Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold52
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: 1774672
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 127110 characters in sequence are not A, C, G, or T
File 9 of 9
Found at i:1645276 original size:29 final size:29
Alignment explanation
Indices: 1645222--1645277 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1645212 TTAACGTTCA
* *
1645222 TTTCATTTCTTTATTCTGTTCTCTTTTTT
1 TTTCATTTCTTTATTCTCTTCACTTTTTT
*
1645251 TTTCCTTTCTTT-TTCTCTTCAACTTTT
1 TTTCATTTCTTTATTCTCTTC-ACTTTT
1645278 CCTTCATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTCATTTCTTTATTCTCTTCACTTTTTT
Found at i:1649843 original size:40 final size:40
Alignment explanation
Indices: 1649723--1649843 Score: 111
Period size: 40 Copynumber: 3.0 Consensus size: 40
1649713 AATAAATTAC
* *
1649723 TACTAAAAATATATCCATAATCATAATTTAAATATGATATT
1 TACTAAAAATACATCTATAATCATAATTTAAATATGATA-T
* * * * * * * **
1649764 TATTATAATTAACTTTTGTAATTATAA--TAAATAAAATAT
1 TACTAAAAAT-ACATCTATAATCATAATTTAAATATGATAT
1649803 TACTAAAAATACATCTATAATCATAATTTAAATATGATAT
1 TACTAAAAATACATCTATAATCATAATTTAAATATGATAT
1649843 T
1 T
1649844 TATCGGCATT
Statistics
Matches: 57, Mismatches: 20, Indels: 7
0.68 0.24 0.08
Matches are distributed among these distances:
38 12 0.21
39 8 0.14
40 20 0.35
41 7 0.12
42 10 0.18
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (40 bp):
TACTAAAAATACATCTATAATCATAATTTAAATATGATAT
Found at i:1650812 original size:3 final size:3
Alignment explanation
Indices: 1650804--1650831 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1650794 CTGATATTTG
1650804 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1650832 TCAAACCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1651017 original size:12 final size:12
Alignment explanation
Indices: 1650984--1651018 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1650974 TACTACTACT
*
1650984 GCTAGGGCTAGG
1 GCTAGGGCTGGG
1650996 GCTAGGGCTGGG
1 GCTAGGGCTGGG
*
1651008 GCTGGGGCTGG
1 GCTAGGGCTGG
1651019 CTGAGACTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.17, G:0.57, T:0.17
Consensus pattern (12 bp):
GCTAGGGCTGGG
Found at i:1653119 original size:2 final size:2
Alignment explanation
Indices: 1653112--1653142 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1653102 GAAATGTTGA
1653112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1653143 CCTGAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1663428 original size:30 final size:32
Alignment explanation
Indices: 1663394--1663460 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
1663384 TATGTATTTG
1663394 TATTTGTAT-TATTTTTT-TATATAAAT-ATT
1 TATTTGTATATATTTTTTATATATAAATAATT
* *
1663423 ATATTTTTATATATTTTTTATATATTAATAATT
1 -TATTTGTATATATTTTTTATATATAAATAATT
1663456 TATTT
1 TATTT
1663461 ATTTTATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 8 0.25
31 8 0.25
32 13 0.41
33 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (32 bp):
TATTTGTATATATTTTTTATATATAAATAATT
Found at i:1663432 original size:8 final size:9
Alignment explanation
Indices: 1663421--1663481 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
1663411 TATATAAATA
1663421 TTATAT-TT
1 TTATATATT
1663429 TTATATATT
1 TTATATATT
* *
1663438 TTTTATATA
1 TTATATATT
*
1663447 TTA-ATAAT
1 TTATATATT
*
1663455 TTATTTATT
1 TTATATATT
1663464 TTATATATAT
1 TTATATAT-T
*
1663474 TTTTATAT
1 TTATATAT
1663482 GTATGTATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 12 0.29
9 21 0.51
10 8 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATATATT
Found at i:1663440 original size:11 final size:11
Alignment explanation
Indices: 1663422--1663481 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
1663412 ATATAAATAT
1663422 TATA-TTTTTA
1 TATATTTTTTA
1663432 TATATTTTTTA
1 TATATTTTTTA
1663443 TATATTAATAATTTA
1 TATATT--T--TTTA
* *
1663458 TTTATTTTATA
1 TATATTTTTTA
1663469 TATA-TTTTTA
1 TATATTTTTTA
1663479 TAT
1 TAT
1663482 GTATGTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 12 0.29
11 18 0.44
13 2 0.05
15 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTTTTA
Found at i:1663443 original size:19 final size:19
Alignment explanation
Indices: 1663400--1663495 Score: 81
Period size: 19 Copynumber: 5.2 Consensus size: 19
1663390 TTTGTATTTG
* **
1663400 TATTATTTTTTTATATAAA
1 TATTATATTTTTATATATT
1663419 TATTATATTTTTATATATT
1 TATTATATTTTTATATATT
* * *
1663438 TTTTATATATTAATA-ATT
1 TATTATATTTTTATATATT
1663456 TATT-TATTTTATATATATT
1 TATTATATTTT-TATATATT
* * *
1663475 T-TTATATGTATGTATATT
1 TATTATATTTTTATATATT
1663493 TAT
1 TAT
1663496 ATTATGTGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
17 5 0.08
18 19 0.31
19 37 0.61
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTATATTTTTATATATT
Found at i:1663462 original size:30 final size:30
Alignment explanation
Indices: 1663394--1663500 Score: 83
Period size: 32 Copynumber: 3.4 Consensus size: 30
1663384 TATGTATTTG
*
1663394 TATTTGTATTATTTTTTTATATAAATATTA
1 TATTTATATTATTTTTTTATATAAATATTA
* *
1663424 TATTTTTATATATTTTTTATATATTAATAATT-
1 TATTTATAT-TATTTTTT-TATATAAAT-ATTA
* **
1663456 TATTTATTTTATATATATTTT-TATATGTATGTA
1 TATTTATATTAT-T-T-TTTTATATAAATAT-TA
1663489 TATTTATATTAT
1 TATTTATATTAT
1663501 GTGTATATTA
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
30 8 0.13
31 13 0.21
32 21 0.34
33 16 0.26
34 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (30 bp):
TATTTATATTATTTTTTTATATAAATATTA
Found at i:1664179 original size:12 final size:12
Alignment explanation
Indices: 1664119--1664250 Score: 55
Period size: 11 Copynumber: 11.0 Consensus size: 12
1664109 TGTATTTAAA
1664119 ATAT-TATTTTT
1 ATATATATTTTT
1664130 ATATAT-TTTTT
1 ATATATATTTTT
*
1664141 ATATATTAATAATTT
1 ATATA-T-AT-TTTT
*
1664156 AT-TTTA-TTTT
1 ATATATATTTTT
*
1664166 ATGTATATTTTT
1 ATATATATTTTT
1664178 ATATATATGTGTATT
1 ATATATAT-T-T-TT
* * *
1664193 A-ATATAATGTG
1 ATATATATTTTT
1664204 AT-TATTATTTTT
1 ATATA-TATTTTT
*
1664216 ATGT-TATATTTT
1 ATATATAT-TTTT
*
1664228 AAATAT-TTTTT
1 ATATATATTTTT
*
1664239 ATAAATATTTTT
1 ATATATATTTTT
1664251 TATGTTATTT
Statistics
Matches: 90, Mismatches: 15, Indels: 31
0.66 0.11 0.23
Matches are distributed among these distances:
10 5 0.06
11 32 0.36
12 32 0.36
13 5 0.06
14 8 0.09
15 8 0.09
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (12 bp):
ATATATATTTTT
Found at i:1664605 original size:33 final size:34
Alignment explanation
Indices: 1664560--1664624 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
1664550 GTCTTAATTT
* * *
1664560 ATTTTATATTTTATATAAATTTTTTATATATTAA
1 ATTTTATATTTTAAATAAATTTATTAAATATTAA
*
1664594 ATTTTA-ATTTTAAATATATTTATTAAATATT
1 ATTTTATATTTTAAATAAATTTATTAAATATT
1664625 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
ATTTTATATTTTAAATAAATTTATTAAATATTAA
Found at i:1665595 original size:2 final size:2
Alignment explanation
Indices: 1665588--1665613 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1665578 AGCCTATACT
1665588 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
1665614 AAATATTGAT
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):
TA
Found at i:1666490 original size:15 final size:15
Alignment explanation
Indices: 1666461--1666497 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1666451 TTTTTTATAT
*
1666461 TTTAA-TTAGAGTTC
1 TTTAATTTAGAATTC
1666475 TTTAATTTAGAATTC
1 TTTAATTTAGAATTC
1666490 TTTAATTT
1 TTTAATTT
1666498 TTTAATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (15 bp):
TTTAATTTAGAATTC
Found at i:1666604 original size:93 final size:95
Alignment explanation
Indices: 1666427--1666604 Score: 204
Period size: 93 Copynumber: 1.9 Consensus size: 95
1666417 TACAAAAATA
* * * * *
1666427 CTTTTCTTCTAATTTTATAACTATTTTTTTATATTTTAATTAGAGTTCTTTAATTTAGAATTCTT
1 CTTTTCTTCTAATTTTATAACTATTTTTTTATATTTTAAGTACAATTCTTTAATTTACAAATCTT
** *
1666492 TAATTTTTTAATTATGTTTATTAAAATAAT
66 TAATCATATAATTATGTTTATTAAAATAAT
*
1666522 CTTTT-TT-TAATTTTATAACTATTTTTTTATATTTTAGGTACAATTCTTTAATTTTTACAAGAT
1 CTTTTCTTCTAATTTTATAACTATTTTTTTATATTTTAAGTACAATTCTTTAA--TTTACAA-AT
*
1666585 -TTTAA-CATATATTTA-GTTTA
63 CTTTAATCATATAATTATGTTTA
1666605 ATCTTAAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
93 45 0.64
94 8 0.11
95 16 0.23
96 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.58
Consensus pattern (95 bp):
CTTTTCTTCTAATTTTATAACTATTTTTTTATATTTTAAGTACAATTCTTTAATTTACAAATCTT
TAATCATATAATTATGTTTATTAAAATAAT
Found at i:1669547 original size:2 final size:2
Alignment explanation
Indices: 1669542--1669571 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1669532 AATAGGAAGA
1669542 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
1669572 TTCATCATGA
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:1671680 original size:23 final size:24
Alignment explanation
Indices: 1671654--1671707 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
1671644 ATTATGAGAA
*
1671654 TTAAAATATGATGT-ATAAAATAT
1 TTAAAATATAATGTGATAAAATAT
* * *
1671677 TTAAAATTTAATGTGATTATATAT
1 TTAAAATATAATGTGATAAAATAT
1671701 TTAAAAT
1 TTAAAAT
1671708 GTGTATCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (24 bp):
TTAAAATATAATGTGATAAAATAT
Found at i:1674296 original size:19 final size:18
Alignment explanation
Indices: 1674272--1674308 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1674262 AATTGATTTG
1674272 ATAATATTTATTAATTAAA
1 ATAATATTT-TTAATTAAA
*
1674291 ATAATATTTTTATTTAAA
1 ATAATATTTTTAATTAAA
1674309 TTTAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAATATTTTTAATTAAA
Found at i:1674905 original size:19 final size:20
Alignment explanation
Indices: 1674873--1674910 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1674863 AAAAAATAAT
1674873 ATAAATATAATATA-AATAC
1 ATAAATATAATATATAATAC
**
1674892 ATAAATATTTTATATAATA
1 ATAAATATAATATATAATA
1674911 TTAATATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAATATAATATATAATAC
Found at i:1674934 original size:46 final size:48
Alignment explanation
Indices: 1674873--1674984 Score: 117
Period size: 46 Copynumber: 2.3 Consensus size: 48
1674863 AAAAAATAAT
*
1674873 ATAAATATAATATAAATACATAAATATTTT-ATATAA-TATTAATAT-ATTC
1 ATAAA-AT-ATATAAATA-ATAAATATTTTAATATAATTA-TAATATAATTA
* *
1674922 A-AAAATATATAAAT-ATAATTTTTTTAAATATAATTATAATATAATTA
1 ATAAAATATATAAATAATAAATATTTT-AATATAATTATAATATAATTA
1674969 ATAAAATATATAAATA
1 ATAAAATATATAAATA
1674985 TAATAAGATA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
44 9 0.17
46 20 0.37
47 8 0.15
48 16 0.30
49 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (48 bp):
ATAAAATATATAAATAATAAATATTTTAATATAATTATAATATAATTA
Found at i:1684558 original size:29 final size:29
Alignment explanation
Indices: 1684499--1684565 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1684489 AAAAGCCACC
* * *
1684499 TTTTTTGTTTGTCAAAAATTGTGGTTTTT
1 TTTTTTGTTTGTCAAAAAATGTGATTCTT
1684528 TTTTTTGTTTGT-AAAAAATGATGATTCTT
1 TTTTTTGTTTGTCAAAAAATG-TGATTCTT
1684557 TTTATTTGT
1 TTT-TTTGT
1684566 CAAAAATAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 7 0.21
29 21 0.64
30 5 0.15
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.61
Consensus pattern (29 bp):
TTTTTTGTTTGTCAAAAAATGTGATTCTT
Found at i:1685145 original size:96 final size:96
Alignment explanation
Indices: 1684981--1685174 Score: 388
Period size: 96 Copynumber: 2.0 Consensus size: 96
1684971 TTTTTATTAC
1684981 AAAACGGAGGAAGATGGAGCTTATAAAAGAAGGCTCCCTCCTCCTTCTCATGTATCCTTCTCCAA
1 AAAACGGAGGAAGATGGAGCTTATAAAAGAAGGCTCCCTCCTCCTTCTCATGTATCCTTCTCCAA
1685046 TTCATTCTCATAATAGAATTGGTAATATCTG
66 TTCATTCTCATAATAGAATTGGTAATATCTG
1685077 AAAACGGAGGAAGATGGAGCTTATAAAAGAAGGCTCCCTCCTCCTTCTCATGTATCCTTCTCCAA
1 AAAACGGAGGAAGATGGAGCTTATAAAAGAAGGCTCCCTCCTCCTTCTCATGTATCCTTCTCCAA
1685142 TTCATTCTCATAATAGAATTGGTAATATCTG
66 TTCATTCTCATAATAGAATTGGTAATATCTG
1685173 AA
1 AA
1685175 GAAGTAGGCA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (96 bp):
AAAACGGAGGAAGATGGAGCTTATAAAAGAAGGCTCCCTCCTCCTTCTCATGTATCCTTCTCCAA
TTCATTCTCATAATAGAATTGGTAATATCTG
Found at i:1687120 original size:39 final size:39
Alignment explanation
Indices: 1687068--1687142 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
1687058 GAACAATGGA
*
1687068 GGGGAATATAAAAGTGATCTGCTCTTTGATGTTTGCTAG
1 GGGGAATATAAAAGTGATCCGCTCTTTGATGTTTGCTAG
1687107 GGGGAATATAAAAGTGATCCGCTCTTTGATGTTTGC
1 GGGGAATATAAAAGTGATCCGCTCTTTGATGTTTGC
1687143 CAGGAGCATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (39 bp):
GGGGAATATAAAAGTGATCCGCTCTTTGATGTTTGCTAG
Found at i:1689571 original size:27 final size:26
Alignment explanation
Indices: 1689514--1689572 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1689504 AAAAACCACC
* *
1689514 ATTTTTGTTTGTCAAAAATGGTGGTT
1 ATTTTTGTTTGTCAAAAATGGTGCTA
* *
1689540 CTTTTTGTTTGTCAAAATTGGTGACTA
1 ATTTTTGTTTGTCAAAAATGGTG-CTA
1689567 ATTTTT
1 ATTTTT
1689573 ATTACAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.53
Consensus pattern (26 bp):
ATTTTTGTTTGTCAAAAATGGTGCTA
Found at i:1695294 original size:16 final size:16
Alignment explanation
Indices: 1695256--1695291 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1695246 TTCGATTTAA
*
1695256 ATAAATAATTTTATTT
1 ATAAATAAATTTATTT
1695272 ATAAATAAATTTA-TT
1 ATAAATAAATTTATTT
1695287 ATAAA
1 ATAAA
1695292 ATATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATAAATTTATTT
Found at i:1695969 original size:13 final size:13
Alignment explanation
Indices: 1695933--1695979 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1695923 ATTTATACTT
*
1695933 ATATATATATTAA
1 ATATAAATATTAA
* *
1695946 ATATGATTATTAA
1 ATATAAATATTAA
1695959 ATATAAATATTTAA
1 ATATAAATA-TTAA
1695973 A-ATAAAT
1 ATATAAAT
1695980 TTTACGTAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 23 0.82
14 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATAAATATTAA
Found at i:1698101 original size:12 final size:12
Alignment explanation
Indices: 1698084--1698108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1698074 CTTATACAAT
1698084 ATTTAAAAAATA
1 ATTTAAAAAATA
1698096 ATTTAAAAAATA
1 ATTTAAAAAATA
1698108 A
1 A
1698109 ACGAGATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTTAAAAAATA
Found at i:1699079 original size:39 final size:40
Alignment explanation
Indices: 1699007--1699082 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
1698997 AATTATGATT
* *
1699007 TATAAAATAATTTTTATTTAAATTTAATTATTAATATTAA
1 TATAAAATAATTTTTATATAAATTTAATAATTAATATTAA
*
1699047 TATAAAATAA-TTTTA-ATATATTTAAATAATTAATAT
1 TATAAAATAATTTTTATATAAATTT-AATAATTAATAT
1699083 CAATTTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 6 0.19
39 16 0.50
40 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (40 bp):
TATAAAATAATTTTTATATAAATTTAATAATTAATATTAA
Found at i:1699120 original size:18 final size:20
Alignment explanation
Indices: 1699094--1699136 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
1699084 AATTTTTGAT
*
1699094 AAATTTAAAT-TTAA-ATAA
1 AAATATAAATATTAACATAA
1699112 AAATATAAATATTAACATAA
1 AAATATAAATATTAACATAA
1699132 AAATA
1 AAATA
1699137 ATATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 4 0.18
20 9 0.41
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAAATATTAACATAA
Found at i:1699145 original size:19 final size:19
Alignment explanation
Indices: 1699094--1699145 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1699084 AATTTTTGAT
*
1699094 AAATTTAAA-TTTAAATAA
1 AAATATAAATTTTAAATAA
*
1699112 AAATATAAATATTAACATAA
1 AAATATAAATTTTAA-ATAA
*
1699132 AAATA-ATATTTTAA
1 AAATATAAATTTTAA
1699146 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 8 0.29
19 11 0.39
20 9 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATAAATTTTAAATAA
Found at i:1699337 original size:19 final size:21
Alignment explanation
Indices: 1699315--1699363 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
1699305 TATTTAAAAA
1699315 ATATTAAAATAT-TAT-TTTT
1 ATATTAAAATATATATATTTT
* *
1699334 ATATTAATATTTATATATTTT
1 ATATTAAAATATATATATTTT
1699355 ATAATTAAA
1 AT-ATTAAA
1699364 TTTAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
20 3 0.12
21 6 0.25
22 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTAAAATATATATATTTT
Found at i:1699417 original size:22 final size:22
Alignment explanation
Indices: 1699367--1699418 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1699357 AATTAAATTT
* * *
1699367 AAATTAAAAAATATTTTTAATA
1 AAATTAAATAATAATTTAAATA
*
1699389 TAA-TAAATAATAATTTAAATA
1 AAATTAAATAATAATTTAAATA
1699410 AAATTAAAT
1 AAATTAAAT
1699419 TAAATTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTAAATAATAATTTAAATA
Found at i:1699902 original size:5 final size:5
Alignment explanation
Indices: 1699886--1699955 Score: 55
Period size: 5 Copynumber: 15.2 Consensus size: 5
1699876 TATCTTATTA
* * *
1699886 TATAT TTTAT TATAT TATAAT TATAT T-TAA AATAT TATA- TAT-T TATAT
1 TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TATAT TATAT
1699934 TAT-T T-T-T TATAT TATAT T-TAT T
1 TATAT TATAT TATAT TATAT TATAT T
1699956 TTTTTATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
3 3 0.06
4 15 0.28
5 30 0.57
6 5 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TATAT
Found at i:1699944 original size:12 final size:13
Alignment explanation
Indices: 1699881--1699950 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 13
1699871 ATTTTTATCT
1699881 TATTATATATTT-
1 TATTATATATTTA
*
1699893 TATTATAT-TATA
1 TATTATATATTTA
*
1699905 -ATTATAT-TTAAAA
1 TATTATATATT--TA
1699918 TATTATATATTTA
1 TATTATATATTTA
*
1699931 TATTAT-TTTTTA
1 TATTATATATTTA
1699943 TATTATAT
1 TATTATAT
1699951 TTATTTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 10 0.21
12 19 0.40
13 9 0.19
14 7 0.15
15 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATATATTTA
Found at i:1699950 original size:17 final size:17
Alignment explanation
Indices: 1699923--1699971 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
1699913 TAAAATATTA
1699923 TATATTTATATTATTTTT
1 TATA-TTATATTATTTTT
1699941 TATATTATATTTATTTTT
1 TATATTATA-TTATTTTT
*
1699959 T-TATAATATTATT
1 TATATTATATTATT
1699972 AAGTTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 5 0.17
17 11 0.38
18 13 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTATATTATTTTT
Found at i:1700110 original size:19 final size:21
Alignment explanation
Indices: 1700071--1700141 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
1700061 TATTTTATTA
1700071 TTTTATAATTAAATTTAAATAAT
1 TTTTA-AATTAAA-TTAAATAAT
*
1700094 TTTT-TATTAAA-TAAATAAT
1 TTTTAAATTAAATTAAATAAT
1700113 TATTTAAATTAAATTAAAT-AT
1 T-TTTAAATTAAATTAAATAAT
*
1700134 ATTTAAAT
1 TTTTAAAT
1700142 CATTAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
19 9 0.21
20 10 0.24
21 14 0.33
22 5 0.12
23 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAATTAAATTAAATAAT
Found at i:1700150 original size:23 final size:21
Alignment explanation
Indices: 1700120--1700163 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1700110 AATTATTTAA
1700120 ATTAAATTAAATATATTTAAATC
1 ATTAAATT--ATATATTTAAATC
*
1700143 ATTAAATTTTATATTTAAATC
1 ATTAAATTATATATTTAAATC
1700164 CCGTTAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
23 8 0.40
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAAATTATATATTTAAATC
Found at i:1700948 original size:21 final size:22
Alignment explanation
Indices: 1700918--1700966 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1700908 GTTTAAAAAA
1700918 ATTTAAAATTTAAAATTTGA-T
1 ATTTAAAATTTAAAATTTGATT
* * *
1700939 ATTTATAATTTATAATTTTATT
1 ATTTAAAATTTAAAATTTGATT
1700961 ATTTAA
1 ATTTAA
1700967 TTATAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTAAAATTTAAAATTTGATT
Found at i:1701828 original size:17 final size:17
Alignment explanation
Indices: 1701803--1701908 Score: 63
Period size: 17 Copynumber: 6.6 Consensus size: 17
1701793 CGAATAATAT
1701803 AAATATATAATATATTA
1 AAATATATAATATATTA
*
1701820 AAATTTAT-ATA-ATATA
1 AAATATATAATATAT-TA
*
1701836 AAATAT-TAATTTATT-
1 AAATATATAATATATTA
1701851 AAA-AT-T--TATA-T-
1 AAATATATAATATATTA
*
1701862 AAATATATAATATTTTA
1 AAATATATAATATATTA
1701879 AATATAATTATAATAT-TTAA
1 AA-AT-A-TATAATATATT-A
1701899 AAATATATAA
1 AAATATATAA
1701909 AAATAATCCA
Statistics
Matches: 71, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
11 4 0.06
12 5 0.07
13 1 0.01
14 3 0.04
15 9 0.13
16 14 0.20
17 16 0.23
18 3 0.04
19 5 0.07
20 11 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATATAATATATTA
Found at i:1701837 original size:32 final size:33
Alignment explanation
Indices: 1701796--1701884 Score: 119
Period size: 32 Copynumber: 2.7 Consensus size: 33
1701786 AAAATTACGA
1701796 ATAATATAAATATA-TAATATATTAAAATTTAT
1 ATAATATAAATATATTAATATATTAAAATTTAT
*
1701828 ATAATATAAA-ATATTAATTTATTAAAATTTAT
1 ATAATATAAATATATTAATATATTAAAATTTAT
*
1701860 ATAAATATATAATATTTTAAATATA
1 AT-AATATA-AATATATT-AATATA
1701885 ATTATAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
31 3 0.06
32 29 0.59
33 6 0.12
34 2 0.04
35 4 0.08
36 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
ATAATATAAATATATTAATATATTAAAATTTAT
Found at i:1702209 original size:18 final size:18
Alignment explanation
Indices: 1702170--1702212 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
1702160 AATTTAAAAT
*
1702170 TTAATATAAAAGATAATA
1 TTAATATAAAAAATAATA
1702188 --AATATAAAAAATAATA
1 TTAATATAAAAAATAATA
1702204 TTAATATAA
1 TTAATATAA
1702213 TATAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 15 0.68
18 7 0.32
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TTAATATAAAAAATAATA
Found at i:1703474 original size:19 final size:18
Alignment explanation
Indices: 1703426--1703474 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1703416 GTAAATTTGC
*
1703426 AAATCTGAAAATCTGTAG
1 AAATCAGAAAATCTGTAG
1703444 AAATCA-AGAAATCTGCTAG
1 AAATCAGA-AAATCTG-TAG
*
1703463 AATTCAGAAAAT
1 AAATCAGAAAAT
1703475 ATGGAAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
19 12 0.46
20 1 0.04
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.24
Consensus pattern (18 bp):
AAATCAGAAAATCTGTAG
Found at i:1708207 original size:16 final size:16
Alignment explanation
Indices: 1708186--1708247 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
1708176 AAATATCTAA
1708186 AAAATCAAAAAATTTC
1 AAAATCAAAAAATTTC
*
1708202 AAAATCAATAAATTT-
1 AAAATCAAAAAATTTC
* * *
1708217 ACAGATCTAAAAATCTC
1 A-AAATCAAAAAATTTC
*
1708234 AAAAATCAAGAAAT
1 -AAAATCAAAAAAT
1708248 CTGAAAATCT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
15 1 0.03
16 24 0.69
17 9 0.26
18 1 0.03
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAATCAAAAAATTTC
Found at i:1708258 original size:33 final size:31
Alignment explanation
Indices: 1708186--1708258 Score: 74
Period size: 33 Copynumber: 2.3 Consensus size: 31
1708176 AAATATCTAA
* * * *
1708186 AAAATCAAAAAATTTCAAAATCAATAAATTT
1 AAAATCTAAAAATCTCAAAATCAAGAAATTG
*
1708217 ACAGATCTAAAAATCTCAAAAATCAAGAAATCTG
1 A-AAATCTAAAAATCTC-AAAATCAAGAAAT-TG
1708251 AAAATCTA
1 AAAATCTA
1708259 CAGAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 1 0.03
32 12 0.36
33 18 0.55
34 2 0.06
ACGTcount: A:0.58, C:0.14, G:0.04, T:0.25
Consensus pattern (31 bp):
AAAATCTAAAAATCTCAAAATCAAGAAATTG
Found at i:1708272 original size:18 final size:19
Alignment explanation
Indices: 1708251--1708295 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1708241 AAGAAATCTG
1708251 AAAATCTAC-AGAAATAAA
1 AAAATCTACTAGAAATAAA
* * *
1708269 AAAATCTGCTAGAATTCAA
1 AAAATCTACTAGAAATAAA
1708288 AAAATCTA
1 AAAATCTA
1708296 GAAATCTGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.58, C:0.13, G:0.07, T:0.22
Consensus pattern (19 bp):
AAAATCTACTAGAAATAAA
Found at i:1708706 original size:28 final size:29
Alignment explanation
Indices: 1708652--1708711 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
1708642 CATGTCTTTA
1708652 TTTAAATGTTATGTCTTTACATAACAA-T
1 TTTAAATGTTATGTCTTTACATAACAACT
*
1708680 TTTAAATGTTGTGTTCTTT-CA-ACACAACT
1 TTTAAATGTTATG-TCTTTACATA-ACAACT
1708709 TTT
1 TTT
1708712 TGATGCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.04
28 18 0.64
29 9 0.32
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (29 bp):
TTTAAATGTTATGTCTTTACATAACAACT
Found at i:1710691 original size:4 final size:4
Alignment explanation
Indices: 1710662--1710735 Score: 55
Period size: 4 Copynumber: 19.2 Consensus size: 4
1710652 AAAAAACCTT
* * * * * *
1710662 ATAC GTAC ATAT ATAC ATAT ATAC ATAC AT-- ATAC ATAC AAAC CT-T
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
1710707 ATGC ATAC ATAC ACAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1710736 AACCTTATAC
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
2 2 0.04
3 1 0.02
4 49 0.94
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1711612 original size:24 final size:23
Alignment explanation
Indices: 1711564--1711608 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1711554 TTTTGACGAA
*
1711564 TAAAAATTCAATCAAAAATTAAT
1 TAAAAAATCAATCAAAAATTAAT
1711587 TAAAAAATCAAAT-AAAAATTAA
1 TAAAAAATC-AATCAAAAATTAA
1711609 ATTATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAAAATCAATCAAAAATTAAT
Found at i:1711884 original size:20 final size:20
Alignment explanation
Indices: 1711850--1711902 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1711840 ATAAAAAATA
* *
1711850 TTTTTATTAATTTAACTCAAT
1 TTTTTATCAA-TTAAATCAAT
*
1711871 TTTTTATCAATTAAATTAAT
1 TTTTTATCAATTAAATCAAT
*
1711891 TTTTTAACAATT
1 TTTTTATCAATT
1711903 TTTAAAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTATCAATTAAATCAAT
Found at i:1712232 original size:29 final size:29
Alignment explanation
Indices: 1712195--1712252 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1712185 TTTTCTGAGA
**
1712195 TACAATGATGTGGTAATCAAATTGAGATT
1 TACAATGATGCAGTAATCAAATTGAGATT
*
1712224 TACAGTGATGCAGTAATCAAATTGAGATT
1 TACAATGATGCAGTAATCAAATTGAGATT
1712253 ATTACATCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (29 bp):
TACAATGATGCAGTAATCAAATTGAGATT
Found at i:1712918 original size:18 final size:18
Alignment explanation
Indices: 1712865--1712921 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1712855 TATTTATAAA
1712865 ATAAAAATTATTTTTTAAT
1 ATAAAAA-TATTTTTTAAT
* * ** *
1712884 TTAAATATAAATATTAAT
1 ATAAAAATATTTTTTAAT
1712902 ATAAAAATATTTTTTAAT
1 ATAAAAATATTTTTTAAT
1712920 AT
1 AT
1712922 TATTTAAAAC
Statistics
Matches: 28, Mismatches: 10, Indels: 1
0.72 0.26 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAAAAATATTTTTTAAT
Found at i:1713248 original size:17 final size:18
Alignment explanation
Indices: 1713188--1713252 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 18
1713178 TATTATATAT
1713188 TACAATTTATATAAAATAA
1 TACAATTTATA-AAAATAA
*
1713207 TA-ATATTT-TAAATATAA
1 TACA-ATTTATAAAAATAA
*
1713224 TTATAATTTATAAAAAT-A
1 -TACAATTTATAAAAATAA
1713242 TACAATTTATA
1 TACAATTTATA
1713253 TTATATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 16 0.41
18 10 0.26
19 13 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TACAATTTATAAAAATAA
Found at i:1713542 original size:14 final size:14
Alignment explanation
Indices: 1713523--1713557 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1713513 AAAGGTGAAA
*
1713523 ATTTATATTTTAAT
1 ATTTATATTTAAAT
1713537 ATTTATATTTAAAT
1 ATTTATATTTAAAT
*
1713551 ATATATA
1 ATTTATA
1713558 ATATGTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTATATTTAAAT
Found at i:1714134 original size:18 final size:20
Alignment explanation
Indices: 1714098--1714136 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
1714088 TTAATATATA
1714098 ATATATCAAAATTTATAAAT
1 ATATATCAAAATTTATAAAT
*
1714118 ATATAT-AATATTT-TAAAT
1 ATATATCAAAATTTATAAAT
1714136 A
1 A
1714137 CATGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATATCAAAATTTATAAAT
Found at i:1714383 original size:2 final size:2
Alignment explanation
Indices: 1714365--1714411 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1714355 TATCAACTTT
* * *
1714365 TA TA TC TA TA CA TA TA TA TA CA 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
1714407 TA TA T
1 TA TA T
1714412 TATTCATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1717379 original size:2 final size:2
Alignment explanation
Indices: 1717374--1717402 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1717364 GTTAAGTGTG
1717374 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1717403 AAAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1719588 original size:27 final size:26
Alignment explanation
Indices: 1719528--1719625 Score: 65
Period size: 27 Copynumber: 3.6 Consensus size: 26
1719518 ATCAAAATTT
* *
1719528 ATATAACATGAAATATTAATTTATTAA
1 ATATAATAT-AAATATTAATATATTAA
*
1719555 A-ATTAATATAAATATATAATATGTTAA
1 ATA-TAATATAAATAT-TAATATATTAA
*
1719582 ATATAAT-TATAATATCTAAAAGTATATAA
1 ATATAATATA-AATAT-TAATA-TAT-TAA
* *
1719611 AAATAATGTAAATAT
1 ATATAATATAAATAT
1719626 ATGAATTATC
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
26 9 0.16
27 29 0.51
28 3 0.05
29 14 0.25
30 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (26 bp):
ATATAATATAAATATTAATATATTAA
Found at i:1719862 original size:20 final size:21
Alignment explanation
Indices: 1719837--1719876 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1719827 GGTTATATGT
*
1719837 TAAAAATTTGATA-AAAATAA
1 TAAAAATTTAATATAAAATAA
1719857 TAAAAATTTAATATAAAATA
1 TAAAAATTTAATATAAAATA
1719877 TGATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
TAAAAATTTAATATAAAATAA
Found at i:1720405 original size:2 final size:2
Alignment explanation
Indices: 1720398--1720430 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1720388 GGGATAAAAG
1720398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1720431 GCAAGTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1722845 original size:35 final size:35
Alignment explanation
Indices: 1722782--1722849 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1722772 ATACATATTT
* * *
1722782 ACACACACATCCATACAAACCTTATACATACATAC
1 ACACAAACATACAAACAAACCTTATACATACATAC
* *
1722817 ACACAAACATACAAACAAGCCTTGTACATACAT
1 ACACAAACATACAAACAAACCTTATACATACAT
1722850 TCATTCATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (35 bp):
ACACAAACATACAAACAAACCTTATACATACATAC
Found at i:1723933 original size:20 final size:20
Alignment explanation
Indices: 1723908--1723960 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1723898 AATAAAAATA
*
1723908 TTTTTATCAATTTAATTTAT
1 TTTTTATCAATTTAATTAAT
* *
1723928 TTTTTATTAATTAAATTAAT
1 TTTTTATCAATTTAATTAAT
*
1723948 TTTTTAACAATTT
1 TTTTTATCAATTT
1723961 TTAAATATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTATCAATTTAATTAAT
Found at i:1728720 original size:20 final size:20
Alignment explanation
Indices: 1728697--1728738 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1728687 ATTTTGATAT
1728697 TAAATATAATAATTAA-TTAA
1 TAAA-ATAATAATTAATTTAA
* *
1728717 TAAAATTATATTTAATTTAA
1 TAAAATAATAATTAATTTAA
1728737 TA
1 TA
1728739 TTATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAATAATAATTAATTTAA
Found at i:1729565 original size:23 final size:25
Alignment explanation
Indices: 1729538--1729591 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
1729528 CGACTTGATT
1729538 TAAATTA-TT-ATTTAATTGAT-AAA
1 TAAATTATTTAATTTAATT-ATAAAA
1729561 TAAATTATTTAAATTTAATTATAAAA
1 TAAATTATTT-AATTTAATTATAAAA
1729587 TAAAT
1 TAAAT
1729592 AAATATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.26
24 2 0.07
25 2 0.07
26 16 0.59
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TAAATTATTTAATTTAATTATAAAA
Found at i:1729862 original size:12 final size:12
Alignment explanation
Indices: 1729845--1729896 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
1729835 ATTTAAAAAA
*
1729845 ATAAAATTTAAT
1 ATAAAATATAAT
1729857 ATAAAATATAAT
1 ATAAAATATAAT
* *
1729869 ATAAAAAATAAC
1 ATAAAATATAAT
1729881 ATAAAA-ATAAT
1 ATAAAATATAAT
1729892 ATAAA
1 ATAAA
1729897 TATTTGAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
11 9 0.25
12 27 0.75
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:1733208 original size:12 final size:11
Alignment explanation
Indices: 1733176--1733209 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
1733166 ATATATATAT
1733176 ATATAATATATA
1 ATATAATA-ATA
1733188 ATATAATAATA
1 ATATAATAATA
1733199 ATAATAATAAT
1 AT-ATAATAAT
1733210 GTTTGACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAATAATA
Found at i:1734631 original size:28 final size:28
Alignment explanation
Indices: 1734600--1734656 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1734590 TTATATTTAT
1734600 TTTATTTTAAAAAATAAAAATTAAATTA
1 TTTATTTTAAAAAATAAAAATTAAATTA
** * *
1734628 TTTATTTTTTAATATAAAAATTAATTTA
1 TTTATTTTAAAAAATAAAAATTAAATTA
1734656 T
1 T
1734657 ATTAAACGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTATTTTAAAAAATAAAAATTAAATTA
Found at i:1735790 original size:22 final size:19
Alignment explanation
Indices: 1735765--1735807 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
1735755 TATTAAAATT
1735765 AATATAAATATATAATATCTTA
1 AATAT-AAT-TATAATAT-TTA
*
1735787 AATATGATTATAATATTTA
1 AATATAATTATAATATTTA
1735806 AA
1 AA
1735808 AATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 2 0.10
22 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATAATTATAATATTTA
Found at i:1736059 original size:2 final size:2
Alignment explanation
Indices: 1736047--1736097 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1736037 TTTTAATTGT
*
1736047 TA TA TA CA 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
1736089 TA TA TA TA T
1 TA TA TA TA T
1736098 GATTGTATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1736142 original size:31 final size:28
Alignment explanation
Indices: 1736107--1736187 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 28
1736097 TGATTGTATG
*
1736107 ATATAAATTTGATAAAAATAATAAAAATTTA
1 ATATAAATATGATAAAAATAA-AAAAA--TA
1736138 ATATAAAATATGATAAAATATAAAAAAATA
1 ATAT-AAATATGATAAAA-ATAAAAAAATA
* *
1736168 ATATTAATATGATATAAATA
1 ATATAAATATGATAAAAATA
1736188 TATGAATGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
28 3 0.07
29 11 0.24
30 6 0.13
31 4 0.09
32 17 0.38
33 4 0.09
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (28 bp):
ATATAAATATGATAAAAATAAAAAAATA
Found at i:1738937 original size:4 final size:4
Alignment explanation
Indices: 1738925--1738997 Score: 58
Period size: 4 Copynumber: 18.5 Consensus size: 4
1738915 AAAAAACCTT
* * * * * *
1738925 ATAC GTAC ATAC ATAC ATAT ATAT ATAT ATAC ACAC ATAC ATAC AAAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
1738973 CT-T ATAC ATAC ATAC ACAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
1738998 TCGTACAAAC
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
3 1 0.02
4 53 0.98
ACGTcount: A:0.48, C:0.23, G:0.01, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1738983 original size:19 final size:19
Alignment explanation
Indices: 1738959--1739015 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
1738949 ATATATACAC
1738959 ACATACATACAAACCTTAT
1 ACATACATACAAACCTTAT
*
1738978 ACATACATACACA-C--AT
1 ACATACATACAAACCTTAT
* *
1738994 ACATTCGTACAAACCTTAT
1 ACATACATACAAACCTTAT
1739013 ACA
1 ACA
1739016 CGCATTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 12 0.39
17 1 0.03
18 1 0.03
19 17 0.55
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.25
Consensus pattern (19 bp):
ACATACATACAAACCTTAT
Found at i:1739824 original size:12 final size:12
Alignment explanation
Indices: 1739807--1739844 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1739797 GTTAATGATG
1739807 AATAAAAAATTA
1 AATAAAAAATTA
1739819 AATAAAAAATT-
1 AATAAAAAATTA
*
1739830 AATCAAAAATTA
1 AATAAAAAATTA
1739842 AAT
1 AAT
1739845 TATTATGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAAAATTA
Found at i:1739837 original size:11 final size:11
Alignment explanation
Indices: 1739807--1739842 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1739797 GTTAATGATG
1739807 AATAAAAAATT
1 AATAAAAAATT
1739818 AAATAAAAAATT
1 -AATAAAAAATT
*
1739830 AATCAAAAATT
1 AATAAAAAATT
1739841 AA
1 AA
1739843 ATTATTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAAAAAATT
Found at i:1740273 original size:2 final size:2
Alignment explanation
Indices: 1740266--1740292 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1740256 TGTAAAGTAT
1740266 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 T
1740293 GCCTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1741432 original size:12 final size:12
Alignment explanation
Indices: 1741410--1741474 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 12
1741400 AAAAATTTAT
1741410 TTTAAAT-TTAA
1 TTTAAATATTAA
1741421 TTTAAATATTAA
1 TTTAAATATTAA
*
1741433 TATAAAATATT--
1 T-TTAAATATTAA
*
1741444 TTTTAATATTAA
1 TTTAAATATTAA
*
1741456 TTTTAAATAATAA
1 -TTTAAATATTAA
*
1741469 TATAAA
1 TTTAAA
1741475 GTTTTAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
10 7 0.16
11 8 0.19
12 10 0.23
13 18 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTAAATATTAA
Found at i:1741449 original size:29 final size:29
Alignment explanation
Indices: 1741416--1741471 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1741406 TTATTTTAAA
1741416 TTTAAT-TTAAATATTAATATAA-AATATTT
1 TTTAATATT-AATATTAA-ATAATAATATTT
*
1741445 TTTAATATTAATTTTAAATAATAATAT
1 TTTAATATTAATATTAAATAATAATAT
1741472 AAAGTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 18 0.75
30 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAATATTAATATTAAATAATAATATTT
Found at i:1741461 original size:36 final size:35
Alignment explanation
Indices: 1741395--1741474 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 35
1741385 TAATATTTAC
1741395 ATAATA-AAAATTTATTTTAAATTTAATTTAAATA
1 ATAATATAAAATTTATTTTAAATTTAATTTAAATA
*
1741429 TTAATATAAAATATT-TTTT-AATATTAATTTTAAATA
1 ATAATATAAAAT-TTATTTTAAAT-TTAA-TTTAAATA
1741465 ATAATATAAA
1 ATAATATAAA
1741475 GTTTTAAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
34 8 0.20
35 13 0.32
36 19 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (35 bp):
ATAATATAAAATTTATTTTAAATTTAATTTAAATA
Found at i:1741463 original size:23 final size:24
Alignment explanation
Indices: 1741399--1741464 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
1741389 ATTTACATAA
* *
1741399 TAAAAATTTATTTTAAAT-TTAATT
1 TAAATATTAATTTTAAATATT-ATT
* *
1741423 TAAATATTAATATAAAATATT-TT
1 TAAATATTAATTTTAAATATTATT
*
1741446 TTAATATTAATTTTAAATA
1 TAAATATTAATTTTAAATA
1741465 ATAATATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 18 0.53
24 14 0.41
25 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAATATTAATTTTAAATATTATT
Found at i:1744676 original size:3 final size:3
Alignment explanation
Indices: 1744668--1744696 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1744658 GTTTACTTAT
1744668 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1744697 GTTTTACTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1746181 original size:2 final size:2
Alignment explanation
Indices: 1746174--1746216 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1746164 TACAACCATC
1746174 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
1746216 T
1 T
1746217 GAAAGAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1746812 original size:18 final size:17
Alignment explanation
Indices: 1746780--1746851 Score: 60
Period size: 19 Copynumber: 4.2 Consensus size: 17
1746770 TAATATATTT
1746780 TATAT-AAA-AATAAAA
1 TATATAAAATAATAAAA
* *
1746795 TATCTTAAATACATAAAAA
1 TATATAAAATA-AT-AAAA
1746814 TATATAAAATAATATAAA
1 TATATAAAATAATA-AAA
* *
1746832 TATA-CAAATAACAAAA
1 TATATAAAATAATAAAA
1746848 TATA
1 TATA
1746852 ATTTTATCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.09
16 10 0.21
17 9 0.19
18 11 0.23
19 13 0.28
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
TATATAAAATAATAAAA
Found at i:1746848 original size:16 final size:16
Alignment explanation
Indices: 1746815--1746852 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1746805 ACATAAAAAT
*
1746815 ATATAAAATAATATAA
1 ATATAAAATAACATAA
1746831 ATATACAAATAACA-AA
1 ATATA-AAATAACATAA
1746847 ATATAA
1 ATATAA
1746853 TTTTATCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 12 0.60
17 7 0.35
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (16 bp):
ATATAAAATAACATAA
Found at i:1747463 original size:35 final size:35
Alignment explanation
Indices: 1747412--1747483 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1747402 TACATATGTT
*
1747412 AAGGGTGATAATGCATGTTTCAAAATTAGAAAGTG
1 AAGGGTGATAATGCATGCTTCAAAATTAGAAAGTG
*
1747447 AAGGTTGATAATGCATGCTTCAAAATTAGAAAGTG
1 AAGGGTGATAATGCATGCTTCAAAATTAGAAAGTG
1747482 AA
1 AA
1747484 AAAATAATCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.28
Consensus pattern (35 bp):
AAGGGTGATAATGCATGCTTCAAAATTAGAAAGTG
Found at i:1750825 original size:67 final size:67
Alignment explanation
Indices: 1750745--1750873 Score: 179
Period size: 67 Copynumber: 1.9 Consensus size: 67
1750735 TAAAAATAAA
* * *
1750745 ATTTTTATGTTAAATGAT-AAAATTAAAATAAAAAATAATTGTTATTACTTAAATAGTAATTTGG
1 ATTTTTATATTAAATAATGAAAATTAAAA-AAAAAATAATTGTTATTACTTAAATAATAATTTGG
1750809 GCT
65 GCT
* * * *
1750812 ATTTTTATATTAAATAATGAAATTTTAAAAAAAAATTATTGTTATTGCTTAAATAATAATTT
1 ATTTTTATATTAAATAATGAAAATTAAAAAAAAAATAATTGTTATTACTTAAATAATAATTT
1750874 AAACTAAACC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 46 0.85
68 8 0.15
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (67 bp):
ATTTTTATATTAAATAATGAAAATTAAAAAAAAAATAATTGTTATTACTTAAATAATAATTTGGG
CT
Found at i:1751814 original size:2 final size:2
Alignment explanation
Indices: 1751807--1751865 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1751797 AATTATAAAT
* *
1751807 TA TA TA TA CA CA TA TA -A 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
1751848 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1751866 AAGCTAGCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1753604 original size:2 final size:2
Alignment explanation
Indices: 1753597--1753621 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1753587 TTACGACCAC
1753597 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
1753622 AGAAAAGACA
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:1753808 original size:11 final size:11
Alignment explanation
Indices: 1753789--1753830 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
1753779 TTATTTACAT
1753789 TTAACTATAAAA
1 TTAA-TATAAAA
*
1753801 TTTATATAAATA
1 TTAATATAAA-A
1753813 TTAATATAAAA
1 TTAATATAAAA
1753824 TTAATAT
1 TTAATAT
1753831 TTAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 14 0.52
12 13 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAATATAAAA
Found at i:1753820 original size:23 final size:25
Alignment explanation
Indices: 1753789--1753839 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1753779 TTATTTACAT
1753789 TTAACTATAAAATT-TATATAAATA
1 TTAACTATAAAATTATATATAAATA
*
1753813 TTAA-TATAAAATTAATATTTAAATA
1 TTAACTATAAAATT-ATATATAAATA
1753838 TT
1 TT
1753840 TTATACAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 4 0.17
25 11 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAACTATAAAATTATATATAAATA
Found at i:1754215 original size:12 final size:13
Alignment explanation
Indices: 1754187--1754228 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1754177 TATCAAAATT
* *
1754187 TATATAAAAATAT
1 TATACAAAAATAA
*
1754200 TATACATAAA-AA
1 TATACAAAAATAA
1754212 TATACAAAAATAA
1 TATACAAAAATAA
1754225 TATA
1 TATA
1754229 AATATATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (13 bp):
TATACAAAAATAA
Found at i:1758997 original size:2 final size:2
Alignment explanation
Indices: 1758990--1759020 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1758980 TTTTGTACCA
*
1758990 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1759021 AACTAGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
AT
Found at i:1760273 original size:2 final size:2
Alignment explanation
Indices: 1760266--1760290 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1760256 CCTATCTATC
1760266 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1760291 CAAACCTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1760617 original size:2 final size:2
Alignment explanation
Indices: 1760610--1760638 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1760600 CTAAAGAAGG
1760610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1760639 ACAATCATGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1761200 original size:7 final size:7
Alignment explanation
Indices: 1761190--1761223 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1761180 ATAAAAATAA
1761190 AAATTTT
1 AAATTTT
1761197 AAATTTT
1 AAATTTT
*
1761204 AAAATTT
1 AAATTTT
*
1761211 AAATTAT
1 AAATTTT
1761218 AAATTT
1 AAATTT
1761224 ATTAGATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTT
Found at i:1761207 original size:21 final size:21
Alignment explanation
Indices: 1761183--1761223 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1761173 TTTAAAAATA
*
1761183 AAAATAAAAATTTTAAATTTT
1 AAAATAAAAATTATAAATTTT
**
1761204 AAAATTTAAATTATAAATTT
1 AAAATAAAAATTATAAATTT
1761224 ATTAGATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATAAAAATTATAAATTTT
Found at i:1761354 original size:20 final size:20
Alignment explanation
Indices: 1761331--1761397 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
1761321 AAAATTTTAG
1761331 TATATTAATAATTATTATTT
1 TATATTAATAATTATTATTT
* *
1761351 TATATAAATATTTATATATTT
1 TATATTAATAATTAT-TATTT
*
1761372 ATATATTTAT-ATTA-TA-TT
1 -TATATTAATAATTATTATTT
1761390 TATATTAA
1 TATATTAA
1761398 GTTTATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 7 0.18
18 2 0.05
19 2 0.05
20 13 0.33
21 8 0.21
22 7 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATTAATAATTATTATTT
Found at i:1761369 original size:8 final size:8
Alignment explanation
Indices: 1761358--1761383 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1761348 TTTTATATAA
1761358 ATATTTAT
1 ATATTTAT
1761366 ATATTTAT
1 ATATTTAT
1761374 ATATTTAT
1 ATATTTAT
1761382 AT
1 AT
1761384 TATATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATTTAT
Found at i:1761389 original size:11 final size:11
Alignment explanation
Indices: 1761373--1761405 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1761363 TATATATTTA
1761373 TATATTTATAT
1 TATATTTATAT
1761384 TATATTTATAT
1 TATATTTATAT
1761395 TA-AGTTTATAT
1 TATA-TTTATAT
1761406 AATTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 1 0.05
11 20 0.95
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1761687 original size:3 final size:3
Alignment explanation
Indices: 1761679--1761704 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1761669 TATTCTTTTG
1761679 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1761705 ATCTTGCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1762510 original size:14 final size:14
Alignment explanation
Indices: 1762466--1762508 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1762456 AGCTTAATTC
1762466 AATTA-ATTTATAA
1 AATTATATTTATAA
* *
1762479 AATTATCTTTATGA
1 AATTATATTTATAA
1762493 AATTATATTTAATAA
1 AATTATATTT-ATAA
1762508 A
1 A
1762509 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 5 0.21
14 15 0.62
15 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
AATTATATTTATAA
Found at i:1762853 original size:19 final size:17
Alignment explanation
Indices: 1762831--1762866 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
1762821 CTTATTTTAC
1762831 TATTTAAAATATATTAAAA
1 TATTTAAAA-A-ATTAAAA
1762850 TATTTAAAAAATTAAAA
1 TATTTAAAAAATTAAAA
1762867 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 1 0.06
19 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATTTAAAAAATTAAAA
Found at i:1766574 original size:6 final size:6
Alignment explanation
Indices: 1766561--1766628 Score: 55
Period size: 6 Copynumber: 12.7 Consensus size: 6
1766551 ATTATATAGG
1766561 ATAT-A ATATAA ATATAA A-A-AA ATAT-A A-A-AA ATATAA ATATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATA-A
*
1766604 A-ATAA AT-TAA A-ATCA ATATAA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATAT
1766629 TTTTATAGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 19
0.71 0.03 0.26
Matches are distributed among these distances:
4 6 0.12
5 18 0.35
6 25 0.49
7 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (6 bp):
ATATAA
Found at i:1766626 original size:10 final size:10
Alignment explanation
Indices: 1766561--1766627 Score: 70
Period size: 10 Copynumber: 6.9 Consensus size: 10
1766551 ATTATATAGG
1766561 ATATAATATAA
1 ATATAA-ATAA
*
1766572 ATATAAAAAA
1 ATATAAATAA
1766582 ATATAAA-AA
1 ATATAAATAA
1766591 ATATAAAT--
1 ATATAAATAA
1766599 ATATAAATAA
1 ATATAAATAA
*
1766609 AT-TAAAATCA
1 ATAT-AAATAA
1766619 ATATAAATA
1 ATATAAATA
1766628 TTTTTATAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
8 8 0.17
9 10 0.21
10 23 0.48
11 7 0.15
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (10 bp):
ATATAAATAA
Found at i:1766757 original size:20 final size:21
Alignment explanation
Indices: 1766724--1766763 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1766714 TATTTTATAT
*
1766724 TAAATTTAATTATAAAATAAA
1 TAAATTTAAATATAAAATAAA
1766745 TAAA-TTAAATATAAAATAA
1 TAAATTTAAATATAAAATAA
1766764 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATTTAAATATAAAATAAA
Found at i:1767175 original size:20 final size:19
Alignment explanation
Indices: 1767150--1767189 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1767140 TATATATTAG
*
1767150 AATTTTATGTAAATTGTTAT
1 AATTTTATATAAATT-TTAT
1767170 AATTTTATATAAATTTTAT
1 AATTTTATATAAATTTTAT
1767189 A
1 A
1767190 TTGTAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
AATTTTATATAAATTTTAT
Found at i:1767186 original size:11 final size:11
Alignment explanation
Indices: 1767150--1767190 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1767140 TATATATTAG
*
1767150 AATTTTATGTA
1 AATTTTATATA
*
1767161 AATTGT-TAT-
1 AATTTTATATA
1767170 AATTTTATATA
1 AATTTTATATA
1767181 AATTTTATAT
1 AATTTTATAT
1767191 TGTAATAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 5 0.20
10 5 0.20
11 15 0.60
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (11 bp):
AATTTTATATA
Found at i:1768457 original size:18 final size:18
Alignment explanation
Indices: 1768431--1768471 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1768421 AAAAGTCCAC
*
1768431 TGAAGTCCCATGCTATAA
1 TGAAATCCCATGCTATAA
1768449 TGAAATCCCATGCTATAA
1 TGAAATCCCATGCTATAA
1768467 TGAAA
1 TGAAA
1768472 AGAAGCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (18 bp):
TGAAATCCCATGCTATAA
Found at i:1769621 original size:22 final size:22
Alignment explanation
Indices: 1769591--1769633 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1769581 TGTCTTAATT
*
1769591 TGCACTTCTAAGAGTAATTTTA
1 TGCAATTCTAAGAGTAATTTTA
1769613 TGCAATTCTAAGAGTAATTTT
1 TGCAATTCTAAGAGTAATTTT
1769634 TGATGGATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (22 bp):
TGCAATTCTAAGAGTAATTTTA
Done.