Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3448_ERROPOS6352467+
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: 66889
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:394 original size:13 final size:13
Alignment explanation
Indices: 376--403 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
366 TGAAAATTCG
376 TTAATGGTACATT
1 TTAATGGTACATT
389 TTAATGGTACATT
1 TTAATGGTACATT
402 TT
1 TT
404 CCCCTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
TTAATGGTACATT
Found at i:10340 original size:21 final size:21
Alignment explanation
Indices: 10316--10359 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10306 GAATCTTTAG
*
10316 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
10337 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
10358 TA
1 TA
10360 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:12610 original size:22 final size:22
Alignment explanation
Indices: 12583--12626 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12573 CTCTCGATTT
12583 TTTTATTGCTCCTTTTCAATCA
1 TTTTATTGCTCCTTTTCAATCA
12605 TTTTATTGCTCCTTTTCAATCA
1 TTTTATTGCTCCTTTTCAATCA
12627 AAAGAGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTTATTGCTCCTTTTCAATCA
Found at i:16781 original size:32 final size:32
Alignment explanation
Indices: 16745--16806 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
16735 AGCTTTTGGT
16745 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
16777 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
16807 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:24990 original size:6 final size:6
Alignment explanation
Indices: 24979--25052 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
24969 GGGATCACTA
24979 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
25022 A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
25053 GAATAGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.05
5 22 0.38
6 27 0.47
8 6 0.10
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (6 bp):
ACTAAT
Found at i:24996 original size:5 final size:5
Alignment explanation
Indices: 24976--25037 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
24966 GCCGGGATCA
24976 CTAA- CTAAT ACTAAT CTAAT CTAA- CTAAT ACTAAT CTAAT ACTAAT
1 CTAAT CTAAT -CTAAT CTAAT CTAAT CTAAT -CTAAT CTAAT -CTAAT
**
25022 AGAAT ACTAAT CTAAT
1 CTAAT -CTAAT CTAAT
25038 ACTCTAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (5 bp):
CTAAT
Found at i:25014 original size:11 final size:11
Alignment explanation
Indices: 24975--25051 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
24965 AGCCGGGATC
24975 ACTAA-CTAAT
1 ACTAATCTAAT
24985 ACTAATCTAAT
1 ACTAATCTAAT
24996 -CTAA-CTAAT
1 ACTAATCTAAT
25005 ACTAATCTAAT
1 ACTAATCTAAT
**
25016 ACTAATAGAAT
1 ACTAATCTAAT
25027 ACTAATCTAAT
1 ACTAATCTAAT
25038 AC---TCTAAT
1 ACTAATCTAAT
25046 ACTAAT
1 ACTAAT
25052 AGAATAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:25030 original size:22 final size:21
Alignment explanation
Indices: 24975--25051 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
24965 AGCCGGGATC
24975 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
24996 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
25016 ACTAA-TAGAATACTAATCTAAT
1 ACTAACT--AATACTAATCTAAT
25038 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
25052 AGAATAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.17
20 21 0.40
21 5 0.10
22 17 0.33
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:25066 original size:14 final size:14
Alignment explanation
Indices: 25049--25076 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25039 CTCTAATACT
25049 AATAGAATAGAAAA
1 AATAGAATAGAAAA
25063 AATAGAATAGAAAA
1 AATAGAATAGAAAA
25077 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:33411 original size:18 final size:18
Alignment explanation
Indices: 33332--33425 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
33322 CAAGGTCACG
*
33332 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
33350 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
33368 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
33386 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
33404 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
33419 ATCAATA
1 ATCAATA
33426 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:33412 original size:9 final size:9
Alignment explanation
Indices: 33332--33412 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
33322 CAAGGTCACG
*
33332 ATCAATAGC
1 ATCAATATC
* *
33341 GTCACTATC
1 ATCAATATC
*
33350 ATCAATAGC
1 ATCAATATC
* * *
33359 GTCACTAGC
1 ATCAATATC
33368 ATCAATATC
1 ATCAATATC
* * *
33377 GTCACTAGC
1 ATCAATATC
33386 ATCAATATC
1 ATCAATATC
* *
33395 GTCACTATC
1 ATCAATATC
33404 ATCAATATC
1 ATCAATATC
33413 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Found at i:35815 original size:21 final size:21
Alignment explanation
Indices: 35785--35873 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
35775 CTCACAAAGA
* *
35785 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
35805 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
35826 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
35847 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
35871 AAA
1 AAA
35874 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:35866 original size:24 final size:21
Alignment explanation
Indices: 35785--35853 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
35775 CTCACAAAGA
* * *
35785 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
35805 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
35826 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
35847 AAAAAGA
1 AAAAAGA
35854 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:40030 original size:14 final size:14
Alignment explanation
Indices: 40011--40039 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40001 TACAATATAT
40011 ATAAGAATTATACG
1 ATAAGAATTATACG
40025 ATAAGAATTATACG
1 ATAAGAATTATACG
40039 A
1 A
40040 ATCCATCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:42455 original size:29 final size:29
Alignment explanation
Indices: 42413--42470 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
42403 TATCTTCTAT
*
42413 TAGGAATAGCGTTTTAATATGATAATAAA
1 TAGGAATAGCGTTTCAATATGATAATAAA
* *
42442 TAGGAATAGCGTTTCGATATGATACTAAA
1 TAGGAATAGCGTTTCAATATGATAATAAA
42471 AATGGGTTGC
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:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (29 bp):
TAGGAATAGCGTTTCAATATGATAATAAA
Found at i:45758 original size:16 final size:16
Alignment explanation
Indices: 45733--45765 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45723 ACGGTATTCT
*
45733 ATATTTTATAGTAGCA
1 ATATTCTATAGTAGCA
45749 ATATTCTATAGTAGCA
1 ATATTCTATAGTAGCA
45765 A
1 A
45766 AGGAATAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (16 bp):
ATATTCTATAGTAGCA
Found at i:46264 original size:15 final size:15
Alignment explanation
Indices: 46231--46264 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
46221 AGTTATGTCT
*
46231 ATGTATGGAATTATA
1 ATGTATGGAATTAGA
*
46246 ATGTATGGAATTAGC
1 ATGTATGGAATTAGA
46261 ATGT
1 ATGT
46265 CAAAAAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (15 bp):
ATGTATGGAATTAGA
Found at i:47287 original size:19 final size:19
Alignment explanation
Indices: 47265--47304 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
47255 TTAAACTTTT
* *
47265 ATTATACTTTTCTATTCTA
1 ATTAAACTTTTCGATTCTA
47284 ATTAAACTTTTCGATTCTA
1 ATTAAACTTTTCGATTCTA
47303 AT
1 AT
47305 AAAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTAAACTTTTCGATTCTA
Found at i:49009 original size:14 final size:14
Alignment explanation
Indices: 48990--49018 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
48980 CTTTTTACTT
48990 TGTTATATAGATTA
1 TGTTATATAGATTA
49004 TGTTATATAGATTA
1 TGTTATATAGATTA
49018 T
1 T
49019 TATTTATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TGTTATATAGATTA
Found at i:49167 original size:21 final size:21
Alignment explanation
Indices: 49143--49182 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49133 TTTATCAGTA
*
49143 ATTCCATTTCATTTATATTCT
1 ATTCCATATCATTTATATTCT
*
49164 ATTCTATATCATTTATATT
1 ATTCCATATCATTTATATT
49183 TTTAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTCCATATCATTTATATTCT
Found at i:57147 original size:220 final size:218
Alignment explanation
Indices: 56725--57353 Score: 930
Period size: 220 Copynumber: 2.9 Consensus size: 218
56715 TTAGGTTAGA
* *
56725 TATATAGTTGTTAGAAACATATCTTTGCTATAAAATCTTATAAATAGGACT-AAAGATTTCCAAG
1 TATATAGTTGTTAGAAACATATCTTCGCTATAAAATCTCATAAATAGGACTCAAAGATTTCCAAG
* * * * *
56789 AAAATGTCCCTCAATAC----AGAG-GGAAACAAACAATCAGAAAAAAATAAAATAAAACAGATA
66 AAAATGTCCCTCAATACAATTACAGAAGAAACAAACAACCAAAAAAAAAT-AAATAAAACACATA
56849 ACAGGCGATAAACTATCAAAAAAATGACGACATCACAAGATTTAAAAAGACGAATATAAGCAGTG
130 ACAGGCGATAAACTATCAAAAAAAT---GACATCACAAGATTTAAAAAGACGAATATAAGCAGTG
*
56914 TTTCATTAGGGTTTTAGGGTAGATACT
192 TTTCATAAGGGTTTTAGGGTAGATACT
* *
56941 TATATAGTTATTAGAAACATATCTTCGCTATAAAATCTCATAAATAGGACTCAAAGATTTCCAAA
1 TATATAGTTGTTAGAAACATATCTTCGCTATAAAATCTCATAAATAGGACTCAAAGATTTCCAAG
57006 AAAATGTCCCTCAATACATATTACAGCAAGAAACAAACAACCAAAAAAAAATAAATAAAACACAT
66 AAAATGTCCCTCAATACA-ATTACAG-AAGAAACAAACAACCAAAAAAAAATAAATAAAACACAT
* * *
57071 AACAGGCAATAAACTATCAAAAAAATGACATCACAAGATTTAAGAAGCCGAATATAAGCAGTGTT
129 AACAGGCGATAAACTATCAAAAAAATGACATCACAAGATTTAAAAAGACGAATATAAGCAGTGTT
57136 TCATAAGGGTTTTAGGGTAGATACT
194 TCATAAGGGTTTTAGGGTAGATACT
* *
57161 GATATAGTTGTTAGAAACATATCTTCGCTATAAAATCTCATAAATAGGACTCAAAGATTTGCAAG
1 TATATAGTTGTTAGAAACATATCTTCGCTATAAAATCTCATAAATAGGACTCAAAGATTTCCAAG
* * *
57226 AAAATGTCCTTCAATACAGATTACAGAGAGAAACAAACAACCGACAAAAAAA-AAACAAAACACA
66 AAAATGTCCCTCAATACA-ATTACAGA-AGAAACAAACAACC-AAAAAAAAATAAATAAAACACA
*
57290 GAACAGGCGATAAACTATCAAAAAAATGACGGCATCACAAGATTTAAAAAGACGAATATAAGCA
128 TAACAGGCGATAAACTATCAAAAAAATGA---CATCACAAGATTTAAAAAGACGAATATAAGCA
57354 TAAATCTGAA
Statistics
Matches: 375, Mismatches: 25, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
216 48 0.13
217 29 0.08
219 1 0.00
220 198 0.53
221 8 0.02
222 3 0.01
223 67 0.18
224 21 0.06
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (218 bp):
TATATAGTTGTTAGAAACATATCTTCGCTATAAAATCTCATAAATAGGACTCAAAGATTTCCAAG
AAAATGTCCCTCAATACAATTACAGAAGAAACAAACAACCAAAAAAAAATAAATAAAACACATAA
CAGGCGATAAACTATCAAAAAAATGACATCACAAGATTTAAAAAGACGAATATAAGCAGTGTTTC
ATAAGGGTTTTAGGGTAGATACT
Found at i:58983 original size:4 final size:4
Alignment explanation
Indices: 58966--58999 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
58956 GAATGATCAT
*
58966 AACA AA-A AAAA AACA AACA AACA AACA AACA AAC
1 AACA AACA AACA AACA AACA AACA AACA AACA AAC
59000 CAACCATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:59824 original size:27 final size:27
Alignment explanation
Indices: 59786--59837 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
59776 CGTGACACAC
*
59786 ACACATACAGATAGAAAGAATATATAT
1 ACACAAACAGATAGAAAGAATATATAT
59813 ACACAAACAGATAGAAAGAATATAT
1 ACACAAACAGATAGAAAGAATATAT
59838 CACAAGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (27 bp):
ACACAAACAGATAGAAAGAATATATAT
Found at i:59899 original size:52 final size:52
Alignment explanation
Indices: 59831--60042 Score: 137
Period size: 52 Copynumber: 3.9 Consensus size: 52
59821 AGATAGAAAG
* ** *
59831 AATATATCACAAGAATATAAATAGATGCAAATTTCACTTACCGATGCATGCA
1 AATATATCACAAGAATATAAATACACACAAATTTCACTTACAGATGCATGCA
* *
59883 AATATATCA-AACGAATATATATACACACACATTTCACTTACAGATGCATGTAGCAA
1 AATATATCACAA-GAATATAAATACACACAAATTTCACTTACAGATGCA--T-GC-A
* * * * ** *
59939 AATTTATAACAGATAGAA-AGAAATATATACATGCAAATTTCACTTATGGATGCACGCA
1 AA--TATATCACA-AGAATA-TAA-ATACACA--CAAATTTCACTTACAGATGCATGCA
* *
59997 AATATATAAAAAGAATATATAA-ACACAC--ATTTCACTTACAGATGCA
1 AATATATCACAAGAATATA-AATACACACAAATTTCACTTACAGATGCA
60043 GGAAGCAAAA
Statistics
Matches: 124, Mismatches: 21, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
50 16 0.13
51 2 0.02
52 40 0.32
54 5 0.04
55 8 0.06
56 11 0.09
58 10 0.08
59 7 0.06
60 7 0.06
62 18 0.15
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (52 bp):
AATATATCACAAGAATATAAATACACACAAATTTCACTTACAGATGCATGCA
Found at i:59967 original size:62 final size:55
Alignment explanation
Indices: 59899--60058 Score: 132
Period size: 50 Copynumber: 2.8 Consensus size: 55
59889 TCAAACGAAT
*
59899 ATATATACACACACATTTCACTTACAGATGCATGTAGCAAAATTTATAACAGATAGAAAGAA
1 ATATATACACACACATTTCACTTACAGATGCA-G-AGCAAAATTTAT---A-ATAAAAAG-A
** * ** *
59961 ATATATACATGCAAATTTCACTTATGGATGCA-CGC-AAA--TAT-ATAAAAAGA
1 ATATATACACACACATTTCACTTACAGATGCAGAGCAAAATTTATAATAAAAAGA
*
60011 ATATATAAACACACATTTCACTTACAGATGCAGGAAGCAAAATTTATA
1 ATATATACACACACATTTCACTTACAGATGCA-G-AGCAAAATTTATA
60059 TGGAATGTGC
Statistics
Matches: 77, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
50 27 0.35
51 7 0.09
53 2 0.03
54 3 0.04
56 6 0.08
58 3 0.04
59 2 0.03
62 27 0.35
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (55 bp):
ATATATACACACACATTTCACTTACAGATGCAGAGCAAAATTTATAATAAAAAGA
Found at i:59991 original size:114 final size:113
Alignment explanation
Indices: 59841--60058 Score: 330
Period size: 114 Copynumber: 1.9 Consensus size: 113
59831 AATATATCAC
* * * *
59841 AAGAATATAAATAGATGCAAATTTCACTTACCGATGCATGCAAATATATCAAACGAATATATATA
1 AAGAATATAAATACATGCAAATTTCACTTACCGATGCACGCAAATATATAAAAAGAATATATA-A
* *
59906 CACACACATTTCACTTACAGATGCATGTAGCAAAATTTATAACAGATAGA
65 -ACACACATTTCACTTACAGATGCAGGAAGCAAAATTTATAACAGATAGA
* **
59956 AAGAA-ATATATACATGCAAATTTCACTTATGGATGCACGCAAATATATAAAAAGAATATATAAA
1 AAGAATATAAATACATGCAAATTTCACTTACCGATGCACGCAAATATATAAAAAGAATATATAAA
60020 CACACATTTCACTTACAGATGCAGGAAGCAAAATTTATA
66 CACACATTTCACTTACAGATGCAGGAAGCAAAATTTATA
60059 TGGAATGTGC
Statistics
Matches: 94, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
112 38 0.40
113 1 0.01
114 50 0.53
115 5 0.05
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (113 bp):
AAGAATATAAATACATGCAAATTTCACTTACCGATGCACGCAAATATATAAAAAGAATATATAAA
CACACATTTCACTTACAGATGCAGGAAGCAAAATTTATAACAGATAGA
Found at i:60424 original size:10 final size:10
Alignment explanation
Indices: 60409--60452 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
60399 GCAACACAAA
60409 AACCACTTGT
1 AACCACTTGT
60419 AACCACTTGT
1 AACCACTTGT
*
60429 AACTACTTGT
1 AACCACTTGT
*
60439 AACTACTTTGT
1 AACCAC-TTGT
60450 AAC
1 AAC
60453 ATTCTTCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (10 bp):
AACCACTTGT
Found at i:61993 original size:24 final size:25
Alignment explanation
Indices: 61950--61998 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
61940 GAGACGTGGA
* *
61950 GAAATTTTGTGCCATGCAAAGTGCT
1 GAAATTTTGAGCCATACAAAGTGCT
61975 GAAATTTT-AGCCATACAAAGTGCT
1 GAAATTTTGAGCCATACAAAGTGCT
61999 CCATTATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (25 bp):
GAAATTTTGAGCCATACAAAGTGCT
Done.