ATTTTTATTAAAATTTAATA
1653554 ATTTTTATT
1 ATTTTTATT
1653563 GATTTTGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTTTATTAAAATTTAATA
Found at i:1653870 original size:87 final size:87
Alignment explanation
Indices: 1653718--1653925 Score: 249
Period size: 87 Copynumber: 2.4 Consensus size: 87
1653708 TGAATGCAAA
* * *
1653718 AAAAAAAAAAGCAAGGGCTTAATTGTTTTTTTTGAAAAAATTTGAGGGTCTTTTTATGCATTTTG
1 AAAAAAAAAAGCAGGGGCTTAATT-TTTTTTTT--AAAAATTTGAGGGCCTTTTGATGCATTTTG
* *
1653783 ACAA-TTTAAGTACTCAATTGAGTGC
63 A-AAGTTTAAGTACCCAATTAAGTGC
* *
1653808 AAAAAAAAAAGCAGGGGCTTAATTTTTTTTTT-TAAGTTTGAGGGCCCTTTTGATGCATTTTGAA
1 AAAAAAAAAAGCAGGGGCTTAATTTTTTTTTTAAAAATTTGAGGG-CCTTTTGATGCATTTTGAA
*
1653872 AGTTTAAGTGCCCAATTAAGTGC
65 AGTTTAAGTACCCAATTAAGTGC
* * * *
1653895 AAAACAAAGAGCAGAGTCTTAATTTTTTTTT
1 AAAAAAAAAAGCAGGGGCTTAATTTTTTTTT
1653926 AATTTGAAGG
Statistics
Matches: 104, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
86 12 0.12
87 61 0.59
89 8 0.08
90 23 0.22
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (87 bp):
AAAAAAAAAAGCAGGGGCTTAATTTTTTTTTTAAAAATTTGAGGGCCTTTTGATGCATTTTGAAA
GTTTAAGTACCCAATTAAGTGC
Found at i:1657764 original size:49 final size:49
Alignment explanation
Indices: 1657692--1657791 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
1657682 GTCTCAGCTA
1657692 AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
1 AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
* *
1657741 AATAGTTGTAATAGTCTAATCCAAAGAATAAAAGAAAGAGCTATTATGT
1 AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
1657790 AA
1 AA
1657792 GTGAACCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (49 bp):
AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
Found at i:1661016 original size:18 final size:18
Alignment explanation
Indices: 1660980--1661017 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1660970 ATGTACTTAA
*
1660980 TTTCTGTACTTTTATAAT
1 TTTCTGTACTTTGATAAT
1660998 TTTCTGTACATTTGA-AAT
1 TTTCTGTAC-TTTGATAAT
1661016 TT
1 TT
1661018 AGTATCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.58
Consensus pattern (18 bp):
TTTCTGTACTTTGATAAT
Found at i:1662962 original size:2 final size:2
Alignment explanation
Indices: 1662957--1662993 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1662947 TTACATCATT
1662957 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1662994 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1662998 original size:2 final size:2
Alignment explanation
Indices: 1662993--1663021 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1662983 TCTCTCTCTC
1662993 TA TA 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 TA TA T
1663022 TTCTATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1664070 original size:20 final size:20
Alignment explanation
Indices: 1664045--1664109 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
1664035 TTATAAATAG
* *
1664045 TTATAAAATTTATATATATT
1 TTATAAAATTTATAGAAATT
*
1664065 TTATAAAAATTATAGAAATT
1 TTATAAAATTTATAGAAATT
* *
1664085 TTAAAAAATTCTAAAGAATATT
1 TTATAAAATT-TATAGAA-ATT
1664107 TTA
1 TTA
1664110 ATTTGACATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 25 0.68
21 6 0.16
22 6 0.16
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (20 bp):
TTATAAAATTTATAGAAATT
Found at i:1664436 original size:28 final size:29
Alignment explanation
Indices: 1664384--1664438 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1664374 TTAACAAATT
* * *
1664384 AAAATATAATTAAAATTTTAGAAAATTAC
1 AAAATATAATTAAAAATATAAAAAATTAC
1664413 AAAATA-AATTAAAAATATAAAAAATT
1 AAAATATAATTAAAAATATAAAAAATT
1664439 GAAATAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATATAATTAAAAATATAAAAAATTAC
Found at i:1664553 original size:17 final size:17
Alignment explanation
Indices: 1664531--1664589 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1664521 AGTTTCTTTT
1664531 TTTTTTAATTTTTTGTA
1 TTTTTTAATTTTTTGTA
* *
1664548 TTTTTTAATTTTATGAA
1 TTTTTTAATTTTTTGTA
* *
1664565 TTTTCTT-CTTTTTTAT-
1 TTTT-TTAATTTTTTGTA
1664581 TTTTTTAAT
1 TTTTTTAAT
1664590 CTTAAATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 2 0.06
16 5 0.15
17 24 0.73
18 2 0.06
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTTTAATTTTTTGTA
Found at i:1666332 original size:25 final size:25
Alignment explanation
Indices: 1666304--1666352 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1666294 CAAACATGTA
* *
1666304 AACGAAAAGCTCTTTCGAGCCATAT
1 AACGAAAAGCTCATCCGAGCCATAT
**
1666329 AACGGGAAGCTCATCCGAGCCATA
1 AACGAAAAGCTCATCCGAGCCATA
1666353 ATTGGGAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (25 bp):
AACGAAAAGCTCATCCGAGCCATAT
Found at i:1666383 original size:24 final size:24
Alignment explanation
Indices: 1666319--1666383 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
1666309 AAAGCTCTTT
* *
1666319 CGAGCCATATAACGGGAAGCTCATC
1 CGAGCCA-ATATCGGGAAGCTCAAC
* * *
1666344 CGAGCC-ATAATTGGGAAGTTCAAG
1 CGAGCCAAT-ATCGGGAAGCTCAAC
1666368 CGAGCCAATATCGGGA
1 CGAGCCAATATCGGGA
1666384 TGGAAGCTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 2 0.06
24 22 0.69
25 8 0.25
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (24 bp):
CGAGCCAATATCGGGAAGCTCAAC
Found at i:1670082 original size:26 final size:28
Alignment explanation
Indices: 1670052--1670107 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
1670042 GTGTTTAAAA
*
1670052 ATAATATGAAAAT-AATAATGAAA-CAT
1 ATAATATGAAAATAAATAATAAAAGCAT
* *
1670078 ATAATTTGAAACTAAATAATAAAAGCAT
1 ATAATATGAAAATAAATAATAAAAGCAT
1670106 AT
1 AT
1670108 GAAATATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 9 0.36
28 5 0.20
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (28 bp):
ATAATATGAAAATAAATAATAAAAGCAT
Found at i:1671677 original size:17 final size:17
Alignment explanation
Indices: 1671624--1671673 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1671614 AATAAATAAA
*
1671624 AAATATATAAAAT-TATT
1 AAATAT-TAAAATAAATT
*
1671641 AAATATTAAAATAAAAT
1 AAATATTAAAATAAATT
*
1671658 AAATATTTAAA-AAATT
1 AAATATTAAAATAAATT
1671674 TAAAAAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATTAAAATAAATT
Found at i:1678960 original size:39 final size:39
Alignment explanation
Indices: 1678880--1678967 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
1678870 GAAAATTATA
* * * * *
1678880 TTTAATACAATAAAATATTTAATATATTTATTTATGTTT
1 TTTAATATAATAAAAAAATTAATATATTTATGTATGATT
*
1678919 TTTAATATAATAAAAAAATTATTATATTTATGTACT-ATT
1 TTTAATATAATAAAAAAATTAATATATTTATGTA-TGATT
1678958 TTTAATATAA
1 TTTAATATAA
1678968 ATACTTTGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 41 0.98
40 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (39 bp):
TTTAATATAATAAAAAAATTAATATATTTATGTATGATT
Found at i:1679485 original size:21 final size:22
Alignment explanation
Indices: 1679456--1679496 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1679446 TTTTAGCCTT
1679456 AAAAGAAAAAAATA-TATAATA
1 AAAAGAAAAAAATATTATAATA
* *
1679477 AAAATAAAATAATATTATAA
1 AAAAGAAAAAAATATTATAA
1679497 ATTATAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAGAAAAAAATATTATAATA
Found at i:1679708 original size:13 final size:13
Alignment explanation
Indices: 1679690--1679715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1679680 TATTCTATTT
1679690 TTTCAACGAAAAA
1 TTTCAACGAAAAA
1679703 TTTCAACGAAAAA
1 TTTCAACGAAAAA
1679716 GTGTAGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
TTTCAACGAAAAA
Found at i:1683371 original size:7 final size:7
Alignment explanation
Indices: 1683361--1683385 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1683351 CTTGTCAAGT
1683361 TTTGAAA
1 TTTGAAA
1683368 TTTGAAA
1 TTTGAAA
1683375 TTTGAAA
1 TTTGAAA
1683382 TTTG
1 TTTG
1683386 GGTTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (7 bp):
TTTGAAA
Found at i:1694938 original size:25 final size:25
Alignment explanation
Indices: 1694909--1694961 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1694899 AGGTAACGGT
1694909 GTTAATTTTTTAGTGTTTAATTCAG
1 GTTAATTTTTTAGTGTTTAATTCAG
1694934 GTTAATTTTTTAGTGTTTAATTCAG
1 GTTAATTTTTTAGTGTTTAATTCAG
1694959 GTT
1 GTT
1694962 TTAAGGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.23, C:0.04, G:0.17, T:0.57
Consensus pattern (25 bp):
GTTAATTTTTTAGTGTTTAATTCAG
Found at i:1695063 original size:16 final size:18
Alignment explanation
Indices: 1695031--1695063 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1695021 TGTTATAGAA
1695031 TAAATTTAGTGTTAATTG
1 TAAATTTAGTGTTAATTG
1695049 TAAATTT-GT-TTAATT
1 TAAATTTAGTGTTAATT
1695064 TTGTGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
TAAATTTAGTGTTAATTG
Found at i:1697953 original size:6 final size:6
Alignment explanation
Indices: 1697942--1697972 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1697932 TTATGGATGT
*
1697942 AATATA AATATA AATATA AATATA TATATA A
1 AATATA AATATA AATATA AATATA AATATA A
1697973 TTATTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:1700024 original size:31 final size:31
Alignment explanation
Indices: 1699986--1700048 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1699976 ATTTGATAAC
1699986 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1700017 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1700048 T
1 T
1700049 AAATTTGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (31 bp):
TTAGAATATTTGTTTTGTTAGTTAGAATAGT
Found at i:1705840 original size:14 final size:16
Alignment explanation
Indices: 1705821--1705853 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1705811 TTAAGTTAAA
1705821 ATAATA-TAAA-CTTT
1 ATAATATTAAACCTTT
1705835 ATAATATTAAACCTTT
1 ATAATATTAAACCTTT
1705851 ATA
1 ATA
1705854 TCTAATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 4 0.24
16 7 0.41
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATATTAAACCTTT
Found at i:1708426 original size:26 final size:26
Alignment explanation
Indices: 1708389--1708438 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1708379 GAATATTTTA
*
1708389 TTATTATCATATTATT-ATTAATTATT
1 TTATTATAATATT-TTAATTAATTATT
1708415 TTATTATAATATTTTAATTAATTA
1 TTATTATAATATTTTAATTAATTA
1708439 AATTAAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATTATAATATTTTAATTAATTATT
Found at i:1708434 original size:14 final size:13
Alignment explanation
Indices: 1708380--1708430 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
1708370 TAATTGGTGG
1708380 AATATTTTATTAT
1 AATATTTTATTAT
* *
1708393 TATCATATTATTATT
1 AAT-ATTTTATTA-T
1708408 AATTATTTTATTAT
1 AA-TATTTTATTAT
1708422 AATATTTTA
1 AATATTTTA
1708431 ATTAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 9 0.29
14 11 0.35
15 10 0.32
16 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
AATATTTTATTAT
Found at i:1710476 original size:31 final size:31
Alignment explanation
Indices: 1710441--1710505 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1710431 AATATAATGT
*
1710441 AATATATATTAAAATTTATTATATTTTTT-AG
1 AATATATATGAAAATTTA-TATATTTTTTGAG
* * *
1710472 AATATTTATGAATATTTATATTTTTTTTGAG
1 AATATATATGAAAATTTATATATTTTTTGAG
1710503 AAT
1 AAT
1710506 TAAAATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 9 0.31
31 20 0.69
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (31 bp):
AATATATATGAAAATTTATATATTTTTTGAG
Found at i:1711321 original size:18 final size:19
Alignment explanation
Indices: 1711286--1711324 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1711276 AATAAACACC
1711286 AAAAAATTATTTTAAAAAT
1 AAAAAATTATTTTAAAAAT
1711305 AAAAAATTATTTTAAAAAT
1 AAAAAATTATTTTAAAAAT
1711324 A
1 A
1711325 TTTTAAAATT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAAATTATTTTAAAAAT
Found at i:1716779 original size:2 final size:2
Alignment explanation
Indices: 1716774--1716801 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1716764 TTTTATGCAG
1716774 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1716802 ATTGTTGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1721336 original size:191 final size:191
Alignment explanation
Indices: 1721012--1721396 Score: 770
Period size: 191 Copynumber: 2.0 Consensus size: 191
1721002 TCTTCACAAT
1721012 TTGTATGGAACTGATGAATGAAATGCTTGTATTATTATTCTTTTTAACTCTCATGTAATCCCTTT
1 TTGTATGGAACTGATGAATGAAATGCTTGTATTATTATTCTTTTTAACTCTCATGTAATCCCTTT
1721077 ATAAATCATCATTTATATTTCTTATTCAAAGTAATAGAATGATAATTTACAAGGTAGTTTTATCA
66 ATAAATCATCATTTATATTTCTTATTCAAAGTAATAGAATGATAATTTACAAGGTAGTTTTATCA
1721142 GGAAATTCCGTCCATTGTTGGTTATGGTGAACGTGCATCAACTTATCTTCACTTCAAACTC
131 GGAAATTCCGTCCATTGTTGGTTATGGTGAACGTGCATCAACTTATCTTCACTTCAAACTC
1721203 TTGTATGGAACTGATGAATGAAATGCTTGTATTATTATTCTTTTTAACTCTCATGTAATCCCTTT
1 TTGTATGGAACTGATGAATGAAATGCTTGTATTATTATTCTTTTTAACTCTCATGTAATCCCTTT
1721268 ATAAATCATCATTTATATTTCTTATTCAAAGTAATAGAATGATAATTTACAAGGTAGTTTTATCA
66 ATAAATCATCATTTATATTTCTTATTCAAAGTAATAGAATGATAATTTACAAGGTAGTTTTATCA
1721333 GGAAATTCCGTCCATTGTTGGTTATGGTGAACGTGCATCAACTTATCTTCACTTCAAACTC
131 GGAAATTCCGTCCATTGTTGGTTATGGTGAACGTGCATCAACTTATCTTCACTTCAAACTC
1721394 TTG
1 TTG
1721397 GTTTTTGTTA
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
191 194 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (191 bp):
TTGTATGGAACTGATGAATGAAATGCTTGTATTATTATTCTTTTTAACTCTCATGTAATCCCTTT
ATAAATCATCATTTATATTTCTTATTCAAAGTAATAGAATGATAATTTACAAGGTAGTTTTATCA
GGAAATTCCGTCCATTGTTGGTTATGGTGAACGTGCATCAACTTATCTTCACTTCAAACTC
Found at i:1725335 original size:24 final size:24
Alignment explanation
Indices: 1725308--1725359 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1725298 TTAGTAAGTC
*
1725308 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1725332 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1725356 AAAT
1 AAAT
1725360 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1726234 original size:14 final size:14
Alignment explanation
Indices: 1726215--1726249 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1726205 CCATCATCTC
1726215 TCTCTCTCTCTCTT
1 TCTCTCTCTCTCTT
*
1726229 TCTCTCACTCTCTT
1 TCTCTCTCTCTCTT
*
1726243 TTTCTCT
1 TCTCTCT
1726250 GTTCTCACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (14 bp):
TCTCTCTCTCTCTT
Found at i:1726234 original size:16 final size:16
Alignment explanation
Indices: 1726213--1726249 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1726203 GCCCATCATC
*
1726213 TCTCTCTCTCTCTCTT
1 TCTCTCACTCTCTCTT
*
1726229 TCTCTCACTCTCTTTT
1 TCTCTCACTCTCTCTT
1726245 TCTCT
1 TCTCT
1726250 GTTCTCACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.57
Consensus pattern (16 bp):
TCTCTCACTCTCTCTT
Found at i:1737885 original size:137 final size:137
Alignment explanation
Indices: 1737634--1737907 Score: 433
Period size: 137 Copynumber: 2.0 Consensus size: 137
1737624 CAAAGTAAAA
*
1737634 AAATACTCACTTTATACTACACTTGAGTTGTCCTGAAAACATGTCTAGATTGTTGTCCAAAAGTT
1 AAATACTCACTTTATACTACACTTGAGTTGTCCTGAAAACATGTCTAGATTGTGGTCCAAAAGTT
* * *
1737699 AGTCTAGACAACTGTTCAAACAATGGATTAAACACAATGACAAAACATGCAATTCAAGGAGCTAT
66 AGCCTAGACAACTGTTCAAACAAGGGATTAAACACAATGACAAAACATGCAATTCAAGAAGCTAT
1737764 CAAACAT
131 CAAACAT
* * * *
1737771 AAATGCTCACTTTATGCTACACTTGAGTTTTCCTGAAAGCATGTCTAGACTT-TGGTCCAAAAGT
1 AAATACTCACTTTATACTACACTTGAGTTGTCCTGAAAACATGTCTAGA-TTGTGGTCCAAAAGT
* * *
1737835 TAGCCTAGGCAACTGTTCAAACAAGGGATTAAACACAATGACAAATCATGCAGTTCAAGAAGCTA
65 TAGCCTAGACAACTGTTCAAACAAGGGATTAAACACAATGACAAAACATGCAATTCAAGAAGCTA
1737900 TCAAACAT
130 TCAAACAT
1737908 GAAGAAAAAC
Statistics
Matches: 125, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
137 123 0.98
138 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (137 bp):
AAATACTCACTTTATACTACACTTGAGTTGTCCTGAAAACATGTCTAGATTGTGGTCCAAAAGTT
AGCCTAGACAACTGTTCAAACAAGGGATTAAACACAATGACAAAACATGCAATTCAAGAAGCTAT
CAAACAT
Found at i:1740166 original size:13 final size:13
Alignment explanation
Indices: 1740148--1740172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1740138 CATAAAATAT
1740148 TTTTTAAAATTTC
1 TTTTTAAAATTTC
1740161 TTTTTAAAATTT
1 TTTTTAAAATTT
1740173 TATAAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAAAATTTC
Found at i:1740179 original size:9 final size:9
Alignment explanation
Indices: 1740162--1740233 Score: 51
Period size: 9 Copynumber: 8.2 Consensus size: 9
1740152 TAAAATTTCT
1740162 TTTTA-AAA
1 TTTTATAAA
1740170 TTTTATAAA
1 TTTTATAAA
1740179 TTTT-TAAA
1 TTTTATAAA
* * *
1740187 ATATATAAG
1 TTTTATAAA
** *
1740196 TTTTGGAAT
1 TTTTATAAA
1740205 TTTTATAAA
1 TTTTATAAA
*
1740214 TATTT-TGAA
1 T-TTTATAAA
1740223 TTTTATAAA
1 TTTTATAAA
1740232 TT
1 TT
1740234 ATTTTGATTT
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
8 14 0.30
9 30 0.64
10 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (9 bp):
TTTTATAAA
Found at i:1740193 original size:17 final size:18
Alignment explanation
Indices: 1740161--1740199 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1740151 TTAAAATTTC
*
1740161 TTTTTAAAATTTTATAAA
1 TTTTTAAAATTATATAAA
*
1740179 TTTTTAAAA-TATATAAG
1 TTTTTAAAATTATATAAA
1740196 TTTT
1 TTTT
1740200 GGAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTTTAAAATTATATAAA
Found at i:1740225 original size:19 final size:20
Alignment explanation
Indices: 1740196--1740245 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1740186 AATATATAAG
1740196 TTTTGGAATTTTTATAAA-TA
1 TTTT-GAATTTTTATAAATTA
1740216 TTTTGAA-TTTTATAAATTA
1 TTTTGAATTTTTATAAATTA
1740235 TTTTG-ATTTTT
1 TTTTGAATTTTT
1740246 TTGTAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.36
19 14 0.50
20 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTGAATTTTTATAAATTA
Found at i:1740243 original size:18 final size:18
Alignment explanation
Indices: 1740168--1740244 Score: 70
Period size: 18 Copynumber: 4.3 Consensus size: 18
1740158 TTCTTTTTAA
*
1740168 AATTTTATAAAT-TTTTA
1 AATTTTATAAATATTTTG
* * * *
1740185 AAATATATAAGT-TTTGG
1 AATTTTATAAATATTTTG
1740202 AATTTTTATAAATATTTTG
1 AA-TTTTATAAATATTTTG
1740221 AATTTTATAAATTATTTTG
1 AATTTTATAAA-TATTTTG
1740240 -ATTTT
1 AATTTT
1740245 TTTGTAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
17 14 0.29
18 21 0.44
19 13 0.27
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
AATTTTATAAATATTTTG
Found at i:1740740 original size:19 final size:18
Alignment explanation
Indices: 1740716--1740762 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
1740706 TTATTATCTT
1740716 ATAACTTTTA-AAAATAATA
1 ATAACTTTTACAAAA-AA-A
1740735 ATAACTTCTTACAAAAAAA
1 ATAACTT-TTACAAAAAAA
*
1740754 AAAACTTTT
1 ATAACTTTT
1740763 CACACCAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 5 0.20
21 4 0.16
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAACTTTTACAAAAAAA
Found at i:1754113 original size:12 final size:12
Alignment explanation
Indices: 1754094--1754124 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1754084 TATATCGCAA
1754094 AAAAATAGAAAT
1 AAAAATAGAAAT
*
1754106 AGAAATAGAAAT
1 AAAAATAGAAAT
1754118 AAAAATA
1 AAAAATA
1754125 AAGAACACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (12 bp):
AAAAATAGAAAT
Found at i:1762406 original size:37 final size:37
Alignment explanation
Indices: 1762356--1762429 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1762346 TTAGTTTTTC
**
1762356 GTGACATTTTATAAATGCCACGGGCTAGAAAATATTT
1 GTGACATTTTATAAATGCCACGAACTAGAAAATATTT
* *
1762393 GTGACATTTTATAAATGTCATGAACTAGAAAATATTT
1 GTGACATTTTATAAATGCCACGAACTAGAAAATATTT
1762430 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (37 bp):
GTGACATTTTATAAATGCCACGAACTAGAAAATATTT
Found at i:1773681 original size:27 final size:26
Alignment explanation
Indices: 1773649--1773702 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
1773639 TTATTTTTTA
1773649 AAATAAAATTATTT-ATTAAATTAATTT
1 AAATAAAATT-TTTAATTAAA-TAATTT
1773676 AAATAAAATTTTTCAATTAAATAATTT
1 AAATAAAATTTTT-AATTAAATAATTT
1773703 TCCCAACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.12
27 16 0.64
28 6 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATAAAATTTTTAATTAAATAATTT
Found at i:1775093 original size:14 final size:14
Alignment explanation
Indices: 1775076--1775127 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
1775066 TAGAACATAT
*
1775076 AACATTAAATCCTA
1 AACACTAAATCCTA
1775090 AACACTAAATCCTA
1 AACACTAAATCCTA
1775104 AAC-CTAGAAT-CTCA
1 AACACTA-AATCCT-A
*
1775118 AACCCTAAAT
1 AACACTAAAT
1775128 AAAAATATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 5 0.15
14 26 0.76
15 3 0.09
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (14 bp):
AACACTAAATCCTA
Found at i:1775563 original size:21 final size:21
Alignment explanation
Indices: 1775526--1775566 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1775516 CTCAAACACA
*
1775526 TTAAACCCATATATCTTAAAC
1 TTAAACCCATACATCTTAAAC
1775547 TTAAACCC-TACACTCTTAAA
1 TTAAACCCATACA-TCTTAAA
1775567 TATATAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAACCCATACATCTTAAAC
Found at i:1775872 original size:83 final size:83
Alignment explanation
Indices: 1775696--1775857 Score: 200
Period size: 83 Copynumber: 2.0 Consensus size: 83
1775686 ATAAACCCTG
* * **
1775696 AACACTACACTTTAAATCTAAAATCTCAAACCTTAAACCCAAAACATAAAAACTTAAACCCTAAA
1 AACACTAAACCTTAAATCTAAAATCTCAAACCTTAAACCCAAAACATAAAAACCCAAACCCTAAA
*
1775761 GTAAAAAATATAACCCCA
66 CTAAAAAATATAACCCCA
* * * * *
1775779 AATACTAAACCTTAAATCTAGAATCTCAAACAC-TAAACCCAAAACATAAAAGCCCAAATCTTAA
1 AACACTAAACCTTAAATCTAAAATCTCAAAC-CTTAAACCCAAAACATAAAAACCCAAACCCTAA
* *
1775843 ACTCAAACATATAAC
65 ACTAAAAAATATAAC
1775858 TTTAAACCCT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
83 65 0.98
84 1 0.02
ACGTcount: A:0.52, C:0.25, G:0.02, T:0.20
Consensus pattern (83 bp):
AACACTAAACCTTAAATCTAAAATCTCAAACCTTAAACCCAAAACATAAAAACCCAAACCCTAAA
CTAAAAAATATAACCCCA
Found at i:1775876 original size:20 final size:19
Alignment explanation
Indices: 1775853--1775911 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1775843 ACTCAAACAT
1775853 ATAACTTTAAACCCTAAACC
1 ATAA-TTTAAACCCTAAACC
1775873 ATAATCTTAAACCCTAAACC
1 ATAAT-TTAAACCCTAAACC
* **
1775893 TTAAATACAAACCCTAAAC
1 AT-AATTTAAACCCTAAAC
1775912 TCGAACCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.88
21 3 0.09
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (19 bp):
ATAATTTAAACCCTAAACC
Found at i:1776068 original size:21 final size:21
Alignment explanation
Indices: 1776044--1776117 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
1776034 CATAACCTTG
1776044 AATCTTAAACCACAAACCCTA
1 AATCTTAAACCACAAACCCTA
* * *
1776065 AATCTAAAAACATAAACCCTA
1 AATCTTAAACCACAAACCCTA
* *
1776086 AA-CTCAAA-CACATAACACTA
1 AATCTTAAACCACA-AACCCTA
*
1776106 AACCCTTAAACC
1 AA-TCTTAAACC
1776118 TTATACCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 13 0.31
21 20 0.48
22 5 0.12
23 1 0.02
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (21 bp):
AATCTTAAACCACAAACCCTA
Found at i:1776652 original size:35 final size:34
Alignment explanation
Indices: 1776552--1776666 Score: 110
Period size: 35 Copynumber: 3.3 Consensus size: 34
1776542 GAACACATTC
* *
1776552 AACCATAAACCCAAACCTTGAATCCTAAACTCAT
1 AACCATAAACCCAAACCTTTAAACCTAAACTCAT
* *
1776586 AACTCAT-AACCCTAAACCATTATACCTTAAACTCA-
1 AAC-CATAAACCC-AAACCTTTAAACC-TAAACTCAT
*
1776621 AACCATAAATCCCAAACCTTTAAACCATAAAC-CTT
1 AACCATAAA-CCCAAACCTTTAAACC-TAAACTCAT
*
1776656 AACCTTAAACC
1 AACCATAAACC
1776667 ATAAACCCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
34 14 0.21
35 41 0.62
36 11 0.17
ACGTcount: A:0.44, C:0.32, G:0.01, T:0.23
Consensus pattern (34 bp):
AACCATAAACCCAAACCTTTAAACCTAAACTCAT
Found at i:1776679 original size:20 final size:20
Alignment explanation
Indices: 1776620--1776684 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
1776610 CCTTAAACTC
1776620 AAACCATAAATCCCAAACCTTT
1 AAACCATAAA-CCCAAACC-TT
**
1776642 AAACCATAAACCTTAACCTT
1 AAACCATAAACCCAAACCTT
*
1776662 AAACCATAAACCCAAACCCT
1 AAACCATAAACCCAAACCTT
1776682 AAA
1 AAA
1776685 TTTAAAATCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 22 0.58
21 6 0.16
22 10 0.26
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.18
Consensus pattern (20 bp):
AAACCATAAACCCAAACCTT
Found at i:1777908 original size:21 final size:22
Alignment explanation
Indices: 1777867--1777909 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1777857 TTAACTATTC
*
1777867 AAATATGATTTATGAGTATTTT
1 AAATATGATTTATGAGAATTTT
1777889 AAATATG-TTTATTGA-AATTTT
1 AAATATGATTTA-TGAGAATTTT
1777910 GTGTATTCAA
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:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
AAATATGATTTATGAGAATTTT
Found at i:1778229 original size:33 final size:31
Alignment explanation
Indices: 1778187--1778265 Score: 106
Period size: 30 Copynumber: 2.5 Consensus size: 31
1778177 TAAATTGTTT
1778187 TTGTATTGGTTATTGTCTATCATGTTGTATTAAA
1 TTGT-TTGGTTATTGTCT-T-ATGTTGTATTAAA
*
1778221 TTGTTTGGTCATT-TCTTATGTTGTATTAAA
1 TTGTTTGGTTATTGTCTTATGTTGTATTAAA
*
1778251 TTGTTTGGTTGTTGT
1 TTGTTTGGTTATTGT
1778266 TTGCTTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 24 0.59
31 2 0.05
32 3 0.07
33 8 0.20
34 4 0.10
ACGTcount: A:0.18, C:0.05, G:0.20, T:0.57
Consensus pattern (31 bp):
TTGTTTGGTTATTGTCTTATGTTGTATTAAA
Found at i:1780727 original size:21 final size:21
Alignment explanation
Indices: 1780701--1780752 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1780691 CAAGTGGTTG
1780701 CCCCAACTCAGCAACAGACTA
1 CCCCAACTCAGCAACAGACTA
* * * *
1780722 CCCCAAATCAGTAAGAGACTG
1 CCCCAACTCAGCAACAGACTA
1780743 CCCCAACTCA
1 CCCCAACTCA
1780753 ATAGGAGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.40, G:0.12, T:0.12
Consensus pattern (21 bp):
CCCCAACTCAGCAACAGACTA
Found at i:1781895 original size:15 final size:15
Alignment explanation
Indices: 1781875--1781905 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1781865 TCTCTTCTCT
*
1781875 TCCTCCTTCTCCTTC
1 TCCTCCTCCTCCTTC
1781890 TCCTCCTCCTCCTTC
1 TCCTCCTCCTCCTTC
1781905 T
1 T
1781906 TTTTCTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (15 bp):
TCCTCCTCCTCCTTC
Found at i:1781911 original size:21 final size:22
Alignment explanation
Indices: 1781861--1781911 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1781851 ACATCTCCAT
*
1781861 TTTTTCTCTTCTCTTCCTCCTTC
1 TTTTTCTC-TCTCCTCCTCCTTC
**
1781884 TCCTTCTC-CTCCTCCTCCTTC
1 TTTTTCTCTCTCCTCCTCCTTC
1781905 TTTTTCT
1 TTTTTCT
1781912 TCTTCTTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 17 0.74
23 6 0.26
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTCTCTCTCCTCCTCCTTC
Found at i:1784518 original size:28 final size:28
Alignment explanation
Indices: 1784468--1784522 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1784458 TAGAATTTAA
*
1784468 TTATTATAAAAATAGTTTAAATTAAATT
1 TTATTATAAAAATAATTTAAATTAAATT
*
1784496 TTATTAT-ATAATAATTTATAATTAAAT
1 TTATTATAAAAATAATTTA-AATTAAAT
1784523 AGACGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TTATTATAAAAATAATTTAAATTAAATT
Found at i:1784666 original size:21 final size:20
Alignment explanation
Indices: 1784640--1784683 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1784630 TATAAATCAA
1784640 ATTATTAAAAATAATAAAAAT
1 ATTATTAAAAATAA-AAAAAT
* *
1784661 ATTATTTAAAATAAAAATAT
1 ATTATTAAAAATAAAAAAAT
1784681 ATT
1 ATT
1784684 GAATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATTAAAAATAAAAAAAT
Found at i:1788187 original size:30 final size:30
Alignment explanation
Indices: 1788152--1788220 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
1788142 CTGACCCGAA
* *
1788152 TATTATTTTCTTGCCATTTTTTTGTTTTTT
1 TATTATTTTCTTGCCATTTTCTTATTTTTT
1788182 TATTATTTTCTTGCCATTTTCTTATTTTTT
1 TATTATTTTCTTGCCATTTTCTTATTTTTT
* *
1788212 CACTATTTT
1 TATTATTTT
1788221 GCTACCAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.13, C:0.13, G:0.04, T:0.70
Consensus pattern (30 bp):
TATTATTTTCTTGCCATTTTCTTATTTTTT
Done.