Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2165
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: 46550
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1950 original size:52 final size:52
Alignment explanation
Indices: 1805--1930 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
1795 AATATGAAAT
* *
1805 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATATGGGCAAA
* *
1857 TTTGCTTGTATGTATCGATACATTTCATAGTGTATCAATACATATGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATATGGGCAAA
1909 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
1931 AAGATCAGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATATGGGCAAA
Found at i:2042 original size:19 final size:18
Alignment explanation
Indices: 2018--2112 Score: 93
Period size: 19 Copynumber: 5.7 Consensus size: 18
2008 CGATACATTA
2018 TATCGATACAAAACTTATG
1 TATCGATAC-AAACTTATG
2037 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
2050 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
2069 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
2082 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
2101 TATCGATACAAA
1 TATCGATACAAA
2113 TCATTGAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 25
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 4 0.06
18 3 0.05
19 33 0.52
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TATCGATACAAACTTATG
Found at i:2054 original size:32 final size:32
Alignment explanation
Indices: 2008--2110 Score: 188
Period size: 32 Copynumber: 3.2 Consensus size: 32
1998 AGCTTCGTAG
* *
2008 CGATACATTATATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
2040 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
2072 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
2104 CGATACA
1 CGATACA
2111 AATCATTGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:4030 original size:20 final size:20
Alignment explanation
Indices: 3986--4043 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3976 ATTTCAACGA
***
3986 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATATTTT
*
4006 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
4026 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
4044 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:4100 original size:13 final size:13
Alignment explanation
Indices: 4082--4106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4072 ATTACTCAAA
4082 TGTATCGATACAT
1 TGTATCGATACAT
4095 TGTATCGATACA
1 TGTATCGATACA
4107 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4208 original size:52 final size:52
Alignment explanation
Indices: 4115--4242 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
4105 CACTGATCTT
*
4115 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
4166 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
4218 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
4243 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:17516 original size:20 final size:19
Alignment explanation
Indices: 17480--17556 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
17470 GTAAAAAGAT
17480 AAAATGTA-CTGATACATTG
1 AAAATGTATC-GATACATTG
* *
17499 AAGAATGTATCGACACATTC
1 AA-AATGTATCGATACATTG
* *
17519 ATACATATATCGATACATTG
1 A-AAATGTATCGATACATTG
17539 AAAAATGTATCGATACAT
1 -AAAATGTATCGATACAT
17557 ATGGGTAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
19 2 0.04
20 41 0.89
21 3 0.07
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:17590 original size:91 final size:91
Alignment explanation
Indices: 17451--17658 Score: 276
Period size: 91 Copynumber: 2.3 Consensus size: 91
17441 TGCATTATTC
* * * *
17451 AATGTATCGATATA-ACTAGGTAAAAAGATAAAATGTACTGATACATTGAAGAATGTATCGACAC
1 AATGTATCGATACATA-TGGGTAAAAAGACAAAATGTACTGACACATTGAAGAATGTATCGACAC
17515 ATTCATACATATATCGATACATTGAAA
65 ATTCATACATATATCGATACATTGAAA
* * *
17542 AATGTATCGATACATATGGGTAAAAAGACAGAATGTA-TCGACATATTGAAGAATGTATCGATAC
1 AATGTATCGATACATATGGGTAAAAAGACAAAATGTACT-GACACATTGAAGAATGTATCGACAC
* *
17606 ATTCATACATGTATCGATATATTGAAA
65 ATTCATACATATATCGATACATTGAAA
* * *
17633 AATGTACCGGTACATCTGGGTAAAAA
1 AATGTATCGATACATATGGGTAAAAA
17659 TGTGACTTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
90 1 0.01
91 101 0.98
92 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (91 bp):
AATGTATCGATACATATGGGTAAAAAGACAAAATGTACTGACACATTGAAGAATGTATCGACACA
TTCATACATATATCGATACATTGAAA
Found at i:17596 original size:20 final size:20
Alignment explanation
Indices: 17571--17638 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
17561 GTAAAAAGAC
*
17571 AGAATGTATCGACATATTGA
1 AGAATGTATCGATATATTGA
* *
17591 AGAATGTATCGATACATTCA
1 AGAATGTATCGATATATTGA
*
17611 TA-CATGTATCGATATATTGA
1 -AGAATGTATCGATATATTGA
*
17631 AAAATGTA
1 AGAATGTA
17639 CCGGTACATC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATATATTGA
Found at i:19390 original size:141 final size:141
Alignment explanation
Indices: 19199--19608 Score: 545
Period size: 141 Copynumber: 2.9 Consensus size: 141
19189 ATTTATCACT
* * * *
19199 AAATAAAAATTATCATCTTAATTTTTCAAGACTTCTAATATTCTTATGGTTTTCCATAGGAGTAT
1 AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAGGGGTAT
* *
19264 AGAAATCTTCAAAACTTTTCGTATATTTTC-TGTCTCCATTAAGATACGAAATGAATTTTCTTAA
66 AGAAATCTTCAAAACTTTTCGTATCTTTTCGT-TCTCCATTAAGGTACGAAATGAATTTTCTTAA
19328 AAATTAAAAATC
130 AAATTAAAAATC
** * * ***
19340 AAATAAAAATTATTATCTTTCTTTTTAAAGATTTTTAATATTCCTATGGTTTTTTGTAGGGGTAT
1 AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAGGGGTAT
* * * **
19405 AGAAATCTTCAAAACTTTTCATATCTTTTCGATTCTCCATTAAGGTATGAAATGAATATT-TTGG
66 AGAAATCTTCAAAACTTTTCGTATCTTTTCG-TTCTCCATTAAGGTACGAAATGAATTTTCTTAA
* *
19469 AAATTAGAAATT
130 AAATTAAAAATC
* * *
19481 AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTACGTTTTTCCTTAGGGGTAT
1 AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAGGGGTAT
*
19546 AGAAATCTTTCAAAACTTTTCGTATCTTTTCAGTTCTCTATTAAGGTACGAAATGAGATTTTC
66 AGAAATC-TTCAAAACTTTTCGTATCTTTTC-GTTCTCCATTAAGGTACGAAATGA-ATTTTC
19609 GAAATTTATA
Statistics
Matches: 230, Mismatches: 33, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
141 157 0.68
142 67 0.29
143 6 0.03
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (141 bp):
AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAGGGGTAT
AGAAATCTTCAAAACTTTTCGTATCTTTTCGTTCTCCATTAAGGTACGAAATGAATTTTCTTAAA
AATTAAAAATC
Found at i:21854 original size:26 final size:27
Alignment explanation
Indices: 21826--21924 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 27
21816 ATCTACGTGT
*
21826 TAAAGA-TTAATTAAAAAATTTATATT
1 TAAAGATTTAATTAAAAAATTTATATG
* *
21852 TAAAGCATTTTAACT-AAAAATTCTACATG
1 TAAAG-A-TTTAATTAAAAAATT-TATATG
*
21881 -AAA-ATTTTAATTAAAAATTTTATATG
1 TAAAGA-TTTAATTAAAAAATTTATATG
*
21907 TAAAAATTTAATTAAAAA
1 TAAAGATTTAATTAAAAA
21925 TCCTATAGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
26 18 0.30
27 22 0.37
28 11 0.18
29 9 0.15
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (27 bp):
TAAAGATTTAATTAAAAAATTTATATG
Found at i:21892 original size:55 final size:54
Alignment explanation
Indices: 21832--22008 Score: 164
Period size: 55 Copynumber: 3.2 Consensus size: 54
21822 GTGTTAAAGA
* *
21832 TTAATTAAAAAATTTATATTTAAAGCATTTTAACTAAAAATTCTACATG-AAAAT-T
1 TTAATTAAAAAATTTATATCTAAA--ATTTTAA-TAAAAATTCTACAGGTAAAATGT
* * * * *
21887 TTAATTAAAAATTTTATATGTAAAAATTTAATTAAAAATCCTATAGGTAAAATGT
1 TTAATTAAAAAATTTATATCTAAAATTTTAA-TAAAAATTCTACAGGTAAAATGT
* *
21942 TTAATT-AAAAATTCTATAACTAAAAATTTTAATAAAAAATTCTACAAGG-AAGATGT
1 TTAATTAAAAAATT-TATATCT-AAAATTTTAAT-AAAAATTCTAC-AGGTAAAATGT
*
21998 CTAATTAAAAA
1 TTAATTAAAAA
22009 TTCTAAATGT
Statistics
Matches: 100, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
53 18 0.18
54 11 0.11
55 35 0.35
56 29 0.29
57 7 0.07
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (54 bp):
TTAATTAAAAAATTTATATCTAAAATTTTAATAAAAATTCTACAGGTAAAATGT
Found at i:21911 original size:27 final size:27
Alignment explanation
Indices: 21832--22122 Score: 172
Period size: 28 Copynumber: 10.5 Consensus size: 27
21822 GTGTTAAAGA
*
21832 TTAATTAAAAAATT-TATATTTAAAGCATT
1 TTAATT-AAAAATTCTATATGTAAA--ATT
* *
21861 TTAACTAAAAATTCTACATG-AAAATT
1 TTAATTAAAAATTCTATATGTAAAATT
* *
21887 TTAATTAAAAATTTTATATGTAAAAAT
1 TTAATTAAAAATTCTATATGTAAAATT
* *
21914 TTAATTAAAAATCCTATAGGTAAAATGT
1 TTAATTAAAAATTCTATATGTAAAAT-T
**
21942 TTAATTAAAAATTCTATAACTAAAAATT
1 TTAATTAAAAATTCTATATGT-AAAATT
* * * * *
21970 TTAATAAAAAATTCTACAAGGAAGATGT
1 TTAATTAAAAATTCTATATGTAAAAT-T
* * *
21998 CTAATTAAAAATTCTAAATGTGAAATGT
1 TTAATTAAAAATTCTATATGTAAAAT-T
* * * * ** * *
22026 TTCATTAGAAATTCCACACATGAAAGT
1 TTAATTAAAAATTCTATATGTAAAATT
* * **
22053 ATAATTAAAAATTCTACATGTAAAGGGT
1 TTAATTAAAAATTCTATATGTAAA-ATT
* * * **
22081 TTAATTAGAAATTTTATTTGTGAAAAAA
1 TTAATTAAAAATTCTATATGT-AAAATT
22109 TTAAGTTAAAAATT
1 TTAA-TTAAAAATT
22123 TAAATGGTAT
Statistics
Matches: 203, Mismatches: 51, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
26 20 0.10
27 49 0.24
28 109 0.54
29 25 0.12
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (27 bp):
TTAATTAAAAATTCTATATGTAAAATT
Found at i:22730 original size:25 final size:24
Alignment explanation
Indices: 22663--22732 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 24
22653 ATTATCAGTG
* *
22663 TATTAAATATAAAGTTTTTTATAT
1 TATTAAATATAAATTTTTTTTTAT
* *
22687 CATTAAAGT-T-AATTATTTTTTTCGT
1 TATTAAA-TATAAATT-TTTTTTT-AT
22712 TATTAAATATAAATTTTTTTT
1 TATTAAATATAAATTTTTTTT
22733 AAGTTTACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
23 3 0.08
24 14 0.39
25 15 0.42
26 4 0.11
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTAAATATAAATTTTTTTTTAT
Found at i:24714 original size:31 final size:31
Alignment explanation
Indices: 24643--24723 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
24633 TCACTATTAA
*
24643 AAATAATAA--TAAATAATTTATTAATATTT
1 AAATAATAATTTAAGTAATTTATTAATATTT
* * *
24672 ATAATTA-AATTTAAGTAATTTTTTATTATTT
1 A-AATAATAATTTAAGTAATTTATTAATATTT
*
24703 AAATAATAATTTGAGTTAATT
1 AAATAATAATTTAAG-TAATT
24724 AAAATTATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
29 3 0.07
30 8 0.20
31 25 0.61
32 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (31 bp):
AAATAATAATTTAAGTAATTTATTAATATTT
Found at i:25042 original size:23 final size:23
Alignment explanation
Indices: 24999--25043 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
24989 ATTTTTATAT
* *
24999 AATTTAATTAATTTATGATACTA
1 AATTTAATCAATTTATAATACTA
25022 AATTTAATCATATTT-TAATACT
1 AATTTAATCA-ATTTATAATACT
25044 GTAAGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (23 bp):
AATTTAATCAATTTATAATACTA
Found at i:30788 original size:22 final size:20
Alignment explanation
Indices: 30749--30819 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
30739 AGAATATATT
30749 GATACAATTAATAATGTATC
1 GATACAATTAATAATGTATC
30769 GATACAATTTAAGTAATGTATC
1 GATACAA-TTAA-TAATGTATC
* *
30791 GATAC-ATTCACTTATGTATC
1 GATACAATT-AATAATGTATC
*
30811 GATATAATT
1 GATACAATT
30820 TCTTTCCAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 21 0.48
21 9 0.20
22 14 0.32
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (20 bp):
GATACAATTAATAATGTATC
Found at i:30872 original size:21 final size:21
Alignment explanation
Indices: 30848--30899 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
30838 TGGTTTTGTT
30848 TCGATACATTTCA-TGCATGTA
1 TCGATACATTTCACT-CATGTA
*
30869 TCGATACA-TTCACTTATGTA
1 TCGATACATTTCACTCATGTA
*
30889 TCAATACATTT
1 TCGATACATTT
30900 ACTATTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (21 bp):
TCGATACATTTCACTCATGTA
Found at i:30887 original size:20 final size:21
Alignment explanation
Indices: 30864--30917 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
30854 CATTTCATGC
30864 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
* *
30884 ATGTATCAATACATTTACTAT
1 ATGTATCGATACATTCACTAT
* *
30905 TTATATCGATACA
1 ATGTATCGATACA
30918 AATTGTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:31560 original size:85 final size:86
Alignment explanation
Indices: 31400--31565 Score: 237
Period size: 85 Copynumber: 1.9 Consensus size: 86
31390 GGTTTTGGTT
31400 TTCTAAAACTTAACCTCCTTAGACAGGTGCCAAGTAATGTGGACTTGACTCAAACTTAGGTGCCA
1 TTCTAAAACTTAACCTCCTTAGACAGGTGCCAAG-AATGTGGACTTGACTCAAACTTAGGTGCCA
*
31465 TCAGCTTGTGTGGGCTTTGACA
65 CCAGCTTGTGTGGGCTTTGACA
* * * * * *
31487 TTCTAAAGCTTGACCTCTTTAGATAGGTGCCAA-AATTTGGACTTGACTCGAACTTAGGTGCCAC
1 TTCTAAAACTTAACCTCCTTAGACAGGTGCCAAGAATGTGGACTTGACTCAAACTTAGGTGCCAC
31551 CAG-TGTGTGTGGGCT
66 CAGCT-TGTGTGGGCT
31566 GACTCAGGTG
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
84 1 0.01
85 41 0.58
87 29 0.41
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (86 bp):
TTCTAAAACTTAACCTCCTTAGACAGGTGCCAAGAATGTGGACTTGACTCAAACTTAGGTGCCAC
CAGCTTGTGTGGGCTTTGACA
Found at i:31757 original size:31 final size:31
Alignment explanation
Indices: 31721--31841 Score: 118
Period size: 31 Copynumber: 3.9 Consensus size: 31
31711 CTTGAACTTA
* * *
31721 GGTGCCACTAGCTTGTGTGGGCTTTGACTAG
1 GGTGCCACCAACTTGTGCGGGCTTTGACTAG
* * *
31752 GGTGCCACCAACTTGTACGAGCTTAGACTCA-
1 GGTGCCACCAACTTGTGCGGGCTTTGACT-AG
* * *
31783 GGTGCTACTAGCTTGTGCGGGCTTTGACTAG
1 GGTGCCACCAACTTGTGCGGGCTTTGACTAG
* * *
31814 GGTGCCACCAACTCGTGTGGCCTTTGAC
1 GGTGCCACCAACTTGTGCGGGCTTTGAC
31842 ATTCTAAGGC
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
30 1 0.01
31 68 0.97
32 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.28
Consensus pattern (31 bp):
GGTGCCACCAACTTGTGCGGGCTTTGACTAG
Found at i:31824 original size:180 final size:180
Alignment explanation
Indices: 31473--31941 Score: 682
Period size: 180 Copynumber: 2.6 Consensus size: 180
31463 CATCAGCTTG
* * *
31473 TGTGGGCTTTGACATTCTAAAGCTTGACCTCTTTAGATAGGTGCCAA--AATTTGGACTTGACTC
1 TGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTT
*
31536 GAACTTAGGTGCCACCAG-TGTGTGTGGGC--TGACTCA-GGTG-CAGCCAACTCATGCGAGCTT
66 GAACTTAGGTGCCACCAGCT-TGTGTGGGCTTTGACT-AGGGTGCCA-CCAACTCATACGAGCTT
* *
31596 AGACTCGGGTGCTGCCAGCTTGTGCGGGCTTTGACTAGGGTACCACCAACTCA
128 AGACTCAGGTGCTACCAGCTTGTGCGGGCTTTGACTAGGGTACCACCAACTCA
*
31649 TGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGATAAGTGCCAACTAATTTGGACTTGACTT
1 TGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTT
* **
31714 GAACTTAGGTGCCACTAGCTTGTGTGGGCTTTGACTAGGGTGCCACCAACTTGTACGAGCTTAGA
66 GAACTTAGGTGCCACCAGCTTGTGTGGGCTTTGACTAGGGTGCCACCAACTCATACGAGCTTAGA
* * *
31779 CTCAGGTGCTACTAGCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTCG
131 CTCAGGTGCTACCAGCTTGTGCGGGCTTTGACTAGGGTACCACCAACTCA
* *
31829 TGTGGCCTTTGACATTCTAAGGCTTGGCCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTT
1 TGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTT
* * * * *
31894 GAACATAGATGCCACCAACTTTTGTGGGCTTTGACTTGGGTGCCACCA
66 GAACTTAGGTGCCACCAGCTTGTGTGGGCTTTGACTAGGGTGCCACCA
31942 GCTCGTGTAG
Statistics
Matches: 264, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
176 44 0.17
178 41 0.16
179 2 0.01
180 175 0.66
181 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.29
Consensus pattern (180 bp):
TGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTT
GAACTTAGGTGCCACCAGCTTGTGTGGGCTTTGACTAGGGTGCCACCAACTCATACGAGCTTAGA
CTCAGGTGCTACCAGCTTGTGCGGGCTTTGACTAGGGTACCACCAACTCA
Found at i:32025 original size:37 final size:36
Alignment explanation
Indices: 31970--32079 Score: 134
Period size: 37 Copynumber: 3.1 Consensus size: 36
31960 AAGAGAAAGA
* *
31970 AAAAGGAGTGGGCGTCCTACTCTTTGGGGACAAAGGG
1 AAAAGGAGTAGGC-TCCTACTCTTTGAGGACAAAGGG
*
32007 AAAAGGAGTAGGCATCCTACTCTTTAAGGACAAA-GG
1 AAAAGGAGTAGGC-TCCTACTCTTTGAGGACAAAGGG
* * *
32043 AAAAAGAGTATG-TCCTGCTCTTTGAGGACAAAGGG
1 AAAAGGAGTAGGCTCCTACTCTTTGAGGACAAAGGG
32078 AA
1 AA
32080 TATAAGAATG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 18 0.28
35 4 0.06
36 12 0.19
37 30 0.47
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (36 bp):
AAAAGGAGTAGGCTCCTACTCTTTGAGGACAAAGGG
Found at i:32142 original size:77 final size:76
Alignment explanation
Indices: 32033--32201 Score: 241
Period size: 77 Copynumber: 2.2 Consensus size: 76
32023 CTACTCTTTA
* * *
32033 AGGACAAAGGAAAAAGAGTATGTCCTGCTCTTTGAGGACAAAGGGAATATAAGAATGAAATGGGT
1 AGGACAAAGGAAAAAGAGTATGTCCTGCTCTTTAAGGACAAAGGGAAAAGAAGAATGAAATGGGT
**
32098 CTTGCTCCTTG
66 CCAGCTCCTTG
* *
32109 AGGACAAAGTAAAAATGAGTATGTCC-GATTCTTTAAGGACAAAGGGAAAAGAAGAATGAAATGG
1 AGGACAAAGGAAAAA-GAGTATGTCCTG-CTCTTTAAGGACAAAGGGAAAAGAAGAATGAAATGG
32173 GTCCAGCTCCTTG
64 GTCCAGCTCCTTG
*
32186 AAGACAAAGGAAAAAG
1 AGGACAAAGGAAAAAG
32202 GAAAAAAAGA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
76 16 0.20
77 66 0.80
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (76 bp):
AGGACAAAGGAAAAAGAGTATGTCCTGCTCTTTAAGGACAAAGGGAAAAGAAGAATGAAATGGGT
CCAGCTCCTTG
Found at i:32277 original size:35 final size:36
Alignment explanation
Indices: 32193--32280 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 36
32183 TTGAAGACAA
* * * *
32193 AGGAAAAAGGAAAAAAAGAATGCATCATGCTCCTTG
1 AGGACAAAGGAAAAAGAGAATACATCATACTCCTTG
*
32229 AGGACAAAGGGAAAAAGAG-ATACATCTTACT-CTTCG
1 AGGACAAA-GGAAAAAGAGAATACATCATACTCCTT-G
32265 AGGACAAAGGAAAAAG
1 AGGACAAAGGAAAAAG
32281 GAAATGAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
35 11 0.24
36 25 0.56
37 9 0.20
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.15
Consensus pattern (36 bp):
AGGACAAAGGAAAAAGAGAATACATCATACTCCTTG
Found at i:32320 original size:42 final size:41
Alignment explanation
Indices: 32220--32320 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
32210 GAATGCATCA
* *
32220 TGCTCCTTGAGGACAAAGGGAAAAA-G-A-G-A-TACATCT
1 TGCTCCTTGAGGACAAAGGGAAAAAGGAATGAAGTGCGTCT
*
32256 TACT-CTTCGAGGACAAA-GGAAAAAGGAAATGAAGTGCGTCT
1 TGCTCCTT-GAGGACAAAGGGAAAAAGG-AATGAAGTGCGTCT
32297 TGCTCCTTGAGGACAAAGGGAAAA
1 TGCTCCTTGAGGACAAAGGGAAAA
32321 GAACTGTGTC
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
35 10 0.19
36 13 0.25
38 1 0.02
39 1 0.02
40 1 0.02
41 17 0.33
42 9 0.17
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.19
Consensus pattern (41 bp):
TGCTCCTTGAGGACAAAGGGAAAAAGGAATGAAGTGCGTCT
Found at i:35901 original size:20 final size:19
Alignment explanation
Indices: 35855--35931 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
35845 TCATACCCTG
* *
35855 ATGTATCGATGCATTTTTCA
1 ATGTATCGATACA-TTATCA
* *
35875 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TATCA
* *
35895 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTAT-CA
35915 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
35932 GTCTTTTTAC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 3 0.07
20 42 0.93
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:35922 original size:40 final size:39
Alignment explanation
Indices: 35855--35932 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
35845 TCATACCCTG
* * *
35855 ATGTATCGATGCATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
35895 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
35933 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:36866 original size:22 final size:22
Alignment explanation
Indices: 36840--36894 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
36830 AGCCTTTGAC
36840 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
36862 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
36884 CATGCATTTTT
1 CATGCATTTTT
36895 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:36901 original size:20 final size:21
Alignment explanation
Indices: 36840--36901 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
36830 AGCCTTTGAC
**
36840 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
36862 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
36884 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
36902 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:38328 original size:97 final size:96
Alignment explanation
Indices: 38139--38314 Score: 243
Period size: 97 Copynumber: 1.8 Consensus size: 96
38129 AAAAATACCA
* *
38139 AAATTTTATTCATCGGGGATACTCCAACCCCATTTTTCCAAGGGGATACTCCAACCCCGCTTTTA
1 AAATTTTATTCATCGGGGACACTCCAACCCCATTCTTCCAAGGGGATACTCCAACCCCGCTTTTA
* * *
38204 TACTTATCAAGATTCAAATCTTATTCTCACTC
66 TAATTA-CAAAATTAAAATCTTATTCTCACTC
*
38236 AAATTTTCA-TCATCGGGGACACTCCAACCCCATTCTTCCGAGGGGATACTCCAACCCCG-TTTT
1 AAATTTT-ATTCATCGGGGACACTCCAACCCCATTCTTCCAAGGGGATACTCCAACCCCGCTTTT
38299 -TCAATTA-AAAATTAAA
65 AT-AATTACAAAATTAAA
38315 TTATTTTCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
94 7 0.10
95 1 0.01
96 8 0.11
97 54 0.76
98 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (96 bp):
AAATTTTATTCATCGGGGACACTCCAACCCCATTCTTCCAAGGGGATACTCCAACCCCGCTTTTA
TAATTACAAAATTAAAATCTTATTCTCACTC
Found at i:43907 original size:13 final size:13
Alignment explanation
Indices: 43888--43965 Score: 70
Period size: 13 Copynumber: 5.8 Consensus size: 13
43878 CCTTTACACC
43888 CAAAAAAAAAACAA
1 CAAAAAAAAAA-AA
43902 -AAAAAAAACAAAA
1 CAAAAAAAA-AAAA
*
43915 CAAAAAAACAAAA
1 CAAAAAAAAAAAA
43928 CAAAAAAATTAAAAA
1 CAAAAAAA--AAAAA
* *
43943 -AAAGAAAAAATAG
1 CAAA-AAAAAAAAA
43956 CAAAAAAAAA
1 CAAAAAAAAA
43966 TAGAAGGGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
13 31 0.57
14 15 0.28
15 8 0.15
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.04
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:43965 original size:1 final size:1
Alignment explanation
Indices: 43889--43952 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
43879 CTTTACACCC
* * * * * ** *
43889 AAAAAAAAAACAAAAAAAAAACAAAACAAAAAAACAAAACAAAAAAATTAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43953 TAGCAAAAAA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.03
Consensus pattern (1 bp):
A
Found at i:45313 original size:28 final size:28
Alignment explanation
Indices: 45183--45654 Score: 548
Period size: 28 Copynumber: 16.4 Consensus size: 28
45173 GAATGTTCAT
45183 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
45211 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
45240 CTCTTTTCAAAGCCCACAAATCAGTGGCG
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
45269 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
45298 CCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
45326 CCCTTTCAGAGCCCACAAGTCAATGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
45354 CCCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
45382 CCATTGCGAAGCCCACAATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
45410 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
45438 CCCTTTTAAAGCTCACACAAGTCAGTGGCA
1 CCCTTTCAAAGC-C-CACAAGTCAGTGGCA
* * *
45468 CTCCTTTTAAAGCTCAAGCAAGTCAGTGGTA
1 C-CCTTTCAAAGC-CCA-CAAGTCAGTGGCA
*
45499 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
45527 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
45555 TCCTTTCAAAGCCCACGAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** * *
45583 TTCTTTCAAAGCCACGCATGTCAGTGGCA
1 CCCTTTCAAAGCC-CACAAGTCAGTGGCA
* *
45612 CCCTTTTAAAAGCCCATGCAAGTCAATGGCAA
1 CCC-TTTCAAAGCCCA--CAAGTCAGTGGC-A
45644 CCCTTTTCAAA
1 CCC-TTTCAAA
45655 TCACCACTGT
Statistics
Matches: 387, Mismatches: 47, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
28 208 0.54
29 97 0.25
30 35 0.09
31 36 0.09
32 11 0.03
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:46177 original size:20 final size:19
Alignment explanation
Indices: 46131--46207 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
46121 TCATACCCTG
* * *
46131 ATGTATCGATGCATTTTTCA
1 ATGTATCGATACA-TTATAA
*
46151 ATATATCGATACATGTATAA
1 ATGTATCGATACAT-TATAA
* *
46171 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTATA-A
46191 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
46208 GTCTTTTTAC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 4 0.09
20 42 0.91
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATAA
Done.