Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 10 of 18
Found at i:1587827 original size:18 final size:18
Alignment explanation
Indices: 1587800--1587834 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1587790 TCTATTTTAT
*
1587800 AATAAAAAAATTTAAAAA
1 AATAAAAAAATATAAAAA
*
1587818 AATAATAAAATATAAAA
1 AATAAAAAAATATAAAA
1587835 TAATTTTGAT
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AATAAAAAAATATAAAAA
Found at i:1588008 original size:23 final size:21
Alignment explanation
Indices: 1587966--1588008 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
1587956 TATATTTATA
* *
1587966 TTTATAAATAAATTATAATAT
1 TTTATAAATAAATAAAAATAT
1587987 TTTATAATATTAAATAAAAATA
1 TTTATAA-A-TAAATAAAAATA
1588009 AAAAATACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTATAAATAAATAAAAATAT
Found at i:1588654 original size:13 final size:14
Alignment explanation
Indices: 1588619--1588673 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
1588609 TTACTTACGG
1588619 TTAGTAAATTATATA
1 TTAGTAAATT-TATA
1588634 TTA-T-AATTT-TA
1 TTAGTAAATTTATA
*
1588645 TTAGTAAATTTATC
1 TTAGTAAATTTATA
* *
1588659 TTAATTAATTTATA
1 TTAGTAAATTTATA
1588673 T
1 T
1588674 AAAAATAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 5 0.15
12 2 0.06
13 9 0.27
14 14 0.42
15 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (14 bp):
TTAGTAAATTTATA
Found at i:1589609 original size:15 final size:16
Alignment explanation
Indices: 1589589--1589618 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1589579 TAAGTAAGAA
1589589 AAAATTA-TAAATATC
1 AAAATTATTAAATATC
1589604 AAAATTATTAAATAT
1 AAAATTATTAAATAT
1589619 TAATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATTATTAAATATC
Found at i:1590157 original size:23 final size:22
Alignment explanation
Indices: 1590130--1590197 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
1590120 ACATTTAATA
1590130 AATAATATATTTAAAATAATTA-
1 AATAATATATTTAAAAT-ATTAT
* *
1590152 ACATAATTTATTTAATATATTAT
1 A-ATAATATATTTAAAATATTAT
* *
1590175 AATATTTATATTTAAAATTTTAT
1 AATA-ATATATTTAAAATATTAT
1590198 CTTATATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
22 8 0.22
23 29 0.78
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
AATAATATATTTAAAATATTAT
Found at i:1590184 original size:14 final size:13
Alignment explanation
Indices: 1590167--1590213 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
1590157 ATTTATTTAA
1590167 TATATTATAATATT
1 TATATT-TAATATT
*
1590181 TATATTTAAAATT
1 TATATTTAATATT
1590194 T-TATCTT-ATATT
1 TATAT-TTAATATT
1590206 TATATTTA
1 TATATTTA
1590214 TATAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 10 0.36
13 12 0.43
14 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTTAATATT
Found at i:1590478 original size:12 final size:13
Alignment explanation
Indices: 1590446--1590479 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1590436 GCATTTGAGA
1590446 AGCATAATTAACG
1 AGCATAATTAACG
*
1590459 AGCATAATTAATG
1 AGCATAATTAACG
1590472 A-CATAATT
1 AGCATAATT
1590480 TTAGGACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (13 bp):
AGCATAATTAACG
Found at i:1591597 original size:13 final size:13
Alignment explanation
Indices: 1591579--1591612 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1591569 TAATAATAAA
1591579 ATAAATAAAATTT
1 ATAAATAAAATTT
1591592 ATAAATAAAATTT
1 ATAAATAAAATTT
1591605 ATAAATAA
1 ATAAATAA
1591613 TGTATATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAATAAAATTT
Found at i:1592004 original size:22 final size:19
Alignment explanation
Indices: 1591979--1592019 Score: 55
Period size: 22 Copynumber: 2.0 Consensus size: 19
1591969 ATTATTTTTA
1591979 AAATATAATATTTAATAATTAT
1 AAATATAA-ATTT--TAATTAT
1592001 AAATATAAATTTTAATTAT
1 AAATATAAATTTTAATTAT
1592020 TTACTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATATAAATTTTAATTAT
Found at i:1592442 original size:22 final size:21
Alignment explanation
Indices: 1592417--1592459 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1592407 CTAATAAATC
*
1592417 TTAAATAATTTTAATATATAAA
1 TTAAATAAATTT-ATATATAAA
* *
1592439 TTAAGTAAATTTATATTTAAA
1 TTAAATAAATTTATATATAAA
1592460 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAAATAAATTTATATATAAA
Found at i:1592495 original size:17 final size:17
Alignment explanation
Indices: 1592449--1592497 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1592439 TTAAGTAAAT
* *
1592449 TTATATTTAAAATTTTA
1 TTATATTTATATTTTTA
* *
1592466 ATATAATTAATATTTTTA
1 TTAT-ATTTATATTTTTA
1592484 TTATATTTATATTT
1 TTATATTTATATTT
1592498 ACACACTTCG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTATATTTTTA
Found at i:1592912 original size:21 final size:21
Alignment explanation
Indices: 1592858--1592959 Score: 60
Period size: 19 Copynumber: 5.0 Consensus size: 21
1592848 ACATATAATT
*
1592858 TTAAAATTATTATGTAATATTTA
1 TTAATATTATT-T-TAATATTTA
*
1592881 TTTATATTATTTTAATATTTA
1 TTAATATTATTTTAATATTTA
*
1592902 TTAA-A-TATATT-ATATTTTA
1 TTAATATTATTTTAATA-TTTA
1592921 TT-ATA-T-TTTT-ATATTATCA
1 TTAATATTATTTTAATATT-T-A
1592940 TTAATTATTA-TTTAAT-TTTA
1 TTAA-TATTATTTTAATATTTA
1592960 AAAATTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
17 2 0.03
18 11 0.17
19 16 0.25
20 3 0.05
21 15 0.23
22 7 0.11
23 11 0.17
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (21 bp):
TTAATATTATTTTAATATTTA
Found at i:1592946 original size:23 final size:24
Alignment explanation
Indices: 1592881--1592952 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
1592871 GTAATATTTA
1592881 TTTATATTAT-TTTAA-TATTTATT
1 TTTATATTATATTTAATTA-TTATT
** *
1592904 AAATATATTATATTTTATTA-TATT
1 -TTTATATTATATTTAATTATTATT
1592928 TTTATATTATCA-TTAATTATTATT
1 TTTATATTAT-ATTTAATTATTATT
1592952 T
1 T
1592953 AATTTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
23 14 0.37
24 18 0.47
25 4 0.11
26 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTATATTATATTTAATTATTATT
Found at i:1592958 original size:39 final size:41
Alignment explanation
Indices: 1592862--1592959 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 41
1592852 ATAATTTTAA
*
1592862 AATTATTATGTAATATTTATTTATATTATTTTAATATTTATT
1 AATTATTATTTAAT-TTTATTTATATTATTTTAATATTTATT
*
1592904 AAATA-TA-TTATATTTTA-TTATA-T-TTTT-ATATTATCATT
1 AATTATTATTTA-ATTTTATTTATATTATTTTAATATT-T-ATT
1592942 AATTATTATTTAATTTTA
1 AATTATTATTTAATTTTA
1592960 AAAATTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
36 5 0.10
37 5 0.10
38 8 0.17
39 13 0.27
40 9 0.19
41 4 0.08
42 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (41 bp):
AATTATTATTTAATTTTATTTATATTATTTTAATATTTATT
Found at i:1595199 original size:9 final size:9
Alignment explanation
Indices: 1595185--1595225 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1595175 CAATAATTTA
1595185 ATTTTATAT
1 ATTTTATAT
1595194 ATTTTATA-
1 ATTTTATAT
*
1595202 ATTTTTTAT
1 ATTTTATAT
1595211 ATTATTA-AT
1 ATT-TTATAT
1595220 ATTTTA
1 ATTTTA
1595226 ATAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 10 0.36
9 16 0.57
10 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTATAT
Found at i:1595224 original size:17 final size:19
Alignment explanation
Indices: 1595185--1595225 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1595175 CAATAATTTA
*
1595185 ATTTTATATATTTTATAAT
1 ATTTTATATATTATATAAT
1595204 -TTTT-TATATTAT-TAAT
1 ATTTTATATATTATATAAT
1595220 ATTTTA
1 ATTTTA
1595226 ATAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.21
17 11 0.58
18 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTATATATTATATAAT
Found at i:1596563 original size:37 final size:37
Alignment explanation
Indices: 1596506--1596604 Score: 102
Period size: 37 Copynumber: 2.7 Consensus size: 37
1596496 TTAAAATTTT
1596506 ATTTTATTATTTAAA-A-TAATATTAAAAATTAAA-AA
1 ATTTT-TTATTTAAATATTAATATTAAAAATTAAATAA
* *
1596541 ATATTTTTATATT-AATATTAATAATT-TAATTTAAATAA
1 AT-TTTTTAT-TTAAATATTAAT-ATTAAAAATTAAATAA
1596579 ATTTTTTATTTAAATATTAAT-TTAAA
1 ATTTTTTATTTAAATATTAATATTAAA
1596605 TTAAGCCTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
35 10 0.19
36 9 0.17
37 27 0.51
38 7 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTTTTTATTTAAATATTAATATTAAAAATTAAATAA
Found at i:1596600 original size:34 final size:37
Alignment explanation
Indices: 1596531--1596608 Score: 101
Period size: 34 Copynumber: 2.2 Consensus size: 37
1596521 ATAATATTAA
1596531 AAATTAAAAAATATTTTTATATTAATATTAATAATTT
1 AAATTAAAAAATATTTTTATATTAATATTAATAATTT
* *
1596568 AATTTAAATAAAT-TTTTTAT-TTAA-A-TATTAATTT
1 AAATTAAA-AAATATTTTTATATTAATATTAATAATTT
1596602 AAATTAA
1 AAATTAA
1596609 GCCTTATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 14 0.38
35 1 0.03
36 4 0.11
37 14 0.38
38 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
AAATTAAAAAATATTTTTATATTAATATTAATAATTT
Found at i:1596924 original size:25 final size:26
Alignment explanation
Indices: 1596896--1596949 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1596886 TTTTATTATT
*
1596896 TTATA-TTATAATTATATT-TAAAATA
1 TTATATTTAT-ATAATATTATAAAATA
1596921 TTATATTTATATAATATTATAAAATA
1 TTATATTTATATAATATTATAAAATA
1596947 TTA
1 TTA
1596950 ATAATCGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTATATTTATATAATATTATAAAATA
Found at i:1596938 original size:16 final size:16
Alignment explanation
Indices: 1596889--1596941 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
1596879 TTATATTTTT
*
1596889 TATTAT-TTTATATTA
1 TATTATATTTATATAA
1596904 TAATTATATTTA-A-AA
1 T-ATTATATTTATATAA
1596919 TATTATATTTATATAA
1 TATTATATTTATATAA
1596935 TATTATA
1 TATTATA
1596942 AAATATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 10 0.30
15 4 0.12
16 15 0.45
17 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATATTTATATAA
Found at i:1596943 original size:26 final size:25
Alignment explanation
Indices: 1596896--1596949 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
1596886 TTTTATTATT
*
1596896 TTATATTATAATTATATTTAAAATA
1 TTATATTATAATAATATTTAAAATA
1596921 TTATATT-TATATAATATTATAAAATA
1 TTATATTATA-ATAATATT-TAAAATA
1596947 TTA
1 TTA
1596950 ATAATCGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 2 0.08
25 14 0.54
26 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATATTATAATAATATTTAAAATA
Found at i:1597286 original size:18 final size:20
Alignment explanation
Indices: 1597257--1597294 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1597247 AATAGTTGAA
1597257 TTAAATAAATATA-AAAATT
1 TTAAATAAATATATAAAATT
1597276 TTAAA-AAATATATAAAATT
1 TTAAATAAATATATAAAATT
1597295 AATTTACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAATAAATATATAAAATT
Found at i:1598422 original size:19 final size:19
Alignment explanation
Indices: 1598395--1598458 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
1598385 AATAATATTT
*
1598395 ATATAAATATAATTATAAA
1 ATATTAATATAATTATAAA
1598414 ATATTAATATTAA-TATAAA
1 ATATTAATA-TAATTATAAA
* *
1598433 A-A-TAATAT-TTTAATAAT
1 ATATTAATATAATT-ATAAA
1598450 ATATTAATA
1 ATATTAATA
1598459 ATAAAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 2 0.05
17 10 0.27
18 2 0.05
19 20 0.54
20 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATTAATATAATTATAAA
Found at i:1598437 original size:25 final size:25
Alignment explanation
Indices: 1598367--1598465 Score: 80
Period size: 25 Copynumber: 4.0 Consensus size: 25
1598357 TCTATTTTAA
1598367 ATTAATATTTAA-A-AATAA-AATAAT
1 ATTAATA-TTAATATAATAATAA-AAT
* * *
1598391 ATTTATATAAATATAATTATAAAAT
1 ATTAATATTAATATAATAATAAAAT
* *
1598416 ATTAATATTAATATAAAAATAATAT
1 ATTAATATTAATATAATAATAAAAT
* *
1598441 TTTAATAAT-ATATTAATAATAAAAT
1 ATTAATATTAATA-TAATAATAAAAT
1598466 GAATTCGAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
23 3 0.05
24 10 0.17
25 44 0.75
26 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTAATATTAATATAATAATAAAAT
Found at i:1598447 original size:11 final size:11
Alignment explanation
Indices: 1598385--1598461 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 11
1598375 TTAAAAATAA
1598385 AATAATAT-TT
1 AATAATATATT
1598395 ATATAAATATAATT
1 A-AT-AATAT-ATT
*
1598409 -ATAAAATATT
1 AATAATATATT
**
1598419 AATATTAATATAAA
1 -A-A-TAATATATT
*
1598433 AATAATATTTT
1 AATAATATATT
1598444 AATAATATATT
1 AATAATATATT
1598455 AATAATA
1 AATAATA
1598462 AAATGAATTC
Statistics
Matches: 51, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
10 4 0.08
11 29 0.57
12 8 0.16
13 2 0.04
14 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AATAATATATT
Found at i:1602956 original size:17 final size:17
Alignment explanation
Indices: 1602908--1602959 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1602898 TATAATTTTA
*
1602908 AAAATAAAAAATAAT-T
1 AAAATTAAAAATAATAT
*
1602924 AAAA-TATAATATAATAT
1 AAAATTA-AAAATAATAT
1602941 AAAATTAAAAATAATAT
1 AAAATTAAAAATAATAT
1602958 AA
1 AA
1602960 TAAAATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 1 0.03
16 11 0.37
17 16 0.53
18 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTAAAAATAATAT
Found at i:1603062 original size:26 final size:28
Alignment explanation
Indices: 1603024--1603088 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 28
1603014 ATTTTATAAC
*
1603024 ATAAAT-TATTAATATTTTAAAT-TTA-T
1 ATAAATATA-TAATATTTTAAATATAATT
1603050 ATAAATATATAATATTTTAAATATAATT
1 ATAAATATATAATATTTTAAATATAATT
1603078 ATAAA-ATATAA
1 ATAAATATATAA
1603089 AAAAACACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 19 0.54
27 10 0.29
28 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAAATATATAATATTTTAAATATAATT
Found at i:1603279 original size:16 final size:16
Alignment explanation
Indices: 1603258--1603332 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 16
1603248 GTATTATAAA
1603258 TATATTTAAAATATTT
1 TATATTTAAAATATTT
1603274 TATATTTATATAA-ATTT
1 TATATTTA-A-AATATTT
*
1603291 TAATATATT--AATAATT
1 T-ATAT-TTAAAATATTT
1603307 TATATTATAAAAT-TTT
1 TATATT-TAAAATATTT
1603323 AATATATTTA
1 --TATATTTA
1603333 TTAATTTCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 19
0.69 0.03 0.28
Matches are distributed among these distances:
14 1 0.02
15 7 0.15
16 14 0.30
17 11 0.23
18 12 0.26
19 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTTAAAATATTT
Found at i:1603296 original size:18 final size:17
Alignment explanation
Indices: 1603258--1603323 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
1603248 GTATTATAAA
1603258 TATATTTA-A-AATATTT
1 TATATTTATATAA-ATTT
1603274 TATATTTATATAAATTT
1 TATATTTATATAAATTT
1603291 TAATATATTA-AT-AA-TT
1 T-ATAT-TTATATAAATTT
1603307 TATA-TTATA-AAATTT
1 TATATTTATATAAATTT
1603322 TA
1 TA
1603324 ATATATTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 7 0.16
16 11 0.26
17 8 0.19
18 8 0.19
19 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTTATATAAATTT
Found at i:1603323 original size:31 final size:33
Alignment explanation
Indices: 1603256--1603345 Score: 112
Period size: 32 Copynumber: 2.7 Consensus size: 33
1603246 ATGTATTATA
*
1603256 AATATATTTAAAATATTTTATATTTATATAAATTTT
1 AATATATTT--AATAATTTATA-TTATATAAATTTT
1603292 AATATA-TTAATAATTTATATTATA-AAATTTT
1 AATATATTTAATAATTTATATTATATAAATTTT
* *
1603323 AATATATTTATTAATTTCTATTA
1 AATATATTTAATAATTTATATTA
1603346 CATTTATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
31 13 0.26
32 19 0.38
33 10 0.20
35 2 0.04
36 6 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
AATATATTTAATAATTTATATTATATAAATTTT
Found at i:1603328 original size:18 final size:18
Alignment explanation
Indices: 1603256--1603330 Score: 65
Period size: 18 Copynumber: 4.4 Consensus size: 18
1603246 ATGTATTATA
1603256 AATATATT-TAAAATATTT
1 AATATATTATAAAAT-TTT
*
1603274 TATAT-TTATATAAATTTT
1 AATATATTATA-AAATTTT
*
1603292 AATATATTA-ATAA--TT
1 AATATATTATAAAATTTT
1603307 --TATATTATAAAATTTT
1 AATATATTATAAAATTTT
1603323 AATATATT
1 AATATATT
1603331 TATTAATTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
13 7 0.16
14 3 0.07
15 2 0.04
16 2 0.04
17 4 0.09
18 20 0.44
19 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATATTATAAAATTTT
Found at i:1603372 original size:28 final size:28
Alignment explanation
Indices: 1603341--1603400 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1603331 TATTAATTTC
1603341 TATTACATTTATATTATTTTTT-ATATAA
1 TATTACATTTA-ATTATTTTTTAATATAA
** *
1603369 TATTATTTTTAATTATTTTTTAATATTA
1 TATTACATTTAATTATTTTTTAATATAA
1603397 TATT
1 TATT
1603401 TAAAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
TATTACATTTAATTATTTTTTAATATAA
Found at i:1604737 original size:14 final size:14
Alignment explanation
Indices: 1604702--1604745 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1604692 TTTGTTAACC
1604702 ATCTTAATTATTAT
1 ATCTTAATTATTAT
*
1604716 ATCTTTAATTATTTT
1 ATC-TTAATTATTAT
*
1604731 ATCTTAATTAATAT
1 ATCTTAATTATTAT
1604745 A
1 A
1604746 ATTAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATCTTAATTATTAT
Found at i:1605579 original size:2 final size:2
Alignment explanation
Indices: 1605572--1605596 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1605562 ATGCTCTTTC
1605572 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1605597 GTTAATTACC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1605790 original size:15 final size:16
Alignment explanation
Indices: 1605765--1605794 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1605755 TATAAGTTTT
1605765 TTATTTATATTAAAAA
1 TTATTTATATTAAAAA
1605781 TTATTT-TATTAAAA
1 TTATTTATATTAAAA
1605795 TTCAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTTATATTAAAAA
Found at i:1605801 original size:21 final size:21
Alignment explanation
Indices: 1605763--1605802 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1605753 TTTATAAGTT
* *
1605763 TTTTATTTATATTAAAAATTA
1 TTTTATTAAAATTAAAAATTA
*
1605784 TTTTATTAAAATTCAAAAT
1 TTTTATTAAAATTAAAAAT
1605803 ATAATTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTATTAAAATTAAAAATTA
Found at i:1607166 original size:19 final size:19
Alignment explanation
Indices: 1607139--1607185 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1607129 ACTGAGAGCA
*
1607139 AAGCTCATCCATTAATGCG
1 AAGCCCATCCATTAATGCG
1607158 AAGCCCATCCATTAATGCG
1 AAGCCCATCCATTAATGCG
1607177 AAGCCCATC
1 AAGCCCATC
1607186 TAACGGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (19 bp):
AAGCCCATCCATTAATGCG
Found at i:1607478 original size:14 final size:14
Alignment explanation
Indices: 1607441--1607481 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1607431 TGTGTGTGTG
*
1607441 TGTATATATTTATA
1 TGTATATATGTATA
*
1607455 TATATATATGTATA
1 TGTATATATGTATA
*
1607469 TGTATGTATGTAT
1 TGTATATATGTAT
1607482 GTATGATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (14 bp):
TGTATATATGTATA
Found at i:1609170 original size:76 final size:73
Alignment explanation
Indices: 1609088--1609243 Score: 222
Period size: 76 Copynumber: 2.1 Consensus size: 73
1609078 TTTCAAACAA
*
1609088 TAACAAATCTAACTTTATTCAATCCAAGACCAAAATAACTATTTCTCATCTTTCCTCTGAATAAT
1 TAACAAATCTAACTTTATTCAATCCAAGACCAAAATAACTATTTCACAT-TTT--TCTGAATAAT
1609153 TATTTGATCTT
63 TATTTGATCTT
* * * * *
1609164 TAACAAATCTAACTTTGTTCCATCCAAGATCAAAATAACTATTTCACATTTTTCTTAATAGTTAT
1 TAACAAATCTAACTTTATTCAATCCAAGACCAAAATAACTATTTCACATTTTTCTGAATAATTAT
*
1609229 TTGATTTT
66 TTGATCTT
1609237 TAACAAA
1 TAACAAA
1609244 ATTATAAAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
73 25 0.34
75 3 0.04
76 45 0.62
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (73 bp):
TAACAAATCTAACTTTATTCAATCCAAGACCAAAATAACTATTTCACATTTTTCTGAATAATTAT
TTGATCTT
Found at i:1609547 original size:18 final size:19
Alignment explanation
Indices: 1609526--1609561 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1609516 TAATTATAAA
1609526 AAATATAA-ATATTAATAT
1 AAATATAATATATTAATAT
*
1609544 AAATATAATATTTTAATA
1 AAATATAATATATTAATA
1609562 ATATAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATATAATATATTAATAT
Found at i:1615906 original size:3 final size:3
Alignment explanation
Indices: 1615898--1615933 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1615888 TTCAATGGAA
1615898 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1615934 CACGCTCACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1616557 original size:2 final size:2
Alignment explanation
Indices: 1616550--1616575 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1616540 GTATATGCAG
1616550 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
1616576 GATGATGATG
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:1622392 original size:19 final size:20
Alignment explanation
Indices: 1622354--1622393 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1622344 TTATTTTTTA
* *
1622354 AAAAAATTTTAAATACATAT
1 AAAAAATTTTAAAAAAATAT
1622374 AAAAAA-TTTAAAAAAATAT
1 AAAAAATTTTAAAAAAATAT
1622393 A
1 A
1622394 TATCGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATTTTAAAAAAATAT
Found at i:1627321 original size:71 final size:71
Alignment explanation
Indices: 1627200--1627331 Score: 246
Period size: 71 Copynumber: 1.9 Consensus size: 71
1627190 ATGGTAAAAT
* *
1627200 AACACATGTCAATTACTGGCAAAGATTCGGAAAAGGCAAATCAATTGGCATAAAGAAAACACATC
1 AACACATGTCAATTACTGACAAAGATTCGGAAAAGGCAAATCAATAGGCATAAAGAAAACACATC
1627265 CGAAAG
66 CGAAAG
1627271 AACACATGTCAATTACTGACAAAGATTCGGAAAAGGCAAATCAATAGGCATAAAGAAAACA
1 AACACATGTCAATTACTGACAAAGATTCGGAAAAGGCAAATCAATAGGCATAAAGAAAACA
1627332 GTCCGTGATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (71 bp):
AACACATGTCAATTACTGACAAAGATTCGGAAAAGGCAAATCAATAGGCATAAAGAAAACACATC
CGAAAG
Found at i:1633101 original size:60 final size:60
Alignment explanation
Indices: 1632983--1633101 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
1632973 TTTTATCTCT
** *
1632983 AAATAAATTTTTAATATTTAATTCATAGTTAAATAAATTTTTAATATTTAATTTATATTC
1 AAATAAATTTTTAATATTTAATTCATAGTTAAATAAATTTTTAATATAAAATTAATATTC
* *
1633043 AAATAAA-TTTTAATATTTTAATTTATATTTAAATAAATTTTTAATATAAAATTAATATT
1 AAATAAATTTTTAATA-TTTAATTCATAGTTAAATAAATTTTTAATATAAAATTAATATT
1633102 TTGTTTATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 8 0.15
60 45 0.85
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (60 bp):
AAATAAATTTTTAATATTTAATTCATAGTTAAATAAATTTTTAATATAAAATTAATATTC
Found at i:1633102 original size:30 final size:30
Alignment explanation
Indices: 1632982--1633089 Score: 173
Period size: 30 Copynumber: 3.6 Consensus size: 30
1632972 TTTTTATCTC
* *
1632982 TAAATAAATTTTTAATATTTAATTCATAGT
1 TAAATAAATTTTTAATATTTAATTTATATT
1633012 TAAATAAATTTTTAATATTTAATTTATATT
1 TAAATAAATTTTTAATATTTAATTTATATT
*
1633042 CAAATAAA-TTTTAATATTTTAATTTATATT
1 TAAATAAATTTTTAATA-TTTAATTTATATT
1633072 TAAATAAATTTTTAATAT
1 TAAATAAATTTTTAATAT
1633090 AAAATTAATA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
29 8 0.11
30 56 0.78
31 8 0.11
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (30 bp):
TAAATAAATTTTTAATATTTAATTTATATT
Found at i:1633244 original size:14 final size:14
Alignment explanation
Indices: 1633222--1633253 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1633212 TTTAATATTT
*
1633222 TAATTTCCTTTTGA
1 TAATCTCCTTTTGA
1633236 TAATCTCCTTTTGA
1 TAATCTCCTTTTGA
1633250 TAAT
1 TAAT
1633254 TACCGTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (14 bp):
TAATCTCCTTTTGA
Found at i:1643259 original size:7 final size:7
Alignment explanation
Indices: 1643247--1643283 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1643237 GGAAGCGACA
1643247 CCAAGTC
1 CCAAGTC
1643254 CCAAGTC
1 CCAAGTC
*
1643261 CCAATTC
1 CCAAGTC
1643268 CCAAGTC
1 CCAAGTC
*
1643275 TCAAGTC
1 CCAAGTC
1643282 CC
1 CC
1643284 GACAATCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.43, G:0.11, T:0.19
Consensus pattern (7 bp):
CCAAGTC
Found at i:1646342 original size:23 final size:22
Alignment explanation
Indices: 1646293--1646360 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
1646283 TATTTTTAAT
* *
1646293 TAAAAATTTATAAT-TTAAAAA
1 TAAAATTTTATAATATTAAATA
1646314 TAAAATTTTATTAATATTAAATA
1 TAAAATTTTA-TAATATTAAATA
* *
1646337 TGAAATTTTATATTTATTAAATA
1 TAAAATTTTATA-ATATTAAATA
1646360 T
1 T
1646361 TATGAATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.22
22 6 0.15
23 25 0.62
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
TAAAATTTTATAATATTAAATA
Found at i:1648905 original size:25 final size:25
Alignment explanation
Indices: 1648850--1648901 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1648840 TTTAAATATA
***
1648850 ATATAATTAATAAATAATTTTAAAT
1 ATATAATTAATAAATAAAAATAAAT
1648875 ATATAATTAATAAATAAAAAT-AAT
1 ATATAATTAATAAATAAAAATAAAT
1648899 ATA
1 ATA
1648902 ATAAATATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATAATTAATAAATAAAAATAAAT
Found at i:1648941 original size:43 final size:42
Alignment explanation
Indices: 1648830--1648944 Score: 105
Period size: 43 Copynumber: 2.8 Consensus size: 42
1648820 ACACAATACA
* * *
1648830 ATATAACATGTTTAAATATAATATAAT-TAATA-AATAATTTT
1 ATATAACATATTTAAATATAAT-TAATATAATATAATAATATG
* * * * *
1648871 AAAT-ATATAATT-AATA-AATAAAAATAATATAATAAATATG
1 ATATAACATATTTAAATATAATTAATATAATATAAT-AATATG
1648911 ATATAACATATTTAAATATAATTAATATAATATA
1 ATATAACATATTTAAATATAATTAATATAATATA
1648945 TTTAATTTAT
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
37 2 0.04
38 8 0.15
39 7 0.13
40 12 0.22
41 9 0.16
42 4 0.07
43 13 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (42 bp):
ATATAACATATTTAAATATAATTAATATAATATAATAATATG
Found at i:1648944 original size:14 final size:14
Alignment explanation
Indices: 1648844--1648950 Score: 72
Period size: 14 Copynumber: 8.2 Consensus size: 14
1648834 AACATGTTTA
1648844 AATATAATATAATT
1 AATATAATATAATT
*
1648858 AATA-AATA-ATTTT
1 AATATAATATA-ATT
1648871 AA-AT-ATATAATT
1 AATATAATATAATT
* *
1648883 AATA-AATAAAAAT
1 AATATAATATAATT
1648896 AATATAATA-AATAT
1 AATATAATATAAT-T
* *
1648910 GATATAACAT-ATT
1 AATATAATATAATT
1648923 --TA-AATATAATT
1 AATATAATATAATT
*
1648934 AATATAATATATTT
1 AATATAATATAATT
1648948 AAT
1 AAT
1648951 TTATGTATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 24
0.69 0.09 0.23
Matches are distributed among these distances:
10 4 0.06
11 5 0.07
12 9 0.12
13 25 0.35
14 29 0.40
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (14 bp):
AATATAATATAATT
Found at i:1648950 original size:9 final size:9
Alignment explanation
Indices: 1648938--1649014 Score: 85
Period size: 9 Copynumber: 9.2 Consensus size: 9
1648928 ATAATTAATA
1648938 TAATATATT
1 TAATATATT
* *
1648947 TAATTTATG
1 TAATATATT
*
1648956 TATTATA-T
1 TAATATATT
1648964 T--TATATT
1 TAATATATT
1648971 TAATAT-TT
1 TAATATATT
1648979 TAATATATT
1 TAATATATT
1648988 TAATA-ATT
1 TAATATATT
1648996 TAATATATT
1 TAATATATT
1649005 TAATA-ATT
1 TAATATATT
1649013 TA
1 TA
1649015 TATTGTATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
6 4 0.07
7 2 0.03
8 22 0.38
9 30 0.52
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (9 bp):
TAATATATT
Found at i:1648982 original size:8 final size:8
Alignment explanation
Indices: 1648969--1649018 Score: 57
Period size: 8 Copynumber: 6.1 Consensus size: 8
1648959 TATATTTATA
1648969 TTTAATAT
1 TTTAATAT
1648977 TTTAATAT
1 TTTAATAT
*
1648985 ATTTAATAA
1 -TTTAATAT
1648994 TTTAATAT
1 TTTAATAT
*
1649002 ATTTAATAA
1 -TTTAATAT
1649011 TTT-ATAT
1 TTTAATAT
1649018 T
1 T
1649019 GTATTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 4 0.11
8 18 0.50
9 14 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TTTAATAT
Found at i:1648987 original size:17 final size:17
Alignment explanation
Indices: 1648965--1649014 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
1648955 GTATTATATT
*
1648965 TATATTTAATATTTTAA
1 TATATTTAATAATTTAA
1648982 TATATTTAATAATTTAA
1 TATATTTAATAATTTAA
1648999 TATATTTAATAATTTA
1 TATATTTAATAATTTA
1649015 TATTGTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTTAATAATTTAA
Found at i:1649041 original size:59 final size:58
Alignment explanation
Indices: 1648933--1649044 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 58
1648923 TAAATATAAT
* *
1648933 TAATATAATATATTTAATTTATGTATTATATTTATATTTAATATTTTAATATATTTAA
1 TAATATAATATATTTAATTTATATATTATATTTATATTTAATATATTAATATATTTAA
* *
1648991 TAATTTAATATATTTAATAATT-TATATTGTATTTATATTTACATA-ATTAATATA
1 TAATATAATATATTTAAT--TTATATATTATATTTATATTTA-ATATATTAATATA
1649045 AAAAATATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 17 0.36
59 25 0.53
60 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (58 bp):
TAATATAATATATTTAATTTATATATTATATTTATATTTAATATATTAATATATTTAA
Found at i:1649251 original size:30 final size:29
Alignment explanation
Indices: 1649194--1649253 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1649184 ATATATTGTC
*
1649194 AAGTATAAAAATTTATAAATAAAATTATT
1 AAGTATAAAAATTTATAAACAAAATTATT
* **
1649223 AAGTGTAAAAAGTTTATAAACAGTATTATT
1 AAGTATAAAAA-TTTATAAACAAAATTATT
1649253 A
1 A
1649254 GAGGAATATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (29 bp):
AAGTATAAAAATTTATAAACAAAATTATT
Found at i:1649915 original size:33 final size:31
Alignment explanation
Indices: 1649878--1649971 Score: 84
Period size: 33 Copynumber: 2.9 Consensus size: 31
1649868 AATTTAAATT
1649878 TATTTAATTAAAAGTATTATTTAATAATAAAAA
1 TATTT-ATTAAAA-TATTATTTAATAATAAAAA
* *
1649911 TATTTTATTTAAAT-TTAATTATAAAAAATAAAAA
1 TA-TTTATTAAAATATT-ATT-T-AATAATAAAAA
* *
1649945 TATTTATTAATATATT-TTAAATAATAA
1 TATTTATTAAAATATTATTTAATAATAA
1649972 TATAAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
30 7 0.14
31 2 0.04
32 6 0.12
33 18 0.36
34 17 0.34
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
TATTTATTAAAATATTATTTAATAATAAAAA
Found at i:1649923 original size:34 final size:34
Alignment explanation
Indices: 1649880--1649949 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 34
1649870 TTTAAATTTA
* *
1649880 TTTAATTAAAAGT-ATTATTTAATAATAAAAATAT
1 TTTAATTAAAAGTAATTA-TAAAAAATAAAAATAT
* **
1649914 TTTATTTAAATTTAATTATAAAAAATAAAAATAT
1 TTTAATTAAAAGTAATTATAAAAAATAAAAATAT
1649948 TT
1 TT
1649950 ATTAATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
TTTAATTAAAAGTAATTATAAAAAATAAAAATAT
Found at i:1650720 original size:13 final size:13
Alignment explanation
Indices: 1650704--1650754 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
1650694 TAAAAATATA
1650704 AATATTTTTATTT
1 AATATTTTTATTT
* *
1650717 AATA-ATTTA-AT
1 AATATTTTTATTT
1650728 AATATTATTTATTT
1 AATATT-TTTATTT
*
1650742 AATATTTATATTT
1 AATATTTTTATTT
1650755 TAATTAAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.17
12 4 0.13
13 14 0.47
14 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATATTTTTATTT
Found at i:1650731 original size:24 final size:24
Alignment explanation
Indices: 1650704--1650749 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1650694 TAAAAATATA
1650704 AATATT-TTTATTTAATAATTTAAT
1 AATATTATTTATTTAAT-ATTTAAT
1650728 AATATTATTTATTTAATATTTA
1 AATATTATTTATTTAATATTTA
1650750 TATTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATATTATTTATTTAATATTTAAT
Found at i:1650779 original size:38 final size:37
Alignment explanation
Indices: 1650704--1650780 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
1650694 TAAAAATATA
* *
1650704 AATATTTTTATTTAATAATTTAATAATATTATTTATTT
1 AATATTTATATTT-ATAATTAAATAATATTATTTATTT
*
1650742 AATATTTATATTT-TAATTAAACTAATATTTTTCTATTT
1 AATATTTATATTTATAATTAAA-TAATATTATT-TATTT
1650780 A
1 A
1650781 TAATATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 7 0.21
37 9 0.26
38 18 0.53
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (37 bp):
AATATTTATATTTATAATTAAATAATATTATTTATTT
Found at i:1651290 original size:30 final size:31
Alignment explanation
Indices: 1651244--1651301 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
1651234 ATTTGACTTA
1651244 ATTTATAAATTAATAAATAA-AAATATTTTT
1 ATTTATAAATTAATAAATAATAAATATTTTT
* *
1651274 ATTTATTAATTTATAAATAATAAATATT
1 ATTTATAAATTAATAAATAATAAATATT
1651302 AATATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATTTATAAATTAATAAATAATAAATATTTTT
Found at i:1652402 original size:124 final size:124
Alignment explanation
Indices: 1652174--1652416 Score: 468
Period size: 124 Copynumber: 2.0 Consensus size: 124
1652164 GAGTTTGAAA
1652174 CACTAAGCCCAAAAAGACCCGAGACAAAACGCCTATTGTATTAATGTCCGTGTAGATATATAATA
1 CACTAAGCCCAAAAAGACCCGAGACAAAACGCCTATTGTATTAATGTCCGTGTAGATATATAATA
*
1652239 ATATAAATTATTAAATATAAAAAATTTTAATGAGGAATATATATATATATACACACGTG
66 ATATAAATTATTAAATATAAAAAATTTTAATGAGCAATATATATATATATACACACGTG
1652298 CACTAAGCCCAAAAAGACCCGAGACAAAACGCCTATTGTATTAATGTCCGTGTAGATATATAATA
1 CACTAAGCCCAAAAAGACCCGAGACAAAACGCCTATTGTATTAATGTCCGTGTAGATATATAATA
*
1652363 ATATAAATTATTAAATATAAAAAATTTTAGTGAGCAATATATATATATATACAC
66 ATATAAATTATTAAATATAAAAAATTTTAATGAGCAATATATATATATATACAC
1652417 GTGTGTGTAT
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 117 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (124 bp):
CACTAAGCCCAAAAAGACCCGAGACAAAACGCCTATTGTATTAATGTCCGTGTAGATATATAATA
ATATAAATTATTAAATATAAAAAATTTTAATGAGCAATATATATATATATACACACGTG
Found at i:1652603 original size:35 final size:33
Alignment explanation
Indices: 1652558--1652625 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
1652548 TACATAAAAA
*
1652558 TTAATATTAAAAAATATAA-TTTTCATTTAAATATT
1 TTAATATT--AAAATATAACTATTCA-TTAAATATT
*
1652593 TTAATTTTAAAATATAACTATTCATTAAATATT
1 TTAATATTAAAATATAACTATTCATTAAATATT
1652626 ACTCACATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 18 0.60
34 5 0.17
35 7 0.23
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (33 bp):
TTAATATTAAAATATAACTATTCATTAAATATT
Found at i:1653174 original size:15 final size:16
Alignment explanation
Indices: 1653144--1653177 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1653134 TTTTAATAAT
1653144 TTAAAAAACTAATTAC
1 TTAAAAAACTAATTAC
*
1653160 TTAAAAAA-TATTTAC
1 TTAAAAAACTAATTAC
1653175 TTA
1 TTA
1653178 TTTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAAAACTAATTAC
Found at i:1660896 original size:22 final size:23
Alignment explanation
Indices: 1660857--1660900 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1660847 AATTTTATTT
1660857 TAATATTTAAAAATTAAATTAAA
1 TAATATTTAAAAATTAAATTAAA
*
1660880 TAATATTT-ATAATTAAATTAA
1 TAATATTTAAAAATTAAATTAA
1660901 TTTAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATATTTAAAAATTAAATTAAA
Found at i:1660928 original size:30 final size:27
Alignment explanation
Indices: 1660867--1660934 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 27
1660857 TAATATTTAA
* *
1660867 AAATTAAATTAAATAATATTTATAATT
1 AAATTAATTTAAATAAAATTTATAATT
1660894 AAATTAATTTAAATTAAAATTTATCAATTT
1 AAATTAATTTAAA-TAAAATTTAT-AA-TT
1660924 AAATTAATTTA
1 AAATTAATTTA
1660935 GCTTATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 12 0.33
28 9 0.25
29 2 0.06
30 13 0.36
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATTAATTTAAATAAAATTTATAATT
Found at i:1660982 original size:23 final size:21
Alignment explanation
Indices: 1660939--1660988 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
1660929 AATTTAGCTT
*
1660939 ATTAATTTTTAAATTTAAAAA
1 ATTATTTTTTAAATTTAAAAA
*
1660960 ATTATTTTTATAATATTTTAAAA
1 ATTATTTTT-TAA-ATTTAAAAA
1660983 ATTATT
1 ATTATT
1660989 GATAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.32
22 3 0.12
23 14 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATTTTTTAAATTTAAAAA
Found at i:1661033 original size:19 final size:19
Alignment explanation
Indices: 1660991--1661034 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1660981 AAATTATTGA
1660991 TAATT-TAAAAATAAATAT
1 TAATTATAAAAATAAATAT
*
1661009 TTATTATAAAAATAAA-AT
1 TAATTATAAAAATAAATAT
1661027 TAAATTAT
1 T-AATTAT
1661035 CACAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTATAAAAATAAATAT
Found at i:1667352 original size:2 final size:2
Alignment explanation
Indices: 1667345--1667376 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1667335 GAGGTTGGGA
1667345 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1667377 GGGAGTTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1670099 original size:2 final size:2
Alignment explanation
Indices: 1670092--1670116 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1670082 AATTAAGCAA
1670092 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1670117 GAATTTGAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1672601 original size:27 final size:26
Alignment explanation
Indices: 1672565--1672706 Score: 100
Period size: 27 Copynumber: 5.5 Consensus size: 26
1672555 TGGTGTAATT
1672565 ATATAATATAAAAATAATTATAATATA
1 ATATAATATAAAAAT-ATTATAATATA
* *
1672592 ATATAATATAATAAAAATAATTAATA-A
1 ATATAATATAA-AAATATTA-TAATATA
* *
1672619 ATAT-ATATTAAAATTTATATAATATA
1 ATATAATATAAAAATAT-TATAATATA
* * * *
1672645 A-AT--TATTAATATATTA-AATTTT
1 ATATAATATAAAAATATTATAATATA
1672667 ATATACATAT-AAAATATTATAAATATA
1 ATATA-ATATAAAAATATTAT-AATATA
1672694 ATTATAATATAAA
1 A-TATAATATAAA
1672707 TGTAAAGATT
Statistics
Matches: 90, Mismatches: 13, Indels: 23
0.71 0.10 0.18
Matches are distributed among these distances:
22 5 0.06
23 4 0.04
24 9 0.10
25 19 0.21
26 11 0.12
27 28 0.31
28 14 0.16
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATAATATAAAAATATTATAATATA
Found at i:1672637 original size:14 final size:14
Alignment explanation
Indices: 1672620--1672671 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
1672610 AATTAATAAA
1672620 TATATATTAAAATT
1 TATATATTAAAATT
1672634 TATATAATATAAATTATT
1 TATAT-AT-TAAA--ATT
* *
1672652 AATATATTAAATTT
1 TATATATTAAAATT
1672666 TATATA
1 TATATA
1672672 CATATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 12 0.39
15 2 0.06
16 8 0.26
17 2 0.06
18 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATTAAAATT
Found at i:1672649 original size:21 final size:22
Alignment explanation
Indices: 1672580--1672703 Score: 69
Period size: 21 Copynumber: 5.5 Consensus size: 22
1672570 ATATAAAAAT
* *
1672580 AATTATAATATAATATAATAT-
1 AATTAAAATATTATATAATATA
*
1672601 AATAAAAATAATTA-ATAAATATA
1 AATTAAAAT-ATTATAT-AATATA
*
1672624 TATTAAAAT-TTATATAATATA
1 AATTAAAATATTATATAATATA
* *
1672645 AATTATTAATATATTAAATTTTATATA
1 AATTA--AA-ATATT--ATATAATATA
*
1672672 CATATAAAATATTATA-AATAT-
1 AAT-TAAAATATTATATAATATA
*
1672693 AATTATAATAT
1 AATTAAAATAT
1672704 AAATGTAAAG
Statistics
Matches: 79, Mismatches: 13, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
20 7 0.09
21 24 0.30
22 14 0.18
23 11 0.14
24 2 0.03
25 7 0.09
26 2 0.03
27 10 0.13
28 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTAAAATATTATATAATATA
Found at i:1672653 original size:38 final size:37
Alignment explanation
Indices: 1672597--1672697 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 37
1672587 ATATAATATA
* *
1672597 ATATAATAAAAATAATTAATAAATATATATTAAAATTT
1 ATATAATATAAATTATT-ATAAATATATATTAAAATTT
*
1672635 ATATAATATAAATTA-T-T--A-ATATATTAAATTTT
1 ATATAATATAAATTATTATAAATATATATTAAAATTT
*
1672667 ATATACATATAAAATATTATAAATATA-ATTA
1 ATATA-ATATAAATTATTATAAATATATATTA
1672698 TAATATAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
32 18 0.34
33 10 0.19
34 1 0.02
35 2 0.04
37 6 0.11
38 16 0.30
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (37 bp):
ATATAATATAAATTATTATAAATATATATTAAAATTT
Found at i:1672676 original size:18 final size:17
Alignment explanation
Indices: 1672619--1672692 Score: 68
Period size: 16 Copynumber: 4.5 Consensus size: 17
1672609 TAATTAATAA
*
1672619 ATAT-ATATTAAAATTT
1 ATATAATATTAAATTTT
1672635 ATATAATA-TAAATTATT
1 ATATAATATTAAATT-TT
1672652 A-AT-ATATTAAATTTT
1 ATATAATATTAAATTTT
* *
1672667 ATATACATATAAAATATT
1 ATATA-ATATTAAATTTT
1672685 ATA-AATAT
1 ATATAATAT
1672693 AATTATAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 6 0.12
16 23 0.47
17 7 0.14
18 13 0.27
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATATTAAATTTT
Found at i:1673074 original size:43 final size:43
Alignment explanation
Indices: 1672993--1673074 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 43
1672983 TACAGTTTTT
* * * *
1672993 TAAAATAAAATAAAATTATAATTAAATAATTATTTTATAAAAA
1 TAAAATAAAATAAAATCATAATCAAATAAATATGTTATAAAAA
1673036 TAAAATAAAATTAAAATCA-AATCAAATCAAATA-GTTATA
1 TAAAATAAAA-TAAAATCATAATCAAAT-AAATATGTTATA
1673075 GAAGTTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
43 22 0.67
44 11 0.33
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (43 bp):
TAAAATAAAATAAAATCATAATCAAATAAATATGTTATAAAAA
Found at i:1673365 original size:3 final size:3
Alignment explanation
Indices: 1673357--1673387 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1673347 TGCTGTTAGT
1673357 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1673388 GAAGAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1674980 original size:12 final size:12
Alignment explanation
Indices: 1674963--1674989 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1674953 AAACTTATTT
1674963 TAATATTAAAAA
1 TAATATTAAAAA
1674975 TAATATTAAAAA
1 TAATATTAAAAA
1674987 TAA
1 TAA
1674990 AAATTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATATTAAAAA
Found at i:1675067 original size:40 final size:40
Alignment explanation
Indices: 1674957--1675069 Score: 108
Period size: 40 Copynumber: 2.8 Consensus size: 40
1674947 ACCTATAAAC
* *
1674957 TTATTTTAATATTAA-AAATAATATTAAAAATAAAAATTATTT
1 TTATATTAATATTAATAATTAATATT--AAAT-AAAATTATTT
* *
1674999 TTATATTAATATTTATAATTAATTTTAAATAAAATTATTT
1 TTATATTAATATTAATAATTAATATTAAATAAAATTATTT
1675039 TTATTATTTAA-A-TAATAATTTAA-ATTAAATA
1 TTA-TA-TTAATATTAATAA-TTAATATTAAATA
1675070 GTAACCCATT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
40 25 0.41
41 11 0.18
42 17 0.28
43 8 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (40 bp):
TTATATTAATATTAATAATTAATATTAAATAAAATTATTT
Found at i:1680893 original size:2 final size:2
Alignment explanation
Indices: 1680888--1680931 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1680878 TTCCTGGGGA
*
1680888 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1680929 AG A
1 AG A
1680932 AGACAGAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1681334 original size:79 final size:79
Alignment explanation
Indices: 1681159--1681310 Score: 241
Period size: 79 Copynumber: 1.9 Consensus size: 79
1681149 TATACAATTT
* * * *
1681159 ATTCAAAATTACATATTTTTGTCATATTTCAATTCATAACACTATTTATCGTAACATATTTTATA
1 ATTCAAAATTACATATTCTTATCATATTTCAATTCATAACAATATTTATCATAACATATTTTATA
1681224 TAATTTATCATTAG
66 TAATTTATCATTAG
* **
1681238 ATTCAAAATTACATATTCTTATCATGTTTCAATTTGTAACAATATTTATCATAACATATTTTATA
1 ATTCAAAATTACATATTCTTATCATATTTCAATTCATAACAATATTTATCATAACATATTTTATA
1681303 TAATTTAT
66 TAATTTAT
1681311 TATAATAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (79 bp):
ATTCAAAATTACATATTCTTATCATATTTCAATTCATAACAATATTTATCATAACATATTTTATA
TAATTTATCATTAG
Found at i:1681769 original size:24 final size:24
Alignment explanation
Indices: 1681734--1681781 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1681724 TTGTTAATTT
*
1681734 AATTAAACA-TTTATAAATATTAAA
1 AATTAAAAATTTTAT-AATATTAAA
1681758 AATTAAAAATTTTATAATATTAAA
1 AATTAAAAATTTTATAATATTAAA
1681782 CATAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AATTAAAAATTTTATAATATTAAA
Found at i:1682021 original size:2 final size:2
Alignment explanation
Indices: 1682016--1682060 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1682006 TGCCTGTGGG
1682016 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1682058 TA T
1 TA T
1682061 GACTGCCTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1683709 original size:125 final size:126
Alignment explanation
Indices: 1683529--1683761 Score: 380
Period size: 125 Copynumber: 1.9 Consensus size: 126
1683519 TTTTCCAAAT
*
1683529 TTAAGCCAGCTCAAGACCAACTGAAAATCTGTTTCACCATTCAATATATCTTTAAAA-ATTATTT
1 TTAAGCCAGCTCAAGACCAACTGAAAATCTGTTTCACCATTCAATATATCATTAAAATATTATTT
*
1683593 TTATATTAATATTAATA-TTTTATAATTAAATTTAAATAAAAATATTATTTTTATCCACAG
66 TCATATTAATATTAATATTTTTATAATTAAATTTAAATAAAAATATTATTTTTATCCACAG
* * * * *
1683653 TTAAGTCAGGTCAAGATCAACCTGAAAATCTGTTTCTCGATTCAATATATCATTAAAATATTATT
1 TTAAGCCAGCTCAAGACCAA-CTGAAAATCTGTTTCACCATTCAATATATCATTAAAATATTATT
1683718 TTCATATTAATATTAATATTTTTATAATTAAATTTAAATAAAAA
65 TTCATATTAATATTAATATTTTTATAATTAAATTTAAATAAAAA
1683762 AATTTTATTA
Statistics
Matches: 99, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
124 17 0.17
125 34 0.34
126 23 0.23
127 25 0.25
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.41
Consensus pattern (126 bp):
TTAAGCCAGCTCAAGACCAACTGAAAATCTGTTTCACCATTCAATATATCATTAAAATATTATTT
TCATATTAATATTAATATTTTTATAATTAAATTTAAATAAAAATATTATTTTTATCCACAG
Found at i:1697032 original size:19 final size:17
Alignment explanation
Indices: 1697000--1697050 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
1696990 AAGTCTAAAA
*
1697000 AAATAAATAAAATATTTT
1 AAATAAA-AAAATAATTT
1697018 ATATATAAAAAAATAATTT
1 A-A-ATAAAAAAATAATTT
*
1697037 AAAAAAAAAAATAA
1 AAATAAAAAAATAA
1697051 AATGATACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 11 0.38
18 2 0.07
19 11 0.38
20 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAAAAAATAATTT
Found at i:1698904 original size:3 final size:3
Alignment explanation
Indices: 1698898--1698929 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1698888 AAAAAATTAA
*
1698898 AAG AAG AAG AAG CAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1698930 TGTTGAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1707155 original size:18 final size:18
Alignment explanation
Indices: 1707105--1707151 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1707095 GAAAGGGAGG
* *
1707105 AAAATATT-TAATTTTTT
1 AAAATATTATAAATATTT
*
1707122 AAAATATTATATATATTT
1 AAAATATTATAAATATTT
1707140 AAAAT-TTATAAA
1 AAAATATTATAAA
1707152 ATATAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATATTATAAATATTT
Found at i:1707161 original size:13 final size:13
Alignment explanation
Indices: 1707145--1707178 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1707135 TATTTAAAAT
1707145 TTATAAAATATAA
1 TTATAAAATATAA
*
1707158 TTATTAAATATAA
1 TTATAAAATATAA
*
1707171 ATATAAAA
1 TTATAAAA
1707179 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTATAAAATATAA
Found at i:1707629 original size:2 final size:2
Alignment explanation
Indices: 1707622--1707675 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
1707612 TTGGTTTTGT
1707622 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1707664 -A TA TA -A TA TA TA
1 TA TA TA TA TA TA TA
1707676 AAAATGTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1707729 original size:3 final size:3
Alignment explanation
Indices: 1707721--1707747 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1707711 AATAGACCAA
1707721 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1707748 GCTTCTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1707846 original size:19 final size:20
Alignment explanation
Indices: 1707805--1707846 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1707795 CGAAAATTAA
*
1707805 TTTTTAAAAATATTGATATT
1 TTTTTAAAAATATAGATATT
* *
1707825 TTTTTAAAATTATAGCTATT
1 TTTTTAAAAATATAGATATT
1707845 TT
1 TT
1707847 ATTATTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTTAAAAATATAGATATT
Found at i:1708036 original size:21 final size:21
Alignment explanation
Indices: 1707984--1708026 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1707974 AAACTAATGA
*
1707984 AATATTATTTATAATTAAAAT
1 AATATAATTTATAATTAAAAT
*
1708005 AATATAATTTATTATTAAAAT
1 AATATAATTTATAATTAAAAT
1708026 A
1 A
1708027 TTAATGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATAATTTATAATTAAAAT
Found at i:1708918 original size:25 final size:25
Alignment explanation
Indices: 1708884--1708939 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
1708874 GCACAGGAAT
1708884 ATTTTTATTACCTTAAAAAATATCA
1 ATTTTTATTACCTTAAAAAATATCA
* *
1708909 ATTTTTATTAGCTTAAAAAATATTA
1 ATTTTTATTACCTTAAAAAATATCA
1708934 ATTTTT
1 ATTTTT
1708940 TTTATTATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTTTTATTACCTTAAAAAATATCA
Found at i:1709559 original size:6 final size:6
Alignment explanation
Indices: 1709548--1709603 Score: 71
Period size: 6 Copynumber: 9.2 Consensus size: 6
1709538 TTAACACAAA
1709548 AAATTT AAATTT AAATTT -AATTT -AATTT AAATTAAT AAAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT--T -AAATTT AAATTT
1709597 AAATTT A
1 AAATTT A
1709604 CTTTAATTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.22
6 29 0.63
7 1 0.02
8 1 0.02
9 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:1709571 original size:5 final size:5
Alignment explanation
Indices: 1709549--1709611 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
1709539 TAACACAAAA
* **
1709549 AATTT AAATTT AAATTT AATTT AATTT AAATT AATAA AATTT AAATTT
1 AATTT -AATTT -AATTT AATTT AATTT AATTT AATTT AATTT -AATTT
*
1709597 AAATTT ACTTT AATT
1 -AATTT AATTT AATT
1709612 CGAATTGAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
5 26 0.54
6 22 0.46
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (5 bp):
AATTT
Found at i:1709760 original size:10 final size:10
Alignment explanation
Indices: 1709745--1709781 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1709735 AAAATTACTA
1709745 TTTTAT-TTT
1 TTTTATATTT
*
1709754 TTTT-TATAT
1 TTTTATATTT
1709763 TTTTATATTT
1 TTTTATATTT
1709773 TTTTATATT
1 TTTTATATT
1709782 ACTTTATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 1 0.04
9 10 0.42
10 13 0.54
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTATATTT
Found at i:1709768 original size:18 final size:18
Alignment explanation
Indices: 1709745--1709781 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1709735 AAAATTACTA
*
1709745 TTTTATTTTTTTTTATAT
1 TTTTATATTTTTTTATAT
1709763 TTTTATATTTTTTTATAT
1 TTTTATATTTTTTTATAT
1709781 T
1 T
1709782 ACTTTATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTATATTTTTTTATAT
Found at i:1712436 original size:2 final size:2
Alignment explanation
Indices: 1712429--1712458 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1712419 TAAACCTGTA
1712429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1712459 TTAAAGCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1718920 original size:34 final size:36
Alignment explanation
Indices: 1718881--1718959 Score: 108
Period size: 34 Copynumber: 2.2 Consensus size: 36
1718871 TTATTTTATG
*
1718881 ATATAAATATAATAATAA-ATATTTATA-TAATATA
1 ATATAAATATAATAATAATATATTAATATTAATATA
* *
1718915 ATATAAATATTATAATAATATATTAATATTTATATA
1 ATATAAATATAATAATAATATATTAATATTAATATA
*
1718951 AAATAAATA
1 ATATAAATA
1718960 ATTAATATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 17 0.44
35 8 0.21
36 14 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (36 bp):
ATATAAATATAATAATAATATATTAATATTAATATA
Found at i:1718923 original size:11 final size:11
Alignment explanation
Indices: 1718881--1718959 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
1718871 TTATTTTATG
1718881 ATATAAATATA
1 ATATAAATATA
1718892 ATAATAAATAT-
1 AT-ATAAATATA
*
1718903 TTATATAATATA
1 ATATA-AATATA
*
1718915 ATATAAATATT
1 ATATAAATATA
1718926 ATAATAATATATTA
1 AT-ATAA-ATA-TA
**
1718940 ATATTTATATA
1 ATATAAATATA
*
1718951 AAATAAATA
1 ATATAAATA
1718960 ATTAATATGT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
10 3 0.06
11 23 0.43
12 19 0.36
13 5 0.09
14 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1720401 original size:10 final size:9
Alignment explanation
Indices: 1720386--1720411 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1720376 ATCGCATGAG
1720386 TTTTTTTCT
1 TTTTTTTCT
1720395 TTTTTTTCT
1 TTTTTTTCT
1720404 TTTTTTTC
1 TTTTTTTC
1720412 CAATTATGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1726072 original size:25 final size:21
Alignment explanation
Indices: 1726033--1726086 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
1726023 AATAAAAAAA
*
1726033 TAATATAAATTTTTATTAAAT
1 TAATATAAATTTTTATCAAAT
1726054 GTAATATAAATTATATTTATCAAAT
1 -TAATATAAA-T-T-TTTATCAAAT
1726079 TAA-ATAAA
1 TAATATAAA
1726087 AGGTAATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 9 0.32
23 6 0.21
24 4 0.14
25 9 0.32
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TAATATAAATTTTTATCAAAT
Found at i:1731264 original size:6 final size:6
Alignment explanation
Indices: 1731255--1731284 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1731245 ACATCTCATC
1731255 CTCAAG CTCAAG CTCAAG CTCAAG CTCAAG
1 CTCAAG CTCAAG CTCAAG CTCAAG CTCAAG
1731285 GCCAATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (6 bp):
CTCAAG
Found at i:1732660 original size:29 final size:29
Alignment explanation
Indices: 1732627--1732684 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1732617 TCCATAAGGC
1732627 GACGTCAATCTCAAGTAAAAATAAAAAGT
1 GACGTCAATCTCAAGTAAAAATAAAAAGT
1732656 GACGTCAATCTCAAGTAAAAATAAAAAGT
1 GACGTCAATCTCAAGTAAAAATAAAAAGT
1732685 AAGAACATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.21
Consensus pattern (29 bp):
GACGTCAATCTCAAGTAAAAATAAAAAGT
Found at i:1737358 original size:2 final size:2
Alignment explanation
Indices: 1737351--1737384 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1737341 AGGCTTAAAC
1737351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1737385 TTGTAAAGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1739092 original size:18 final size:19
Alignment explanation
Indices: 1739061--1739118 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
1739051 ATATTTATTT
* *
1739061 AAAATTTAACATATATA-A
1 AAAATATAATATATATATA
*
1739079 AAAATATAATATAT-TATT
1 AAAATATAATATATATATA
1739097 AAAATATTAATTATATATATA
1 AAAATA-TAA-TATATATATA
1739118 A
1 A
1739119 TTAAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 2 0.06
18 18 0.56
19 3 0.09
20 5 0.16
21 4 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATATAATATATATATA
Found at i:1739099 original size:36 final size:38
Alignment explanation
Indices: 1739044--1739115 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 38
1739034 AATATGTTAT
*
1739044 AAATATTATATTTATTTAAAAT-TTAA-CATATATAAA
1 AAATATAATATTTATTTAAAATATTAATCATATATAAA
*
1739080 AAATATAATATATTA-TTAAAATATTAATTATATATA
1 AAATATAATAT-TTATTTAAAATATTAATCATATATA
1739116 TAATTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 17 0.55
37 7 0.23
38 7 0.23
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (38 bp):
AAATATAATATTTATTTAAAATATTAATCATATATAAA
Found at i:1740121 original size:15 final size:16
Alignment explanation
Indices: 1740101--1740137 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1740091 TTTAAGTAAG
1740101 AATTTAAATTTT-TTA
1 AATTTAAATTTTATTA
*
1740116 AATTTAAATTTTATTT
1 AATTTAAATTTTATTA
1740132 AATTTA
1 AATTTA
1740138 TAAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTAAATTTTATTA
Found at i:1740145 original size:17 final size:18
Alignment explanation
Indices: 1740105--1740145 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
1740095 AGTAAGAATT
1740105 TAAATTT-TTTAAATTTA
1 TAAATTTATTTAAATTTA
*
1740122 -AATTTTATTT-AATTTA
1 TAAATTTATTTAAATTTA
1740138 TAAATTTA
1 TAAATTTA
1740146 AATTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAAATTTATTTAAATTTA
Found at i:1740170 original size:29 final size:23
Alignment explanation
Indices: 1740111--1740157 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
1740101 AATTTAAATT
1740111 TTTTAAATTTAAATTTTATTTAA
1 TTTTAAATTTAAATTTTATTTAA
1740134 TTTATAAATTTAAATTATTATTTA
1 TTT-TAAATTTAAATT-TTATTTA
1740158 TAAAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.14
24 12 0.55
25 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAAATTTAAATTTTATTTAA
Found at i:1742718 original size:21 final size:21
Alignment explanation
Indices: 1742669--1742718 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1742659 TTATGTATAT
1742669 TTTAAATTTTTAAAATTTTTA
1 TTTAAATTTTTAAAATTTTTA
* * *
1742690 -TAATAATTTTTTAATTTTTTA
1 TTTA-AATTTTTAAAATTTTTA
1742711 TTTAAATT
1 TTTAAATT
1742719 AATATTACGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTAAATTTTTAAAATTTTTA
Found at i:1742975 original size:2 final size:2
Alignment explanation
Indices: 1742941--1742965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1742931 GTGGATGGAA
1742941 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1742966 ACACATATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1743346 original size:15 final size:17
Alignment explanation
Indices: 1743326--1743358 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1743316 ATTTGACATT
1743326 TATAAAT-AT-TATTAC
1 TATAAATAATATATTAC
1743341 TATAAATAATATATTAC
1 TATAAATAATATATTAC
1743358 T
1 T
1743359 TAACTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TATAAATAATATATTAC
Found at i:1743528 original size:11 final size:11
Alignment explanation
Indices: 1743497--1743538 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
1743487 TTAAATTAAA
1743497 TTTAATTAATTT
1 TTTAATT-ATTT
*
1743509 ATGTAATTATTT
1 -TTTAATTATTT
1743521 TTTAATTATTT
1 TTTAATTATTT
1743532 TTTAATT
1 TTTAATT
1743539 TTTAATCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 4 0.15
13 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TTTAATTATTT
Found at i:1743803 original size:2 final size:2
Alignment explanation
Indices: 1743796--1743844 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1743786 CCATCACATT
*
1743796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1743838 TA TA TA T
1 TA TA TA T
1743845 GCAAAAACCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1744932 original size:21 final size:20
Alignment explanation
Indices: 1744903--1744942 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1744893 ATATATCGTT
1744903 TTAACTTTTGAAAAATAATC
1 TTAACTTTTGAAAAATAATC
* *
1744923 TTAACCTTTTTAAATATAAT
1 TTAA-CTTTTGAAAAATAAT
1744943 ATAGTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (20 bp):
TTAACTTTTGAAAAATAATC
Found at i:1746133 original size:3 final size:3
Alignment explanation
Indices: 1746127--1746160 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1746117 GAAATGGCTG
1746127 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1746161 ATTTTCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1746693 original size:2 final size:2
Alignment explanation
Indices: 1746688--1746719 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1746678 AAAATAGATC
*
1746688 AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1746720 GGAGGAGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Done.