Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 39 of 39
Found at i:5870913 original size:16 final size:16
Alignment explanation
Indices: 5870894--5870951 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
5870884 TTAAAATTCG
5870894 AAATAATTCGAACTCA
1 AAATAATTCGAACTCA
5870910 AAATAA-TCTGAACTCA
1 AAATAATTC-GAACTCA
* * *
5870926 AAATGATTCAAACTTAA
1 AAATAATTCGAAC-TCA
5870943 AAATAATTC
1 AAATAATTC
5870952 AAAACTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 2 0.06
16 21 0.60
17 12 0.34
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.28
Consensus pattern (16 bp):
AAATAATTCGAACTCA
Found at i:5875985 original size:18 final size:18
Alignment explanation
Indices: 5875958--5876001 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5875948 TTTAGAGTAT
*
5875958 GAAAGTAATGGTAAATGA
1 GAAAGTAATGATAAATGA
*
5875976 GAAGGTAATGATAAATGA
1 GAAAGTAATGATAAATGA
5875994 GAAAGTAA
1 GAAAGTAA
5876002 GAGTAGAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.20
Consensus pattern (18 bp):
GAAAGTAATGATAAATGA
Found at i:5877672 original size:16 final size:16
Alignment explanation
Indices: 5877651--5877687 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
5877641 GAGAGCAATT
5877651 GTGAAGATATTGTAGA
1 GTGAAGATATTGTAGA
5877667 GTGAAGATATTGTAGA
1 GTGAAGATATTGTAGA
5877683 GTGAA
1 GTGAA
5877688 AGAGATGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (16 bp):
GTGAAGATATTGTAGA
Found at i:5880348 original size:68 final size:68
Alignment explanation
Indices: 5880255--5880499 Score: 260
Period size: 68 Copynumber: 3.6 Consensus size: 68
5880245 ATTGGTAAGA
* *
5880255 GTGACTTGATGTCCCTTGCTTTTTTATTGTAATGTCAATCAGACCTTGATGGTCACTTATTAGCA
1 GTGACTTGATGTCACTTGCTTTTTTATTGAAATGTCAATCAGACCTTGATGGTCACTTATTAGCA
5880320 AAG
66 AAG
* * * *
5880323 GTGATTTGGTGTCACTTGCTTTTTTATTGAAATGTCAATTAGACCTTTATGGTCACTTATTAGCA
1 GTGACTTGATGTCACTTGCTTTTTTATTGAAATGTCAATCAGACCTTGATGGTCACTTATTAGCA
5880388 AAG
66 AAG
* ** * * * * ** * * *
5880391 ATGACTCAATGCCACTTG-TTTGTTTGTTAAAATATCGGTTAGAACTTTG-TGGTAACTTATTAG
1 GTGACTTGATGTCACTTGCTTT-TTTATTGAAATGTCAATCAG-ACCTTGATGGTCACTTATTAG
5880454 CAAAG
64 CAAAG
** * *
5880459 GTGACTCAATGTCATTTGCTTTTTTGTTGAAATGTCAATCA
1 GTGACTTGATGTCACTTGCTTTTTTATTGAAATGTCAATCA
5880500 AGATTTTGAT
Statistics
Matches: 146, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
67 3 0.02
68 136 0.93
69 7 0.05
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (68 bp):
GTGACTTGATGTCACTTGCTTTTTTATTGAAATGTCAATCAGACCTTGATGGTCACTTATTAGCA
AAG
Found at i:5891642 original size:21 final size:21
Alignment explanation
Indices: 5891616--5891670 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
5891606 TAATTTAAAC
5891616 AAATTTATATAATTAT-AATTT
1 AAATTT-TATAATTATAAATTT
*
5891637 AAATTTTTTAAATTATAAATTT
1 AAATTTTAT-AATTATAAATTT
*
5891659 AATTTTTTATAA
1 AA-ATTTTATAA
5891671 GTTTTGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 12 0.43
22 9 0.32
23 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATTTTATAATTATAAATTT
Found at i:5891660 original size:22 final size:20
Alignment explanation
Indices: 5891626--5891667 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
5891616 AAATTTATAT
5891626 AATTATAATTTAAATTTTTTA
1 AATTATAATTT-AATTTTTTA
5891647 AATTATAAATTTAATTTTTTA
1 AATTAT-AATTTAATTTTTTA
5891668 TAAGTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTATAATTTAATTTTTTA
Found at i:5894730 original size:43 final size:42
Alignment explanation
Indices: 5894645--5894735 Score: 98
Period size: 43 Copynumber: 2.1 Consensus size: 42
5894635 ATAATTTTTT
*
5894645 ATTTATATTTAATTATAAAATATAAAATTATTAATTTAAAATA
1 ATTTATATTT-ATTATAAAATATAAAATTATTAAATTAAAATA
*
5894688 TTTTATATTT-TTAATAATAATAT-AAATTAAATTAAATT-AAATA
1 ATTTATATTTATT-ATAA-AATATAAAATT--ATTAAATTAAAATA
5894731 ATTTA
1 ATTTA
5894736 AAAAATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
41 2 0.05
42 9 0.22
43 23 0.56
44 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (42 bp):
ATTTATATTTATTATAAAATATAAAATTATTAAATTAAAATA
Found at i:5896112 original size:12 final size:11
Alignment explanation
Indices: 5896053--5896121 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
5896043 TAAAAATAAG
5896053 TAAA-AATTAT
1 TAAATAATTAT
* *
5896063 TAAATAATCACA
1 TAAATAATTA-T
5896075 TAAATAA-T-T
1 TAAATAATTAT
*
5896084 TAATTAA--AT
1 TAAATAATTAT
5896093 TAAA-AATTAT
1 TAAATAATTAT
5896103 ATAAATAATTAT
1 -TAAATAATTAT
5896115 TAAATAA
1 TAAATAA
5896122 AGATAATGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
8 2 0.04
9 10 0.22
10 6 0.13
11 15 0.33
12 13 0.28
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATAATTAT
Found at i:5896872 original size:15 final size:14
Alignment explanation
Indices: 5896827--5896876 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
5896817 TTCCACTACT
5896827 TTTTATTTTTATT-
1 TTTTATTTTTATTA
*
5896840 TTTTCTCTTTTAGTTA
1 TTTTAT-TTTTA-TTA
5896856 TTTTATTTTTA-TA
1 TTTTATTTTTATTA
*
5896869 TATTATTT
1 TTTTATTT
5896877 AACTATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 14 0.45
14 5 0.16
15 7 0.23
16 5 0.16
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:5897950 original size:54 final size:54
Alignment explanation
Indices: 5897868--5897975 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
5897858 TTAGGTGTAC
5897868 ATGTTCTTTAACTTTTTTCTATTACTTTTGTTTGCTCTTGAAAATAATAAGCTA
1 ATGTTCTTTAACTTTTTTCTATTACTTTTGTTTGCTCTTGAAAATAATAAGCTA
5897922 ATGTTCTTTAACTTTTTTCTATTACTTTTGTTTGCTCTTGAAAATAATAAGCTA
1 ATGTTCTTTAACTTTTTTCTATTACTTTTGTTTGCTCTTGAAAATAATAAGCTA
5897976 TCATCTACGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (54 bp):
ATGTTCTTTAACTTTTTTCTATTACTTTTGTTTGCTCTTGAAAATAATAAGCTA
Found at i:5905646 original size:2 final size:2
Alignment explanation
Indices: 5905639--5905675 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5905629 GGCATGATGC
*
5905639 AT AT AT 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 AT AT AT A
5905676 ATCGCCACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5905988 original size:23 final size:23
Alignment explanation
Indices: 5905961--5906004 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5905951 ATTTGTTTCA
*
5905961 TAATTTATATT-ACATTAATTATT
1 TAATTT-TATTAAAATTAATTATT
5905984 TAATTTTATTAAAATTAATTA
1 TAATTTTATTAAAATTAATTA
5906005 AATATATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATTTTATTAAAATTAATTATT
Found at i:5906058 original size:17 final size:17
Alignment explanation
Indices: 5906036--5906111 Score: 79
Period size: 17 Copynumber: 4.5 Consensus size: 17
5906026 TTAACTAAAA
*
5906036 AATAAAATATTTTTTTT
1 AATAAAATATTATTTTT
*
5906053 AATAAATTTATT-TTTTT
1 AATAAA-ATATTATTTTT
5906070 AA-AAAATTAATTATTTTT
1 AATAAAA-T-ATTATTTTT
5906088 -A-AAAATATTATTTTT
1 AATAAAATATTATTTTT
5906103 AATAAAATA
1 AATAAAATA
5906112 ATCACCTTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
15 9 0.18
16 6 0.12
17 27 0.53
18 9 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATAAAATATTATTTTT
Found at i:5906108 original size:18 final size:18
Alignment explanation
Indices: 5906039--5906109 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 18
5906029 ACTAAAAAAT
*
5906039 AAAATATTTTTTTTAATA
1 AAAATATTATTTTTAATA
**
5906057 AATTTATT-TTTTTAA-A
1 AAAATATTATTTTTAATA
*
5906073 AAATTAATTA-TTTT--TA
1 AAAAT-ATTATTTTTAATA
5906089 AAAATATTATTTTTAATA
1 AAAATATTATTTTTAATA
5906107 AAA
1 AAA
5906110 TAATCACCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
15 4 0.09
16 14 0.33
17 14 0.33
18 11 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAAATATTATTTTTAATA
Found at i:5906761 original size:18 final size:18
Alignment explanation
Indices: 5906735--5906776 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5906725 AAATTATATA
*
5906735 AAAAT-TAAAATAAATTT
1 AAAATATAAAATAAAATT
*
5906752 ATAATATAAAATAAAATT
1 AAAATATAAAATAAAATT
5906770 AAAATAT
1 AAAATAT
5906777 TTAAGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATATAAAATAAAATT
Found at i:5907094 original size:19 final size:19
Alignment explanation
Indices: 5907070--5907127 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
5907060 TATTTTTTTA
5907070 ATTTTTATATTTTAAAATT
1 ATTTTTATATTTTAAAATT
**
5907089 ATTTTTAATGATTTT--TTTT
1 ATTTTT-AT-ATTTTAAAATT
5907108 ATTTTTATATTTTATAAATT
1 ATTTTTATATTTTA-AAATT
5907128 TTAATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
17 5 0.17
18 2 0.07
19 14 0.47
20 4 0.13
21 5 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTATATTTTAAAATT
Found at i:5907923 original size:7 final size:7
Alignment explanation
Indices: 5907911--5907944 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
5907901 ATTACTTTAA
5907911 AAAAATT
1 AAAAATT
5907918 AAAAATT
1 AAAAATT
5907925 AAAAATT
1 AAAAATT
5907932 -AAAA-T
1 AAAAATT
5907937 AAAAATT
1 AAAAATT
5907944 A
1 A
5907945 TTATTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.04
6 8 0.32
7 16 0.64
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:5907928 original size:14 final size:13
Alignment explanation
Indices: 5907911--5907944 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
5907901 ATTACTTTAA
5907911 AAAAATTAAAAATT
1 AAAAATTAAAAA-T
5907925 AAAAATT-AAAAT
1 AAAAATTAAAAAT
5907937 AAAAATTA
1 AAAAATTA
5907945 TTATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.42
13 4 0.21
14 7 0.37
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAATTAAAAAT
Found at i:5908537 original size:40 final size:40
Alignment explanation
Indices: 5908493--5908569 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
5908483 AAAAGGTAAT
5908493 AAAGACACAAAAACCTTAATTTTATATTTATTTTAAAGGA
1 AAAGACACAAAAACCTTAATTTTATATTTATTTTAAAGGA
* * *
5908533 AAAGACATAAAAACTTTAATTTTATGTTTATTTTAAA
1 AAAGACACAAAAACCTTAATTTTATATTTATTTTAAA
5908570 ATTTGATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (40 bp):
AAAGACACAAAAACCTTAATTTTATATTTATTTTAAAGGA
Found at i:5908936 original size:16 final size:18
Alignment explanation
Indices: 5908911--5908956 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
5908901 AATTTTTACT
*
5908911 TATATAATTTT-A-TTAA
1 TATATTATTTTAATTTAA
5908927 TATATTATTTTAATTTAA
1 TATATTATTTTAATTTAA
5908945 TAATATTATTTT
1 T-ATATTATTTT
5908957 TTATTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 5 0.19
19 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTATTTTAATTTAA
Found at i:5908943 original size:21 final size:21
Alignment explanation
Indices: 5908919--5908959 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5908909 CTTATATAAT
*
5908919 TTTATTAATA-TATTATTTTAA
1 TTTAATAATATTATT-TTTTAA
5908940 TTTAATAATATTATTTTTTA
1 TTTAATAATATTATTTTTTA
5908960 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAATAATATTATTTTTTAA
Found at i:5909521 original size:9 final size:9
Alignment explanation
Indices: 5909507--5909535 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5909497 TTATAGTCTC
5909507 AAAATAAAA
1 AAAATAAAA
5909516 AAAAT-AAA
1 AAAATAAAA
5909524 AAAATAAAA
1 AAAATAAAA
5909533 AAA
1 AAA
5909536 TATTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAATAAAA
Found at i:5909524 original size:8 final size:8
Alignment explanation
Indices: 5909507--5909537 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
5909497 TTATAGTCTC
5909507 AAAATAAAA
1 AAAAT-AAA
5909516 AAAATAAA
1 AAAATAAA
5909524 AAAATAAA
1 AAAATAAA
5909532 AAAATA
1 AAAATA
5909538 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAATAAA
Found at i:5909659 original size:13 final size:13
Alignment explanation
Indices: 5909623--5909662 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5909613 ATATATAATT
5909623 TAATTTTTTATTTA
1 TAATTTTTTA-TTA
*
5909637 TAATTATTTATTA
1 TAATTTTTTATTA
*
5909650 TATTTTTTTATTA
1 TAATTTTTTATTA
5909663 ACGTTAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TAATTTTTTATTA
Found at i:5910305 original size:2 final size:2
Alignment explanation
Indices: 5910298--5910323 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5910288 TTTATAAATG
5910298 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
5910324 TTTTATCTTC
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:5919874 original size:14 final size:14
Alignment explanation
Indices: 5919855--5919884 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5919845 CCCAACCCTC
*
5919855 AAGCCCAAAGCTCG
1 AAGCCCAAAACTCG
5919869 AAGCCCAAAACTCG
1 AAGCCCAAAACTCG
5919883 AA
1 AA
5919885 ACCTCAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.33, G:0.17, T:0.07
Consensus pattern (14 bp):
AAGCCCAAAACTCG
Found at i:5919940 original size:14 final size:14
Alignment explanation
Indices: 5919909--5919982 Score: 62
Period size: 14 Copynumber: 5.3 Consensus size: 14
5919899 CCTTAACCCT
5919909 AACCTCTAAACCTT-A
1 AACCT-TAAA-CTTCA
5919924 AACCTTAAACTTCA
1 AACCTTAAACTTCA
*
5919938 AACC-CAAACTTCA
1 AACCTTAAACTTCA
* * *
5919951 AACCCTAGACCTCA
1 AACCTTAAACTTCA
* *
5919965 AACCTCAAAATTCA
1 AACCTTAAACTTCA
5919979 AACC
1 AACC
5919983 ACAAATCCTA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
13 15 0.31
14 28 0.58
15 5 0.10
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.20
Consensus pattern (14 bp):
AACCTTAAACTTCA
Found at i:5919946 original size:27 final size:28
Alignment explanation
Indices: 5919909--5920023 Score: 80
Period size: 28 Copynumber: 4.1 Consensus size: 28
5919899 CCTTAACCCT
* *
5919909 AACCTCTAAACCTT-AAACCTTAAACTTCA
1 AACCTC-AAA-CTTCAAACCCTAAACCTCA
*
5919938 AACC-CAAACTTCAAACCCTAGACCTCA
1 AACCTCAAACTTCAAACCCTAAACCTCA
*
5919965 AACCTCAAAATTCAAACCAC-AAATCCT-A
1 AACCTCAAACTTCAAACC-CTAAA-CCTCA
* *
5919993 AATCCT-AAACTTTAAACTCCCAAACCT-A
1 AA-CCTCAAACTTCAAAC-CCTAAACCTCA
5920021 AAC
1 AAC
5920024 ATTAAACCTA
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
26 3 0.04
27 20 0.28
28 34 0.47
29 15 0.21
ACGTcount: A:0.44, C:0.34, G:0.01, T:0.21
Consensus pattern (28 bp):
AACCTCAAACTTCAAACCCTAAACCTCA
Found at i:5919969 original size:7 final size:7
Alignment explanation
Indices: 5919909--5920039 Score: 56
Period size: 7 Copynumber: 18.7 Consensus size: 7
5919899 CCTTAACCCT
5919909 AACCTCTA
1 AACCTC-A
*
5919917 AACCTTA
1 AACCTCA
*
5919924 AACCTTA
1 AACCTCA
*
5919931 AACTTCA
1 AACCTCA
5919938 AACC-CA
1 AACCTCA
*
5919944 AACTTCA
1 AACCTCA
5919951 AACC-CTA
1 AACCTC-A
*
5919958 GACCTCA
1 AACCTCA
5919965 AACCTCA
1 AACCTCA
**
5919972 AAATTCA
1 AACCTCA
*
5919979 AACCACA
1 AACCTCA
5919986 AATCCT-A
1 AA-CCTCA
5919993 AATCCT-A
1 AA-CCTCA
* *
5920000 AACTTTA
1 AACCTCA
*
5920007 AACTCCCA
1 AAC-CTCA
5920015 AACCT-A
1 AACCTCA
* *
5920021 AACATTA
1 AACCTCA
*
5920028 AACCTAA
1 AACCTCA
5920035 AACCT
1 AACCT
5920040 TAATCTAAGT
Statistics
Matches: 94, Mismatches: 22, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
6 13 0.14
7 69 0.73
8 12 0.13
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (7 bp):
AACCTCA
Found at i:5920054 original size:39 final size:40
Alignment explanation
Indices: 5920004--5920141 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 40
5919994 ATCCTAAACT
5920004 TTAAACTCCCAAACC-TAAACATTAAACCTAAAACCTT-AATC
1 TTAAA-TCCCAAACCTTAAACA-TAAA-CTAAAACCTTAAATC
* * *
5920045 -TAAGTCCCAAACCTTAATCATAAACTATAACCTTAAATC
1 TTAAATCCCAAACCTTAAACATAAACTAAAACCTTAAATC
* * * * * *
5920084 TTAAATCCCAAACCCTAACCTTAGACTATAACCTTAAACC
1 TTAAATCCCAAACCTTAAACATAAACTAAAACCTTAAATC
*
5920124 ATAAA-CCTCAAACCTTAA
1 TTAAATCC-CAAACCTTAA
5920142 GCCATAATCC
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
38 9 0.11
39 19 0.23
40 54 0.66
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.25
Consensus pattern (40 bp):
TTAAATCCCAAACCTTAAACATAAACTAAAACCTTAAATC
Found at i:5920112 original size:40 final size:40
Alignment explanation
Indices: 5920004--5920121 Score: 125
Period size: 40 Copynumber: 3.0 Consensus size: 40
5919994 ATCCTAAACT
* *
5920004 TTAAACTCCCAAA-CCTAAACATTAAACCTAAAACCTT-AATC
1 TTAAA-TCCCAAACCCT-AACCTTAAA-CTATAACCTTAAATC
* * * *
5920045 -TAAGTCCCAAACCTTAATCATAAACTATAACCTTAAATC
1 TTAAATCCCAAACCCTAACCTTAAACTATAACCTTAAATC
*
5920084 TTAAATCCCAAACCCTAACCTTAGACTATAACCTTAAA
1 TTAAATCCCAAACCCTAACCTTAAACTATAACCTTAAA
5920122 CCATAAACCT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
38 9 0.14
39 17 0.27
40 37 0.59
ACGTcount: A:0.44, C:0.28, G:0.02, T:0.26
Consensus pattern (40 bp):
TTAAATCCCAAACCCTAACCTTAAACTATAACCTTAAATC
Found at i:5920216 original size:27 final size:27
Alignment explanation
Indices: 5920158--5920288 Score: 79
Period size: 27 Copynumber: 4.7 Consensus size: 27
5920148 ATCCTTGAAT
* *** *
5920158 CTTAAACCTTAAATCTTAATTTTAAAT
1 CTTAAACCCTAAATCTTAAACCTAAAC
*
5920185 ATTAAACCCTAAATCTTAAACCCT-AAC
1 CTTAAACCCTAAATCTTAAA-CCTAAAC
** *
5920212 CTTAAACTTTAAATCTTGAA-CTAATAC
1 CTTAAACCCTAAATCTTAAACCTAA-AC
*
5920239 CTTAAAACCTTAAA-CTTTAAAACTCTAAAC
1 CTT-AAACCCTAAATC-TT-AAAC-CTAAAC
* *
5920269 TTTAAACCCTAAACCTTAAA
1 CTTAAACCCTAAATCTTAAA
5920289 TTGTTATCCT
Statistics
Matches: 81, Mismatches: 14, Indels: 17
0.72 0.12 0.15
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 41 0.51
28 15 0.19
29 13 0.16
30 5 0.06
31 4 0.05
ACGTcount: A:0.44, C:0.22, G:0.01, T:0.34
Consensus pattern (27 bp):
CTTAAACCCTAAATCTTAAACCTAAAC
Found at i:5920260 original size:15 final size:15
Alignment explanation
Indices: 5920240--5920288 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
5920230 AACTAATACC
5920240 TTAAAACCTTAAACT
1 TTAAAACCTTAAACT
5920255 TTAAAA-CTCTAAACT
1 TTAAAACCT-TAAACT
* *
5920270 TT-AAACCCTAAACC
1 TTAAAACCTTAAACT
5920284 TTAAA
1 TTAAA
5920289 TTGTTATCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAACCTTAAACT
Found at i:5920322 original size:6 final size:7
Alignment explanation
Indices: 5920113--5920453 Score: 124
Period size: 7 Copynumber: 48.4 Consensus size: 7
5920103 CTTAGACTAT
5920113 AACCTTA
1 AACCTTA
*
5920120 AACCATA
1 AACCTTA
*
5920127 AACCTCA
1 AACCTTA
5920134 AACCTTA
1 AACCTTA
* *
5920141 AGCCATA
1 AACCTTA
* *
5920148 ATCCTTG
1 AACCTTA
*
5920155 AATCTTA
1 AACCTTA
5920162 AACCTTA
1 AACCTTA
*
5920169 AATCTT-
1 AACCTTA
**
5920175 AATTTTA
1 AACCTTA
**
5920182 AATATTA
1 AACCTTA
*
5920189 AACCCTA
1 AACCTTA
*
5920196 AATCTTA
1 AACCTTA
*
5920203 AACCCT-
1 AACCTTA
5920209 AACCTTA
1 AACCTTA
*
5920216 AACTTTA
1 AACCTTA
* *
5920223 AATCTTG
1 AACCTTA
5920230 AA-C-TA
1 AACCTTA
5920235 ATACCTTAA
1 A-ACCTT-A
5920244 AACCTTA
1 AACCTTA
*
5920251 AACTTTA
1 AACCTTA
*
5920258 AAACTCTA
1 AACCT-TA
*
5920266 AACTTTA
1 AACCTTA
*
5920273 AACCCTA
1 AACCTTA
5920280 AACCTTA
1 AACCTTA
* *
5920287 AA-TTGTT
1 AACCT-TA
*
5920294 ATCCTTA
1 AACCTTA
*
5920301 AATCTTA
1 AACCTTA
5920308 AACCTTA
1 AACCTTA
5920315 AA-CTTAA
1 AACCTT-A
*
5920322 AACC-CA
1 AACCTTA
*
5920328 TAACCTAA
1 -AACCTTA
5920336 AACCTTA
1 AACCTTA
*
5920343 AA-CTCCA
1 AACCT-TA
*
5920350 AATCCGTA
1 AA-CCTTA
5920358 AACACTAATA
1 AAC-CT--TA
**
5920368 AAATTTA
1 AACCTTA
* *
5920375 AAACTTG
1 AACCTTA
*
5920382 AACCATA
1 AACCTTA
*
5920389 AATCTTA
1 AACCTTA
*
5920396 AATCTTA
1 AACCTTA
*
5920403 AACTTTA
1 AACCTTA
* *
5920410 AACCCTC
1 AACCTTA
5920417 AACCTTA
1 AACCTTA
*
5920424 AA-CTTT
1 AACCTTA
*
5920430 AATCTTA
1 AACCTTA
*
5920437 ACCCTTA
1 AACCTTA
*
5920444 AACCCTA
1 AACCTTA
5920451 AAC
1 AAC
5920454 TCGATCATTG
Statistics
Matches: 240, Mismatches: 74, Indels: 40
0.68 0.21 0.11
Matches are distributed among these distances:
5 2 0.01
6 24 0.10
7 188 0.78
8 18 0.08
9 4 0.02
10 4 0.02
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (7 bp):
AACCTTA
Found at i:5920435 original size:34 final size:35
Alignment explanation
Indices: 5920382--5920449 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
5920372 TTAAAACTTG
*
5920382 AACCATAAATCTTAAATCTTAAACTTTAAACCCTC
1 AACCATAAATCTTAAATCTTAAACCTTAAACCCTC
* * *
5920417 AACCTTAAA-CTTTAATCTTAACCCTTAAACCCT
1 AACCATAAATCTTAAATCTTAAACCTTAAACCCT
5920450 AAACTCGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (35 bp):
AACCATAAATCTTAAATCTTAAACCTTAAACCCTC
Found at i:5920633 original size:7 final size:7
Alignment explanation
Indices: 5920617--5920671 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
5920607 TATTAACTCC
*
5920617 TAAACTT
1 TAAACCT
5920624 TAAACCT
1 TAAACCT
5920631 TAAATCCT
1 TAAA-CCT
5920639 TAAACCT
1 TAAACCT
5920646 TAAACC-
1 TAAACCT
*
5920652 CAAACCT
1 TAAACCT
* *
5920659 TATACCC
1 TAAACCT
5920666 TAAACC
1 TAAACC
5920672 AACCCCTAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 5 0.12
7 28 0.70
8 7 0.17
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACCT
Done.