Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold271
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: 858520
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 36313 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:831609 original size:3 final size:3
Alignment explanation
Indices: 831601--831633 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
831591 ACTATTCAGT
*
831601 TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
831634 GTAATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:833048 original size:19 final size:21
Alignment explanation
Indices: 833024--833065 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
833014 AACACGATAA
*
833024 TTTTGAAA-CAC-AACTTTTT
1 TTTTGAAAGCACGAAATTTTT
833043 TTTTGAAAGCACGAAATTTTT
1 TTTTGAAAGCACGAAATTTTT
833064 TT
1 TT
833066 AAAACACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTTGAAAGCACGAAATTTTT
Found at i:833081 original size:17 final size:16
Alignment explanation
Indices: 833061--833098 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
833051 GCACGAAATT
833061 TTTTTAAAACACAATAA
1 TTTTTAAAACACAA-AA
*
833078 TTTTAAAAACACAAAA
1 TTTTTAAAACACAAAA
833094 TTTTT
1 TTTTT
833099 TTTTAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTTTAAAACACAAAA
Found at i:833102 original size:21 final size:20
Alignment explanation
Indices: 833024--833138 Score: 66
Period size: 19 Copynumber: 6.0 Consensus size: 20
833014 AACACGATAA
* *
833024 TTTTGAAACAC-AACTTTTT
1 TTTTAAAACACAAAATTTTT
* *
833043 TTTTGAAAGCACGAAA--TTT
1 TTTT-AAAACACAAAATTTTT
833062 TTTTAAAACACAATAA----T
1 TTTTAAAACACAA-AATTTTT
*
833079 TTTAAAAACACAAAATTTTT
1 TTTTAAAACACAAAATTTTT
*
833099 TTTT-AAATACAAAATTTTAT
1 TTTTAAAACACAAAATTTT-T
* *
833119 TTTGAGAACACAAAAATTTT
1 TTTTAAAACAC-AAAATTTT
833139 GATAAATTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
16 2 0.03
17 13 0.17
18 7 0.09
19 26 0.35
20 13 0.17
21 6 0.08
22 8 0.11
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTTAAAACACAAAATTTTT
Found at i:833114 original size:54 final size:54
Alignment explanation
Indices: 833011--833116 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
833001 GTGATCCGGA
* * * *
833011 TAAAACACGATAATTTTGAAACACAACTTTTTTTTTGAAAGCACGAAATTTTTT
1 TAAAACACAATAATTTTAAAACACAAATTTTTTTTTGAAAGCACAAAATTTTTT
*
833065 TAAAACACAATAATTTTAAAAACACAAAATTTTTTTTT-AAA-TACAAAATTTT
1 TAAAACACAATAATTTT-AAAACAC-AAATTTTTTTTTGAAAGCACAAAATTTT
833117 ATTTTGAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
54 25 0.56
55 9 0.20
56 11 0.24
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (54 bp):
TAAAACACAATAATTTTAAAACACAAATTTTTTTTTGAAAGCACAAAATTTTTT
Found at i:833218 original size:36 final size:35
Alignment explanation
Indices: 833160--833284 Score: 114
Period size: 36 Copynumber: 3.4 Consensus size: 35
833150 AAACACGAGG
*
833160 ATTTTTTT-AGAAACACGGAAATTTATGAAACACTGTCA
1 ATTTTTTTGA-AAACAC-GAAATTTATAAAACACTG--A
* *
833198 ATTTTTTTGAAAACAC-AAATTTTTAAAAGACATGA
1 ATTTTTTTGAAAACACGAAATTTATAAAACAC-TGA
833233 A-TTTTTTGAAAACACGAAAATTTATAAAACA-TGGAA
1 ATTTTTTTGAAAACACG-AAATTTATAAAACACT-G-A
833269 ATTTTTTCTGAAAACA
1 ATTTTTT-TGAAAACA
833285 AAGAAATTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
34 15 0.20
35 3 0.04
36 26 0.35
37 7 0.09
38 22 0.30
39 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.35
Consensus pattern (35 bp):
ATTTTTTTGAAAACACGAAATTTATAAAACACTGA
Found at i:833354 original size:17 final size:18
Alignment explanation
Indices: 833201--833395 Score: 120
Period size: 18 Copynumber: 10.9 Consensus size: 18
833191 ACTGTCAATT
833201 TTTTTGAAAACAC--AAA
1 TTTTTGAAAACACGAAAA
* * *
833217 TTTTTAAAAGACATG-AAT
1 TTTTTGAAA-ACACGAAAA
833235 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
833253 TTTAT-AAAACATGGAAATT
1 TTTTTGAAAACA-CGAAA-A
833272 TTTTCTGAAAACA--AAGAA
1 TTTT-TGAAAACACGAA-AA
* ** * *
833290 ATTACG-AAATACGAGAA
1 TTTTTGAAAACACGAAAA
*
833307 TTTTTGAAAACACGGGAAATT
1 TTTTTGAAAACAC--GAAA-A
833328 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
833346 TTTTT-AAAACACGGAAA
1 TTTTTGAAAACACGAAAA
* *
833363 TTTTTAAAAACACGGAAA
1 TTTTTGAAAACACGAAAA
833381 TTTTTG-AAACACGAA
1 TTTTTGAAAACACGAA
833396 GTTTTTTTAA
Statistics
Matches: 138, Mismatches: 26, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
16 12 0.09
17 43 0.31
18 52 0.38
19 8 0.06
20 4 0.03
21 19 0.14
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:833362 original size:18 final size:18
Alignment explanation
Indices: 833170--833393 Score: 135
Period size: 17 Copynumber: 12.4 Consensus size: 18
833160 ATTTTTTTAG
*
833170 AAACACGGAAATTTATG-
1 AAACACGGAAATTTTTGA
* *
833187 AAACACTGTCAATTTTTTTGA
1 AAACAC-G-GAA-ATTTTTGA
833208 AAACAC--AAATTTTT-A
1 AAACACGGAAATTTTTGA
* * *
833223 AAAGACATGAATTTTTTGA
1 AAACAC-GGAAATTTTTGA
* *
833242 AAACACGAAAATTTAT-A
1 AAACACGGAAATTTTTGA
*
833259 AAACATGGAAATTTTTTCTGA
1 AAACACGGAAA--TTTT-TGA
** **
833280 AAACAAAGAAA-TTACG-
1 AAACACGGAAATTTTTGA
*
833296 AAATAC-GAGAATTTTTGA
1 AAACACGGA-AATTTTTGA
833314 AAACACGGGAAATTTTTTTGA
1 AAACAC-GGAAA--TTTTTGA
*
833335 AAACACGAAAATTTTT-A
1 AAACACGGAAATTTTTGA
*
833352 AAACACGGAAATTTTTAA
1 AAACACGGAAATTTTTGA
833370 AAACACGGAAATTTTTG-
1 AAACACGGAAATTTTTGA
833387 AAACACG
1 AAACACG
833394 AAGTTTTTTT
Statistics
Matches: 161, Mismatches: 26, Indels: 40
0.71 0.11 0.18
Matches are distributed among these distances:
15 8 0.05
16 11 0.07
17 45 0.28
18 43 0.27
19 13 0.08
20 12 0.07
21 29 0.18
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (18 bp):
AAACACGGAAATTTTTGA
Found at i:833380 original size:55 final size:54
Alignment explanation
Indices: 833235--833385 Score: 146
Period size: 56 Copynumber: 2.7 Consensus size: 54
833225 AGACATGAAT
* * *
833235 TTTTTGAAAACACGAAAATTTATAAAACATGGAAATTTTTTCTGAAAACAAAGAA
1 TTTTT-AAAACACGGAAATTTTTAAAACACGGAAATTTTTTCTGAAAACAAAGAA
* *** *
833290 ATTACGAAATAC-GAGAATTTTTGAAAACACGGGAAATTTTTT-TGAAAACACGAA-AA
1 TTTTTAAAACACGGA-AATTTTT-AAAACAC-GGAAATTTTTTCTGAAAACA--AAGAA
833346 TTTTTAAAACACGGAAATTTTTAAAAACACGGAAATTTTT
1 TTTTTAAAACACGGAAATTTTT-AAAACACGGAAATTTTT
833386 GAAACACGAA
Statistics
Matches: 76, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
53 1 0.01
54 11 0.14
55 26 0.34
56 34 0.45
57 4 0.05
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (54 bp):
TTTTTAAAACACGGAAATTTTTAAAACACGGAAATTTTTTCTGAAAACAAAGAA
Found at i:833402 original size:35 final size:35
Alignment explanation
Indices: 833300--833408 Score: 112
Period size: 35 Copynumber: 3.0 Consensus size: 35
833290 ATTACGAAAT
* *
833300 ACGAGAATTTTTGAAAACACGGGAAATTTTTTTGAAAAC
1 ACGAAAATTTTT-AAAACAC-GG-AA-TTTTTTAAAAAC
*
833339 ACGAAAATTTTTAAAACACGGAAATTTTTAAAAAC
1 ACGAAAATTTTTAAAACACGGAATTTTTTAAAAAC
* * *
833374 ACGGAAATTTTTGAAACAC-GAAGTTTTTTTAAAAC
1 ACGAAAATTTTTAAAACACGGAA-TTTTTTAAAAAC
833409 GAATATAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
34 3 0.05
35 37 0.60
36 2 0.03
37 2 0.03
38 7 0.11
39 11 0.18
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (35 bp):
ACGAAAATTTTTAAAACACGGAATTTTTTAAAAAC
Found at i:833463 original size:17 final size:17
Alignment explanation
Indices: 833440--833486 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
833430 TTAGTATTAT
833440 TTTTTGAAACACGAGAAA
1 TTTTTGAAACACGA-AAA
*
833458 -TTTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
833475 TTTTTGAAACAC
1 TTTTTGAAACAC
833487 AATTAGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:833467 original size:18 final size:18
Alignment explanation
Indices: 833440--833483 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
833430 TTAGTATTAT
833440 TTTTTG-AAACACGAGAAA
1 TTTTTGAAAACACGA-AAA
*
833458 -TTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
833475 TTTTTGAAA
1 TTTTTGAAA
833484 CACAATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:833796 original size:5 final size:5
Alignment explanation
Indices: 833786--833812 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
833776 GATTTTAACG
833786 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
833813 ACATAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:833829 original size:17 final size:17
Alignment explanation
Indices: 833786--833836 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
833776 GATTTTAACG
*
833786 AATAAAAT-AAAATA-A
1 AATAAAATAAAAACATA
833801 AATAAAATAAAAACATA
1 AATAAAATAAAAACATA
*
833818 AATACAAA-AAAAACTTA
1 AATA-AAATAAAAACATA
833835 AA
1 AA
833837 AATATGCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 8 0.26
16 5 0.16
17 15 0.48
18 3 0.10
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AATAAAATAAAAACATA
Found at i:834537 original size:24 final size:23
Alignment explanation
Indices: 834510--834559 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
834500 CTCTCTCTTT
834510 TTTCTTCTTTGCTGTTTTTTGTTG
1 TTTCTTCTTTGCTGTTTTTT-TTG
*
834534 TTTCTTGTTTGCTGTTTTTTTTG
1 TTTCTTCTTTGCTGTTTTTTTTG
834557 TTT
1 TTT
834560 ATGCTTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.00, C:0.10, G:0.16, T:0.74
Consensus pattern (23 bp):
TTTCTTCTTTGCTGTTTTTTTTG
Found at i:834929 original size:29 final size:29
Alignment explanation
Indices: 834882--834982 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
834872 TTCTGGGGCA
* *
834882 AAAATGTAATGTCACGAAAATATA-GGGTT
1 AAAATGTAATTTTA-GAAAATATAGGGGTT
* * *
834911 AAAATGTAATTTATAGAAAGTTTAGGGGCT
1 AAAATGTAATTT-TAGAAAATATAGGGGTT
** *
834941 CGAATGTAA-TTTACAAAATATTAGGGGTT
1 AAAATGTAATTTTAGAAAATA-TAGGGGTT
834970 AAAATGTAATTTT
1 AAAATGTAATTTT
834983 TATTTTTTGC
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
28 6 0.11
29 34 0.62
30 15 0.27
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAATATAGGGGTT
Found at i:835401 original size:80 final size:80
Alignment explanation
Indices: 835307--835591 Score: 212
Period size: 80 Copynumber: 3.6 Consensus size: 80
835297 GATTCGAAAT
* *
835307 TCAATTCACCTCTCG-AGCCATGAGTTAATTTTTTTTTAAAAAACGA-AAATTGAAAAATACATC
1 TCAACTCACCTCTCGCA-CCATGAGTTAATTTTTTTTGAAAAAA-GAGAAATTGAAAAATACATC
*
835370 GGCATGTGACCCAAGGC
64 GACATGTGACCCAAGGC
* ** * * * *
835387 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGAAAAAATAGAAATTGGAAAATACCTCGA
1 TCAACTCACCTCTCGCACCATGAGTTAATTTTTTTTGAAAAAAGAGAAATTGAAAAATACATCGA
** *
835452 TGTGTGACCCGAGGC
66 CATGTGACCCAAGGC
* * ** * * * *
835467 ACAACTCACCTCT-GTATTATGAGTTGA--TTTTTTGAAAAAAATAGAAATTTAAAAATACCTC-
1 TCAACTCACCTCTCGCACCATGAGTTAATTTTTTTTG-AAAAAAGAGAAATTGAAAAATACATCG
*
835528 AGC--GTGACCCGAGGC
65 A-CATGTGACCCAAGGC
* * ** * *
835543 TCAACTCACATCT-GTATTATGAGTTGA-TTTTTTTGAAAAAATAGAAATT
1 TCAACTCACCTCTCGCACCATGAGTTAATTTTTTTTGAAAAAAGAGAAATT
835592 AAATTAAAAG
Statistics
Matches: 179, Mismatches: 21, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
76 51 0.28
77 15 0.08
78 24 0.13
79 14 0.08
80 74 0.41
81 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (80 bp):
TCAACTCACCTCTCGCACCATGAGTTAATTTTTTTTGAAAAAAGAGAAATTGAAAAATACATCGA
CATGTGACCCAAGGC
Found at i:835627 original size:83 final size:83
Alignment explanation
Indices: 835375--836343 Score: 1320
Period size: 83 Copynumber: 11.7 Consensus size: 83
835365 ACATCGGCAT
* * *
835375 GTGACCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGAAAAAATAG-----AA
1 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTTTGAAAAAATAGAAATTAA
** *
835435 ATT-GGA-AAATACCTCGATGT
64 ATTAAAAGAAATACCTC-A-GC
*
835455 GTGACCCGAGGCACAACTCACCTCTGTATTATGAGTTGA-TTTTTTGAAAAAAATAGAAA-T---
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTG-AAAAAATAGAAATTAAA
835515 TT--AA-AAATACCTCAGC
65 TTAAAAGAAATACCTCAGC
*
835531 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
835596 TAAAAGAAATACCTCAGC
66 TAAAAGAAATACCTCAGC
* *
835614 GTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAAAATAGAATTTAA
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTG--AAAAAATAGAAATTAA
*
835679 ATTTAAAAAAAATACCTCAGC
64 A-TTAAAAGAAATACCTCAGC
*
835700 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
835765 TAAAAGAAATACCTCAGC
66 TAAAAGAAATACCTCAGC
* *
835783 GTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAAAATAGAATTTAA
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTG--AAAAAATAGAAATTAA
*
835848 ATTTAAAAAAAATACCTCAGC
64 A-TTAAAAGAAATACCTCAGC
*
835869 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
835934 TAAAAGAAATACCTCAGC
66 TAAAAGAAATACCTCAGC
* *
835952 GTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAAAATAGAATTTAA
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTG--AAAAAATAGAAATTAA
*
836017 ATTTAAAAAAAATACCTCAGC
64 A-TTAAAAGAAATACCTCAGC
*
836038 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
836103 TAAAAGAAATACCTCAGC
66 TAAAAGAAATACCTCAGC
* *
836121 GTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAAAATAGAATTTAA
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTG--AAAAAATAGAAATTAA
*
836186 ATTTAAAAAAAATACCTCAGC
64 A-TTAAAAGAAATACCTCAGC
* * *
836207 GTGACCCGAGGCTCAACTCACCTCTCATATTATGAGTTGA----TTT-AAAAAACAGATATT---
1 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAA
*
836264 TT-AAAGAAATACCTCATC
65 TTAAAAGAAATACCTCAGC
* * * *
836282 ATGACCCAAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTTTAAAAAATATAAATT
1 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTGAAAAAATAGAAATT
836344 GAAAAATATA
Statistics
Matches: 809, Mismatches: 49, Indels: 62
0.88 0.05 0.07
Matches are distributed among these distances:
75 51 0.06
76 52 0.06
77 16 0.02
78 19 0.02
79 18 0.02
80 46 0.06
82 2 0.00
83 249 0.31
84 48 0.06
85 64 0.08
86 231 0.29
87 13 0.02
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (83 bp):
GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
TAAAAGAAATACCTCAGC
Found at i:835712 original size:169 final size:169
Alignment explanation
Indices: 835375--836343 Score: 1533
Period size: 169 Copynumber: 5.9 Consensus size: 169
835365 ACATCGGCAT
* * *
835375 GTGACCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGAAAAAATAG-----AA
1 GTGACCCGAGGCTCAACTCACATCT-GTATTATGAGTTGA-TTTTTTTGAAAAAATAGAAATTAA
** * * *
835435 ATT-GGA-AAATACCTCGATGTGTGACCCGAGGCACAACTCACCTCTGTATTATGAGTTGA-TTT
64 ATTAAAAGAAATACCTC-A-GCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTT
835497 TTTG-AAAAAAATAG-----AAATTT---AAAAATACCTCAGC
127 TTTGAAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
835531 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
1 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
835596 TAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTG
66 TAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTG
835661 AAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
131 AAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
835700 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
1 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
835765 TAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTG
66 TAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTG
835830 AAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
131 AAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
835869 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
1 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
835934 TAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTG
66 TAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTG
835999 AAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
131 AAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
836038 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
1 GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
836103 TAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTG
66 TAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTG
836168 AAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
131 AAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
* * * *
836207 GTGACCCGAGGCTCAACTCACCTCTCATATTATGAGTTGA----TTT-AAAAAACAGATATT---
1 GTGACCCGAGGCTCAACTCACATCT-GTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAA
* * * *
836264 TT-AAAGAAATACCTCATCATGACCCAAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTT
65 TTAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCT-GTATTATGAGTTGATTTTTT
* *
836328 TTAAAAAATATA-AATT
129 TGAAAAAAAATAGAATT
836344 GAAAAATATA
Statistics
Matches: 776, Mismatches: 18, Indels: 33
0.94 0.02 0.04
Matches are distributed among these distances:
154 17 0.02
155 13 0.02
156 23 0.03
159 43 0.06
160 9 0.01
161 60 0.08
162 32 0.04
165 12 0.02
166 9 0.01
169 545 0.70
170 13 0.02
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (169 bp):
GTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTTGAAAAAATAGAAATTAAAT
TAAAAGAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTGTATTATGAGTTGATTTTTTTG
AAAAAAAATAGAATTTAAATTTAAAAAAAATACCTCAGC
Found at i:837139 original size:18 final size:17
Alignment explanation
Indices: 837118--837185 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 17
837108 TTGATTTTTC
*
837118 TTTTTCTTTTCTTTGTT
1 TTTTTTTTTTCTTTGTT
*
837135 TTTTTTTATTTTTTTGTT
1 TTTTTTT-TTTCTTTGTT
*
837153 TTTATTTTTTTATTT-TT
1 TTT-TTTTTTTCTTTGTT
837170 ATTTTTTTTTGTCTTT
1 -TTTTTTTTT-TCTTT
837186 TTTAGGCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 14 0.33
18 25 0.58
19 4 0.09
ACGTcount: A:0.06, C:0.04, G:0.04, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTTCTTTGTT
Found at i:837148 original size:8 final size:8
Alignment explanation
Indices: 837135--837189 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
837125 TTTCTTTGTT
837135 TTTTTTTA
1 TTTTTTTA
837143 -TTTTTT-
1 TTTTTTTA
*
837149 TGTTTTTA
1 TTTTTTTA
837157 TTTTTTTA
1 TTTTTTTA
837165 TTTTTATT-
1 TTTTT-TTA
*
837173 TTTTTTTG
1 TTTTTTTA
837181 TCTTTTTTA
1 T-TTTTTTA
837190 GGCATAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
7 13 0.33
8 18 0.46
9 8 0.21
ACGTcount: A:0.09, C:0.02, G:0.04, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:837149 original size:22 final size:22
Alignment explanation
Indices: 837111--837178 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
837101 TTTCATCTTG
837111 ATTTTTCTT-TTTCTTTTCTTTGTT
1 ATTTTT-TTATTT-TTTTCTTT-TT
*
837135 -TTTTTTTATTTTTTTGTTTTT
1 ATTTTTTTATTTTTTTCTTTTT
*
837156 ATTTTTTTATTTTTATTTTTTTT
1 ATTTTTTTATTTTT-TTCTTTTT
837179 TGTCTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 2 0.05
22 22 0.56
23 15 0.38
ACGTcount: A:0.07, C:0.04, G:0.03, T:0.85
Consensus pattern (22 bp):
ATTTTTTTATTTTTTTCTTTTT
Found at i:837188 original size:1 final size:1
Alignment explanation
Indices: 837112--837179 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
837102 TTCATCTTGA
* * * * * * * * *
837112 TTTTTCTTTTTCTTTTCTTTGTTTTTTTTTATTTTTTTGTTTTTATTTTTTTATTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
837177 TTT
1 TTT
837180 GTCTTTTTTA
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.06, C:0.04, G:0.03, T:0.87
Consensus pattern (1 bp):
T
Found at i:837188 original size:14 final size:13
Alignment explanation
Indices: 837118--837179 Score: 79
Period size: 14 Copynumber: 4.5 Consensus size: 13
837108 TTGATTTTTC
* *
837118 TTTTTCTTTTCTT
1 TTTTTTTTTTATT
837131 TGTTTTTTTTTATT
1 T-TTTTTTTTTATT
837145 TTTTTGTTTTTATT
1 TTTTT-TTTTTATT
837159 TTTTTATTTTTATT
1 TTTTT-TTTTTATT
837173 TTTTTTT
1 TTTTTTT
837180 GTCTTTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
13 7 0.16
14 37 0.84
ACGTcount: A:0.06, C:0.03, G:0.03, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTTATT
Found at i:843715 original size:17 final size:17
Alignment explanation
Indices: 843695--843748 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
843685 GCATGAAATT
843695 TTTTTAAAACACAATAA
1 TTTTTAAAACACAATAA
* **
843712 TTTTAAAAACACAATTT
1 TTTTTAAAACACAATAA
* *
843729 TTTTTTAAATACAA-AA
1 TTTTTAAAACACAATAA
843745 TTTT
1 TTTT
843749 ATTTTGAGAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 4 0.14
17 25 0.86
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTTAAAACACAATAA
Found at i:843746 original size:19 final size:20
Alignment explanation
Indices: 843712--843753 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
843702 AACACAATAA
*
843712 TTTTAAAAACACAATTTT-T
1 TTTTAAAAACAAAATTTTAT
*
843731 TTTTAAATACAAAATTTTAT
1 TTTTAAAAACAAAATTTTAT
843751 TTT
1 TTT
843754 GAGAACACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTAAAAACAAAATTTTAT
Found at i:843822 original size:17 final size:17
Alignment explanation
Indices: 843796--844027 Score: 117
Period size: 17 Copynumber: 12.8 Consensus size: 17
843786 ACGAGGATTT
843796 TTTTTGAAACACGGAAA
1 TTTTTGAAACACGGAAA
* *
843813 TTTATGAAACACGGTCAATT
1 TTTTTGAAACACGG--AA-A
**
843833 TTTTTGAAACCACAAAAA
1 TTTTTGAAA-CACGGAAA
* * *
843851 TTTTTAAAAGACAGGAAT
1 TTTTTGAAACAC-GGAAA
843869 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGGAAA
* * *
843887 TTTATAAAACATGGAAA
1 TTTTTGAAACACGGAAA
* *
843904 TTTTTTCTAAAAACAAGGAAA
1 --TTTT-T-GAAACACGGAAA
** *
843925 -TTACGAAATAC-GAGAA
1 TTTTTGAAACACGGA-AA
843941 TTTTTGAAAACACGGGAAA
1 TTTTTG-AAACAC-GGAAA
*
843960 TTTTTTTGAAAACACGAAAA
1 --TTTTTG-AAACACGGAAA
* * *
843980 TTTTTAAAACGCGAAAA
1 TTTTTGAAACACGGAAA
*
843997 TTTTTAAAAACACGGAAA
1 TTTTT-GAAACACGGAAA
844015 TTTTTGAAACACG
1 TTTTTGAAACACG
844028 AAGTTTTTTT
Statistics
Matches: 164, Mismatches: 33, Indels: 36
0.70 0.14 0.15
Matches are distributed among these distances:
15 2 0.01
16 6 0.04
17 50 0.30
18 50 0.30
19 14 0.09
20 15 0.09
21 27 0.16
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGGAAA
Found at i:843823 original size:37 final size:36
Alignment explanation
Indices: 843777--843897 Score: 111
Period size: 37 Copynumber: 3.3 Consensus size: 36
843767 TTTTGATAAA
*
843777 TTATGAAACACGAGGATTTTTTTTGAAACACGGAAAT
1 TTATAAAACACGAGGA-TTTTTTTGAAACACGGAAAT
* * **
843814 TTATGAAACACG-GTCAATTTTTTTGAAACCACAAAAAT
1 TTATAAAACACGAG--GATTTTTTTGAAA-CACGGAAAT
* * *
843852 TTTTAAAAGAC-AGGAATTTTTTGAAAACACGGAAAT
1 TTATAAAACACGAGGATTTTTTTG-AAACACGGAAAT
843888 TTATAAAACA
1 TTATAAAACA
843898 TGGAAATTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
36 24 0.36
37 26 0.39
38 17 0.25
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (36 bp):
TTATAAAACACGAGGATTTTTTTGAAACACGGAAAT
Found at i:843909 original size:37 final size:35
Alignment explanation
Indices: 843789--843926 Score: 118
Period size: 38 Copynumber: 3.8 Consensus size: 35
843779 ATGAAACACG
* *
843789 AGGATTTTTTTTG-AAACACGGAAATTTATGAAAC
1 AGGAATTTTTTTGAAAACACGGAAATTTATAAAAC
* ** *
843823 ACGGTCAATTTTTTTGAAACCACAAAAATTTTTAAAAGAC
1 A-GG--AATTTTTTTGAAAACACGGAAATTTAT-AAA-AC
843863 AGGAA-TTTTTTGAAAACACGGAAATTTATAAAAC
1 AGGAATTTTTTTGAAAACACGGAAATTTATAAAAC
* *
843897 ATGGAAATTTTTTCTAAAAACAAGGAAATT
1 A-GG-AATTTTTT-TGAAAACACGGAAATT
843927 ACGAAATACG
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
34 4 0.05
35 7 0.09
36 22 0.27
37 16 0.20
38 26 0.32
39 4 0.05
40 3 0.04
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (35 bp):
AGGAATTTTTTTGAAAACACGGAAATTTATAAAAC
Found at i:843966 original size:21 final size:20
Alignment explanation
Indices: 843941--844044 Score: 80
Period size: 17 Copynumber: 5.5 Consensus size: 20
843931 AATACGAGAA
*
843941 TTTTTGAAAACACGGGAAATT
1 TTTTTGAAAACAC-GAAAATT
843962 TTTTTGAAAACACGAAAA--
1 TTTTTGAAAACACGAAAATT
*
843980 TTTTT-AAAACGCGAAAA--
1 TTTTTGAAAACACGAAAATT
* *
843997 TTTTTAAAAACACGGAAA--
1 TTTTTGAAAACACGAAAATT
**
844015 TTTTTG-AAACACGAAGTTT
1 TTTTTGAAAACACGAAAATT
*
844034 TTTTTTAAAAC
1 TTTTTGAAAAC
844045 GAATATAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
17 24 0.34
18 20 0.29
19 5 0.07
20 8 0.11
21 13 0.19
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:844035 original size:17 final size:17
Alignment explanation
Indices: 843934--844036 Score: 82
Period size: 18 Copynumber: 5.7 Consensus size: 17
843924 ATTACGAAAT
*
843934 ACGAGAATTTTTGAAAAC
1 ACGA-AATTTTTTAAAAC
843952 ACGGGAAATTTTTTTGAAAAC
1 AC--GAAA-TTTTTT-AAAAC
*
843973 ACGAAAATTTTTAAAAC
1 ACGAAATTTTTTAAAAC
* *
843990 GCGAAAATTTTTAAAAAC
1 ACG-AAATTTTTTAAAAC
*
844008 ACGGAAA-TTTTTGAAAC
1 AC-GAAATTTTTTAAAAC
*
844025 ACGAAGTTTTTT
1 ACGAAATTTTTT
844037 TTTAAAACGA
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
16 3 0.04
17 22 0.32
18 23 0.33
19 7 0.10
20 7 0.10
21 7 0.10
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (17 bp):
ACGAAATTTTTTAAAAC
Found at i:844036 original size:35 final size:35
Alignment explanation
Indices: 843934--844036 Score: 107
Period size: 35 Copynumber: 2.8 Consensus size: 35
843924 ATTACGAAAT
* *
843934 ACGAGAATTTTTGAAAACACGGGAAATTTTTTTGAAAAC
1 ACGAAAATTTTT-AAAACAC--GAAA-TTTTTTAAAAAC
* *
843973 ACGAAAATTTTTAAAACGCGAAAATTTTTAAAAAC
1 ACGAAAATTTTTAAAACACGAAATTTTTTAAAAAC
* * *
844008 ACGGAAATTTTTGAAACACGAAGTTTTTT
1 ACGAAAATTTTTAAAACACGAAATTTTTT
844037 TTTAAAACGA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 34 0.62
36 4 0.07
38 6 0.11
39 11 0.20
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (35 bp):
ACGAAAATTTTTAAAACACGAAATTTTTTAAAAAC
Found at i:844099 original size:17 final size:17
Alignment explanation
Indices: 844076--844122 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
844066 TTAGTATTAT
844076 TTTTTGAAACACGAGAAA
1 TTTTTGAAACACGA-AAA
*
844094 -TTTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
844111 TTTTTGAAACAC
1 TTTTTGAAACAC
844123 AATTAGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:844103 original size:18 final size:18
Alignment explanation
Indices: 844076--844119 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
844066 TTAGTATTAT
844076 TTTTTG-AAACACGAGAAA
1 TTTTTGAAAACACGA-AAA
*
844094 -TTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
844111 TTTTTGAAA
1 TTTTTGAAA
844120 CACAATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:844438 original size:5 final size:5
Alignment explanation
Indices: 844428--844454 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
844418 GATTTTAACG
844428 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
844455 ACATAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:845164 original size:24 final size:23
Alignment explanation
Indices: 845137--845186 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
845127 CTCTCTCCTT
845137 TTTCTTCTTTGCTGTTTTTTGTTG
1 TTTCTTCTTTGCTGTTTTTT-TTG
*
845161 TTTCTTGTTTGCTGTTTTTTTTG
1 TTTCTTCTTTGCTGTTTTTTTTG
845184 TTT
1 TTT
845187 ATGCTTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.00, C:0.10, G:0.16, T:0.74
Consensus pattern (23 bp):
TTTCTTCTTTGCTGTTTTTTTTG
Found at i:845247 original size:17 final size:17
Alignment explanation
Indices: 845227--845259 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
845217 CGGTGGAGCG
*
845227 ACGATGGTGGTGGCGCA
1 ACGACGGTGGTGGCGCA
845244 ACGACGGTGGTGGCGC
1 ACGACGGTGGTGGCGC
845260 GACGGTGGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (17 bp):
ACGACGGTGGTGGCGCA
Found at i:845559 original size:29 final size:29
Alignment explanation
Indices: 845527--845626 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
845517 TTCTGGGGCA
845527 AAAATGTAATTTCATGAAAATAT-GGGGTT
1 AAAATGTAATTT-ATGAAAATATAGGGGTT
* * *
845556 AAAATGTAATTTATAGAAAGTTTAGGGGCT
1 AAAATGTAATTTAT-GAAAATATAGGGGTT
** *
845586 CGAATGTAATTTA-CAAAATATTAGGGGTT
1 AAAATGTAATTTATGAAAATA-TAGGGGTT
845615 AAAATGTAATTT
1 AAAATGTAATTT
845627 TTATTTTTTG
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
28 6 0.11
29 35 0.61
30 16 0.28
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTATGAAAATATAGGGGTT
Found at i:847424 original size:13 final size:12
Alignment explanation
Indices: 847406--847452 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
847396 CTATAGATTG
847406 AATTAATTTATA
1 AATTAATTTATA
847418 CAATTAAATTT-TA
1 -AATT-AATTTATA
* *
847431 AAATATTTTATA
1 AATTAATTTATA
847443 AATTAATTTA
1 AATTAATTTA
847453 ATCTATAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 4 0.14
12 13 0.46
13 6 0.21
14 5 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTAATTTATA
Found at i:849446 original size:13 final size:13
Alignment explanation
Indices: 849428--849476 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
849418 AATGGCATAG
849428 AAATAATATAAAC
1 AAATAATATAAAC
849441 AAATAA-ATAAAC
1 AAATAATATAAAC
*
849453 GAAATTAATATACAAA
1 -AAA-TAATATA-AAC
849469 AAATAATA
1 AAATAATA
849477 ACCTATGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.19
13 9 0.29
14 8 0.26
15 6 0.19
16 2 0.06
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (13 bp):
AAATAATATAAAC
Found at i:849842 original size:24 final size:24
Alignment explanation
Indices: 849815--849869 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
849805 ATTAGAAAAA
* *
849815 ATATATAAATAT-ATACATGTACAT
1 ATATATAAAAATAAT-CATATACAT
* *
849839 ATATAAAAAAATAATTATATACAT
1 ATATATAAAAATAATCATATACAT
849863 ATATATA
1 ATATATA
849870 GATTATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATATAAAAATAATCATATACAT
Found at i:849859 original size:30 final size:33
Alignment explanation
Indices: 849819--849904 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 33
849809 GAAAAAATAT
* *
849819 ATAAATATATACATGTACAT-A-TATAAAAAA-
1 ATAATTATATACATATACATAATTATAAAAAAG
*
849849 ATAATTATATACATATATATAGATTATAAAAAAG
1 ATAATTATATACATATACATA-ATTATAAAAAAG
* * *
849883 ATAATTACATATATATATATAA
1 ATAATTATATACATATACATAA
849905 ACAAATAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 17 0.36
32 1 0.02
33 10 0.21
34 19 0.40
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (33 bp):
ATAATTATATACATATACATAATTATAAAAAAG
Found at i:849881 original size:34 final size:35
Alignment explanation
Indices: 849838--849903 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
849828 TACATGTACA
*
849838 TATATAAAAAAATAATTATATACATATATATAGAT
1 TATATAAAAAAATAATTACATACATATATATAGAT
* *
849873 TATA-AAAAAGATAATTACATATATATATATA
1 TATATAAAAAAATAATTACATACATATATATA
849904 AACAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (35 bp):
TATATAAAAAAATAATTACATACATATATATAGAT
Found at i:849919 original size:32 final size:31
Alignment explanation
Indices: 849810--849928 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 31
849800 TATTCATTAG
* *
849810 AAAAAATATATAA-ATATATACATGTACATATAT
1 AAAAAATA-ATAATA-AT-TACATATATATATAT
* *
849843 -AAAAA-AATAATTATATACATATATATAGATT
1 AAAAAATAATAATAAT-TACATATATATATA-T
* *
849874 ATAAAA-AA-GATAATTACATATATATATAT
1 AAAAAATAATAATAATTACATATATATATAT
*
849903 AAACAAATAATAATAATTACAAATAT
1 AAA-AAATAATAATAATTACATATAT
849929 TAAAATTAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
29 3 0.04
30 34 0.49
31 8 0.12
32 24 0.35
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAAAATAATAATAATTACATATATATATAT
Found at i:849926 original size:16 final size:16
Alignment explanation
Indices: 849883--849936 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
849873 TATAAAAAAG
*
849883 ATAATTACATATATATA
1 ATAATTACAAATA-ATA
849900 TATAA--ACAAATAATA
1 -ATAATTACAAATAATA
*
849915 ATAATTACAAATATTA
1 ATAATTACAAATAATA
849931 A-AATTA
1 ATAATTA
849937 ATTAATTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 4 0.12
15 8 0.25
16 16 0.50
18 4 0.12
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATTACAAATAATA
Found at i:849989 original size:3 final size:3
Alignment explanation
Indices: 849981--850013 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
849971 ATGTAGGTAC
849981 AAT AAT AAT AAT AAT ATAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
850014 GATTAATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:850008 original size:18 final size:18
Alignment explanation
Indices: 849985--850032 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
849975 AGGTACAATA
849985 ATAATAATAAT-ATATAAT
1 ATAATAATAATGAT-TAAT
850003 ATAATAATAATGATTAAT
1 ATAATAATAATGATTAAT
* *
850021 ACAATAAGAATG
1 ATAATAATAATG
850033 TAAAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (18 bp):
ATAATAATAATGATTAAT
Found at i:850027 original size:21 final size:21
Alignment explanation
Indices: 849978--850027 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
849968 TATATGTAGG
849978 TACAATAATAATAATAATATA
1 TACAATAATAATAATAATATA
*
849999 TA-ATATAATAATAATGAT-TAA
1 TACA-ATAATAATAATAATAT-A
850020 TACAATAA
1 TACAATAA
850028 GAATGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
TACAATAATAATAATAATATA
Found at i:856339 original size:22 final size:24
Alignment explanation
Indices: 856297--856340 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
856287 TAACTAAGTT
856297 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
856321 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
856341 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Done.