Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold485
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: 999764
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 8 of 8
Found at i:922548 original size:17 final size:17
Alignment explanation
Indices: 922483--922548 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 17
922473 TTTTTAAAAA
*
922483 AAAAAATTA-ATAATTT
1 AAAAAATAATATAATTT
* *
922499 TAAATATAATATAATTATAT
1 AAAAAATAATATAA-T-T-T
922519 AAAAAATAAAATATAATTT
1 AAAAAAT--AATATAATTT
922538 AAAAAATAATA
1 AAAAAATAATA
922549 CGAATATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
16 6 0.15
17 8 0.21
18 1 0.03
19 9 0.23
20 7 0.18
21 1 0.03
22 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAAATAATATAATTT
Found at i:922760 original size:18 final size:17
Alignment explanation
Indices: 922730--922763 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
922720 TATACATTTT
922730 TTTGATTAATTTTTATA
1 TTTGATTAATTTTTATA
*
922747 TTTGTATTATTTTTTAT
1 TTTG-ATTAATTTTTAT
922764 TTCATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTGATTAATTTTTATA
Found at i:926437 original size:2 final size:2
Alignment explanation
Indices: 926432--926462 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
926422 GTTTGTCCCT
926432 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
926463 GTTCGTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:928302 original size:15 final size:15
Alignment explanation
Indices: 928268--928302 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
928258 TTAACCTGTC
*
928268 AAAAACAAAGCAACA
1 AAAAACAAAGCAAAA
*
928283 AAAAACAAAGGAAAA
1 AAAAACAAAGCAAAA
928298 AAAAA
1 AAAAA
928303 AACATCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAACAAAGCAAAA
Found at i:929381 original size:17 final size:18
Alignment explanation
Indices: 929349--929387 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
929339 AAAATAAAAT
929349 TAATTAAATATATATTTA
1 TAATTAAATATATATTTA
*
929367 TAATT-AATATTTATTTA
1 TAATTAAATATATATTTA
929384 -AATT
1 TAATT
929388 TTAAATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 11 0.55
18 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTAAATATATATTTA
Found at i:929570 original size:2 final size:2
Alignment explanation
Indices: 929559--929593 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
929549 GAGAGGTAAC
929559 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
929594 GTAAATCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:929717 original size:15 final size:15
Alignment explanation
Indices: 929699--929735 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
929689 TTTGACTTGA
929699 TAAATTT-TTATAATT
1 TAAATTTATT-TAATT
929714 TAAATTTATTTAATT
1 TAAATTTATTTAATT
929729 T-AATTTA
1 TAAATTTA
929736 AATTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 13 0.62
16 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATTTATTTAATT
Found at i:929964 original size:14 final size:14
Alignment explanation
Indices: 929945--929985 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
929935 AATTTTTTTA
929945 ATTTTTTAAAAAAT
1 ATTTTTTAAAAAAT
* *
929959 ATTTTTTTAAATAT
1 ATTTTTTAAAAAAT
929973 ATTTTTTAAAAAA
1 ATTTTTTAAAAAA
929986 GTTCATTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTTTTAAAAAAT
Found at i:930095 original size:9 final size:9
Alignment explanation
Indices: 930072--930104 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
930062 TCAATTGCGT
930072 ATAAA-TTA
1 ATAAATTTA
930080 ATAAAATTTA
1 AT-AAATTTA
930090 ATAAATTTA
1 ATAAATTTA
930099 ATAAAT
1 ATAAAT
930105 AATATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 16 0.70
10 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
ATAAATTTA
Found at i:930146 original size:21 final size:20
Alignment explanation
Indices: 930122--930167 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
930112 TAATTATTAT
930122 TTTTAATAAAATAAAAATAAA
1 TTTTAATAAAATAAAAA-AAA
* **
930143 TTTTAATTAAATTTAAAAAA
1 TTTTAATAAAATAAAAAAAA
930163 TTTTA
1 TTTTA
930168 TATTAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTTAATAAAATAAAAAAAA
Found at i:930154 original size:77 final size:76
Alignment explanation
Indices: 930073--930218 Score: 190
Period size: 75 Copynumber: 1.9 Consensus size: 76
930063 CAATTGCGTA
* *
930073 TAAA-TTAATAAAATTTAATAAATTTAATAAA-TAATATATTAATTATTA-TTTTTAATAAAATA
1 TAAATTTAA-AAAATTT--TAAA-TTAATAAATTAAAATATTAATTATTATTTTTTAAAAAAATA
930135 AAAATAAATTTTAAT
62 AAAATAAATTTTAAT
* * *
930150 TAAATTTAAAAAATTTTATATTAATAAATTAAAATATTAATTATTATTTTTTAAAAAAATTAAAT
1 TAAATTTAAAAAATTTTAAATTAATAAATTAAAATATTAATTATTATTTTTTAAAAAAATAAAAA
930215 TAAA
66 TAAA
930219 AAAATAAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
74 8 0.13
75 19 0.31
76 19 0.31
77 11 0.18
78 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (76 bp):
TAAATTTAAAAAATTTTAAATTAATAAATTAAAATATTAATTATTATTTTTTAAAAAAATAAAAA
TAAATTTTAAT
Found at i:930530 original size:19 final size:19
Alignment explanation
Indices: 930478--930530 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
930468 AATTATTATT
*
930478 TTTAATAAAATAAAAAATA
1 TTTAATAAAATTAAAAATA
*
930497 TTTAATTAAATTTAAAAATA
1 TTTAA-TAAAATTAAAAATA
930517 TATTAA-AAAATTAA
1 T-TTAATAAAATTAA
930531 TTATTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 12 0.41
20 13 0.45
21 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTAATAAAATTAAAAATA
Found at i:934389 original size:13 final size:15
Alignment explanation
Indices: 934362--934393 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
934352 TTCGCCTCTT
934362 TTTCTTCTTTCTTCC
1 TTTCTTCTTTCTTCC
934377 TTTC-TCTTT-TTCC
1 TTTCTTCTTTCTTCC
934390 TTTC
1 TTTC
934394 CTCTGTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCTTCTTTCTTCC
Found at i:934397 original size:14 final size:15
Alignment explanation
Indices: 934362--934402 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
934352 TTCGCCTCTT
*
934362 TTTCTTCTTTCTTCC
1 TTTCCTCTTTCTTCC
934377 TTT-CTCTTT-TTCC
1 TTTCCTCTTTCTTCC
*
934390 TTTCCTCTGTCTT
1 TTTCCTCTTTCTT
934403 TCTCTCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.32
14 10 0.45
15 5 0.23
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTCCTCTTTCTTCC
Found at i:934554 original size:11 final size:12
Alignment explanation
Indices: 934520--934562 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
934510 GAATTTTTAG
934520 ATTTTTTTTTGA
1 ATTTTTTTTTGA
*
934532 ATTTTAGGTTTTTTA
1 ATTTT---TTTTTGA
934547 ATTTTTTTTTGA
1 ATTTTTTTTTGA
934559 ATTT
1 ATTT
934563 CATAGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 15 0.58
15 11 0.42
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:934573 original size:28 final size:28
Alignment explanation
Indices: 934507--934562 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
934497 TTATATATAC
*
934507 TTAGAATTTTTAGATTTTTTTTTGAATT
1 TTAGGATTTTTAGATTTTTTTTTGAATT
*
934535 TTAGGTTTTTTA-ATTTTTTTTTGAATT
1 TTAGGATTTTTAGATTTTTTTTTGAATT
934562 T
1 T
934563 CATAGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (28 bp):
TTAGGATTTTTAGATTTTTTTTTGAATT
Found at i:934582 original size:21 final size:23
Alignment explanation
Indices: 934560--934607 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
934550 TTTTTTTGAA
934560 TTTCATAGATTTTTT-TAAAAAT
1 TTTCATAGATTTTTTATAAAAAT
** *
934582 TTTTTTAGATTTTTTATAAAATT
1 TTTCATAGATTTTTTATAAAAAT
934605 TTT
1 TTT
934608 GAAATTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTCATAGATTTTTTATAAAAAT
Found at i:934590 original size:22 final size:22
Alignment explanation
Indices: 934565--934607 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
934555 TTGAATTTCA
934565 TAGATTTTTT-TAAAAATTTTTT
1 TAGATTTTTTAT-AAAATTTTTT
934587 TAGATTTTTTATAAAATTTTT
1 TAGATTTTTTATAAAATTTTT
934608 GAAATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (22 bp):
TAGATTTTTTATAAAATTTTTT
Found at i:934632 original size:18 final size:18
Alignment explanation
Indices: 934594--934628 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
934584 TTTTAGATTT
*
934594 TTTATAAAATTTTTGAAA
1 TTTATAAAATTTTTAAAA
934612 TTTAT-AAATTTTTAAAA
1 TTTATAAAATTTTTAAAA
934629 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTATAAAATTTTTAAAA
Found at i:935118 original size:2 final size:2
Alignment explanation
Indices: 935111--935138 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
935101 GTTTCGATAG
935111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
935139 TTGTGAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:946435 original size:33 final size:34
Alignment explanation
Indices: 946312--946436 Score: 116
Period size: 33 Copynumber: 3.6 Consensus size: 34
946302 GACTTATTTT
* *
946312 TAATTGTTAAATTATTTATATTTTTTAATATAAATA
1 TAATT-TTTAATTATTT-TATTATTTAATATAAATA
* *
946348 T-ATTTTTAATAATATTTTATTATTTAAAATGAATA
1 TAATTTTTAAT--TATTTTATTATTTAATATAAATA
*
946383 TAA--TTT-ACTATTTGCTATTATTTAATATAAATA
1 TAATTTTTAATTATTT--TATTATTTAATATAAATA
946416 TAATTTTTAATTA-TTTATTAT
1 TAATTTTTAATTATTTTATTAT
946437 ATATATTTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
31 5 0.07
33 26 0.36
34 8 0.11
35 24 0.33
36 10 0.14
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (34 bp):
TAATTTTTAATTATTTTATTATTTAATATAAATA
Found at i:948129 original size:21 final size:20
Alignment explanation
Indices: 948089--948127 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
948079 TTACAAAGTT
*
948089 TATTTTTACATTAATATTTA
1 TATTTTTAAATTAATATTTA
948109 TATTTTTATAATTAA-ATTT
1 TATTTTTA-AATTAATATTT
948128 TAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTAAATTAATATTTA
Found at i:951156 original size:33 final size:33
Alignment explanation
Indices: 951119--951185 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
951109 TTCAACGATT
951119 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
951152 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
951185 T
1 T
951186 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:951157 original size:13 final size:13
Alignment explanation
Indices: 951139--951163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
951129 CATAAAATGT
951139 TGTATCGATACAA
1 TGTATCGATACAA
951152 TGTATCGATACA
1 TGTATCGATACA
951164 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:951244 original size:13 final size:13
Alignment explanation
Indices: 951226--951250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
951216 ATTACTCAAA
951226 TGTATCGATACAT
1 TGTATCGATACAT
951239 TGTATCGATACA
1 TGTATCGATACA
951251 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:951352 original size:52 final size:52
Alignment explanation
Indices: 951259--951386 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
951249 CACTGATCTT
*
951259 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATA-CATTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACCATATT-AAA
*
951310 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACCCTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACCATATTAAA
951362 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
951387 TCATATTTCG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 19 0.26
52 50 0.68
53 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACCATATTAAA
Found at i:955399 original size:19 final size:18
Alignment explanation
Indices: 955352--955437 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 18
955342 ATTTCAACAA
*
955352 TTTGTATCGATACAAACAG
1 TTTGTATCGATACATA-AG
*
955371 TAACTGTATCGATACATAAG
1 T--TTGTATCGATACATAAG
955391 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
955407 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
955423 TATTGTATTGATACA
1 T-TTGTATCGATACA
955438 ATGTATCGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 23 0.43
20 3 0.06
21 13 0.24
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:955412 original size:13 final size:13
Alignment explanation
Indices: 955394--955418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
955384 ACATAAGTGT
955394 TGTATCGATACAA
1 TGTATCGATACAA
955407 TGTATCGATACA
1 TGTATCGATACA
955419 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:955416 original size:32 final size:32
Alignment explanation
Indices: 955375--955450 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
955365 AAACAGTAAC
*
955375 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
955407 TGTATCGATACATAAGTATTGTATTGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
955439 TGTATCGCTACA
1 TGTATCGATACA
955451 AAGCTACTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:955507 original size:13 final size:13
Alignment explanation
Indices: 955489--955516 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
955479 CATTACTCAA
955489 TGTATCGATACAT
1 TGTATCGATACAT
955502 TGTATCGATACAT
1 TGTATCGATACAT
955515 TG
1 TG
955517 ATCTTTGTAT
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:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:955512 original size:33 final size:33
Alignment explanation
Indices: 955469--955534 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
955459 GCCAAGGAAA
955469 TGTATAGATACATT-ACTCAATGTATCGATACAT
1 TGTATAGATACATTGA-TCAATGTATCGATACAT
* **
955502 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATAGATACATTGATCAATGTATCGATACAT
955535 CTGGGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATAGATACATTGATCAATGTATCGATACAT
Found at i:960323 original size:52 final size:52
Alignment explanation
Indices: 960249--960349 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
960239 AAAAGTCACA
* *
960249 TTTTTACTCAGATGTATCGATACATTTTTCAATATATCGATACATTCTATTT
1 TTTTTACCCAGATGTATCGATACATTCTTCAATATATCGATACATTCTATTT
* *
960301 TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCGATATATTCTA
1 TTTTTACCCAGATGTATCGATACATTCTTCAATATATCGATACATTCTA
960350 CCTAGATGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.46
Consensus pattern (52 bp):
TTTTTACCCAGATGTATCGATACATTCTTCAATATATCGATACATTCTATTT
Found at i:960337 original size:20 final size:20
Alignment explanation
Indices: 960312--960388 Score: 100
Period size: 20 Copynumber: 3.7 Consensus size: 20
960302 TTTTACCCAG
960312 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* *
960332 ATGTATCGATATATTCTACCTA
1 ATGTATCGATACATTCT-TC-A
*
960354 GATGTATCGATACATTGTTCA
1 -ATGTATCGATACATTCTTCA
960375 ATGTATCGATACAT
1 ATGTATCGATACAT
960389 CTTGTTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
20 30 0.61
21 2 0.04
22 2 0.04
23 15 0.31
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:965639 original size:16 final size:17
Alignment explanation
Indices: 965602--965640 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
965592 TCATTAAACC
965602 AATGAATCTTTTCATCTA
1 AATGAATCTTTTCA-CTA
*
965620 AATGCATCTTTTCA-TA
1 AATGAATCTTTTCACTA
965636 AATGA
1 AATGA
965641 TGATAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (17 bp):
AATGAATCTTTTCACTA
Found at i:966028 original size:16 final size:15
Alignment explanation
Indices: 965989--966032 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
965979 TTAACATTTA
965989 TATATTATT-ATAAT
1 TATATTATTAATAAT
* *
966003 TTTTTTATTAATAAT
1 TATATTATTAATAAT
966018 CTATATTATTAATAA
1 -TATATTATTAATAA
966033 AGTCTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 7 0.29
15 5 0.21
16 12 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTATTAATAAT
Found at i:967953 original size:14 final size:14
Alignment explanation
Indices: 967876--967979 Score: 52
Period size: 14 Copynumber: 7.3 Consensus size: 14
967866 TTGCTGTCTA
*
967876 AAAGTACCTATGTA
1 AAAGTACCTATGTC
*
967890 AAAATA-C-ATGTGC
1 AAAGTACCTATGT-C
* *
967903 AGAAGGTATCTATGTT
1 A-AA-GTACCTATGTC
** *
967919 AAAGTATTTATATC
1 AAAGTACCTATGTC
967933 GAAAGTACCTATGTC
1 -AAAGTACCTATGTC
* * *
967948 AAAGTACTTGTGTTG
1 AAAGTACCTATG-TC
967963 AAA-TACCTATGTC
1 AAAGTACCTATGTC
967976 AAAG
1 AAAG
967980 GTACTTGTGC
Statistics
Matches: 66, Mismatches: 16, Indels: 16
0.67 0.16 0.16
Matches are distributed among these distances:
12 4 0.06
13 6 0.09
14 31 0.47
15 19 0.29
16 2 0.03
17 4 0.06
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (14 bp):
AAAGTACCTATGTC
Found at i:967975 original size:28 final size:30
Alignment explanation
Indices: 967933--967988 Score: 98
Period size: 28 Copynumber: 1.9 Consensus size: 30
967923 TATTTATATC
967933 GAAAGTACCTATGTCAAA-GTACTTGTGTT
1 GAAAGTACCTATGTCAAAGGTACTTGTGTT
967962 GAAA-TACCTATGTCAAAGGTACTTGTG
1 GAAAGTACCTATGTCAAAGGTACTTGTG
967989 CTATAATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (30 bp):
GAAAGTACCTATGTCAAAGGTACTTGTGTT
Found at i:967986 original size:29 final size:29
Alignment explanation
Indices: 967876--967988 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 29
967866 TTGCTGTCTA
* * * **
967876 AAAGTACCTATGTAAAAATACATGTGCAG
1 AAAGTACCTATGTCAAAGTACTTGTGTTG
* * * * * * *
967905 AAGGTATCTATGTTAAAGTATTTATATCG
1 AAAGTACCTATGTCAAAGTACTTGTGTTG
967934 AAAGTACCTATGTCAAAGTACTTGTGTTG
1 AAAGTACCTATGTCAAAGTACTTGTGTTG
967963 AAA-TACCTATGTCAAAGGTACTTGTG
1 AAAGTACCTATGTCAAA-GTACTTGTG
967989 CTATAATACT
Statistics
Matches: 66, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
28 13 0.20
29 53 0.80
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (29 bp):
AAAGTACCTATGTCAAAGTACTTGTGTTG
Found at i:968484 original size:2 final size:2
Alignment explanation
Indices: 968475--968507 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
968465 ATGAATTTTA
968475 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
968508 TTGAGTGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:969282 original size:20 final size:19
Alignment explanation
Indices: 969257--969318 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
969247 GTATGAGGAT
969257 TATTTTTTATATTATAATTA
1 TATTTTTTATATT-TAATTA
* *
969277 TATTTTATATATTTTA-TA
1 TATTTTTTATATTTAATTA
*
969295 TAAATTTTTATAATTTAATTA
1 T-ATTTTTTAT-ATTTAATTA
969316 TAT
1 TAT
969319 ATGTTATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 3 0.09
19 9 0.27
20 18 0.55
21 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTTTATATTTAATTA
Found at i:969320 original size:34 final size:32
Alignment explanation
Indices: 969268--969333 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
969258 ATTTTTTATA
*
969268 TTATAATTATATTTTATATATTTTATATAAATTT
1 TTATAATTATA--TTATATATGTTATATAAATTT
969302 TTATAATT-TAATTATATATGTTATATAAATTT
1 TTATAATTAT-ATTATATATGTTATATAAATTT
969334 AAGTAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 20 0.67
33 1 0.03
34 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
TTATAATTATATTATATATGTTATATAAATTT
Found at i:969341 original size:32 final size:32
Alignment explanation
Indices: 969281--969343 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
969271 TAATTATATT
* *
969281 TTATATATTTTATATAAATTTTTATAATTTAA
1 TTATATATGTTATATAAATTTTAATAATTTAA
969313 TTATATATGTTATATAAA-TTTAAGTAATTTA
1 TTATATATGTTATATAAATTTTAA-TAATTTA
969344 TATATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (32 bp):
TTATATATGTTATATAAATTTTAATAATTTAA
Found at i:969342 original size:41 final size:38
Alignment explanation
Indices: 969260--969360 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 38
969250 TGAGGATTAT
*
969260 TTTTTATATTATAATTATATTTTATATATTTTATATAAA
1 TTTTTATATT-TAATTATATTTTATATAATTTATATAAA
969299 TTTTTATAATTTAATTATATATGTTATATAAATTTA-AGT-AA
1 TTTTTAT-ATTTAATTATAT-T-TTATAT-AATTTATA-TAAA
*
969340 TTTATATATTTATATTATATT
1 TTTTTATATTTA-ATTATATT
969361 AATATTATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
39 16 0.30
40 10 0.19
41 22 0.41
42 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (38 bp):
TTTTTATATTTAATTATATTTTATATAATTTATATAAA
Found at i:969358 original size:32 final size:32
Alignment explanation
Indices: 969281--969359 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
969271 TAATTATATT
* *
969281 TTATATATTTTATATAAATTTTTATAATTTAA
1 TTATATATATTATATAAATTTTAATAATTTAA
*
969313 TTATATATGTTATATAAA-TTTAAGTAATTT-A
1 TTATATATATTATATAAATTTTAA-TAATTTAA
*
969344 TATATTTATATTATAT
1 T-TATATATATTATAT
969360 TAATATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.15
32 35 0.85
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (32 bp):
TTATATATATTATATAAATTTTAATAATTTAA
Found at i:969392 original size:21 final size:23
Alignment explanation
Indices: 969348--969396 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
969338 AATTTATATA
*
969348 TTTATATTATATTAATATTATTT
1 TTTATATTATATTAATACTATTT
* *
969371 TTTATATTAT-TTTATACTTTTT
1 TTTATATTATATTAATACTATTT
969393 TTTA
1 TTTA
969397 CAAAAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATATTATATTAATACTATTT
Found at i:969551 original size:24 final size:25
Alignment explanation
Indices: 969524--969570 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
969514 TTATAAATAT
* *
969524 TAAAATTTAAA-TATTTTTTAAAAA
1 TAAAAATTAAATTATATTTTAAAAA
969548 TAAAAATTAAATTATATTTTAAA
1 TAAAAATTAAATTATATTTTAAA
969571 TTTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAAAAATTAAATTATATTTTAAAAA
Found at i:969575 original size:13 final size:12
Alignment explanation
Indices: 969554--969591 Score: 53
Period size: 10 Copynumber: 3.2 Consensus size: 12
969544 AAAATAAAAA
969554 TTAAATTATATT
1 TTAAATTATATT
969566 TTAAATTTATATT
1 TTAAA-TTATATT
969579 TT--ATTATATT
1 TTAAATTATATT
969589 TTA
1 TTA
969592 TATCACATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
12 5 0.21
13 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTAAATTATATT
Found at i:970734 original size:29 final size:29
Alignment explanation
Indices: 970702--970765 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
970692 ATTTATATTT
*
970702 ATATTCAAATATAAAA-TTTAAAATTATCA
1 ATATT-AAATATAAAAGTTTAAAATTATAA
* *
970731 ATATTTAATGTAAAAGTTTTAAAATTATAA
1 ATATTAAATATAAAAG-TTTAAAATTATAA
970761 ATATT
1 ATATT
970766 TTAAAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 8 0.27
29 5 0.17
30 17 0.57
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (29 bp):
ATATTAAATATAAAAGTTTAAAATTATAA
Found at i:970771 original size:26 final size:29
Alignment explanation
Indices: 970717--970785 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 29
970707 CAAATATAAA
* *
970717 ATTTAAAATTATCAATATTTAATGTAAAAG
1 ATTTAAAATTATAAATATTT-ATGTAAAAC
*
970747 TTTTAAAATTATAAATA-TT-T-TAAAAC
1 ATTTAAAATTATAAATATTTATGTAAAAC
970773 ATTTAAAATTATA
1 ATTTAAAATTATA
970786 CTCAAACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 17 0.49
27 1 0.03
29 2 0.06
30 15 0.43
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (29 bp):
ATTTAAAATTATAAATATTTATGTAAAAC
Found at i:970827 original size:25 final size:26
Alignment explanation
Indices: 970799--970856 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
970789 AAACAATGCA
970799 AATTTAAAATTA-TCCAAACTT-AAAT
1 AATTTAAAATTAGT-CAAACTTAAAAT
* *
970824 AATTT-AAATTAGTTAAATTTAAAAT
1 AATTTAAAATTAGTCAAACTTAAAAT
970849 AATTTAAA
1 AATTTAAA
970857 TTCAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 11 0.39
25 15 0.54
26 2 0.07
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (26 bp):
AATTTAAAATTAGTCAAACTTAAAAT
Found at i:972276 original size:33 final size:36
Alignment explanation
Indices: 972225--972298 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 36
972215 ATTTTTATAT
*
972225 TTTTTATTTTCTTTAAAATTTTTAAAATT-TATTTA
1 TTTTTATTTTCTTAAAAATTTTTAAAATTATATTTA
*
972260 TTTTTA-TTT-TTAAAAATTTTTAAAATTATTTTTA
1 TTTTTATTTTCTTAAAAATTTTTAAAATTATATTTA
972294 TTTTT
1 TTTTT
972299 TAATTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 17 0.47
34 13 0.36
35 6 0.17
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTTTATTTTCTTAAAAATTTTTAAAATTATATTTA
Found at i:972715 original size:32 final size:32
Alignment explanation
Indices: 972679--972830 Score: 85
Period size: 32 Copynumber: 5.0 Consensus size: 32
972669 AGTATATATA
*
972679 TTTTATTTTTAATT-AATATTAAA-AATTATAAT
1 TTTTATTTATAATTAAATA-TAAATAATTA-AAT
*
972711 TTTTATTTATATTTAAATATAAATAATTAAA-
1 TTTTATTTATAATTAAATATAAATAATTAAAT
* *
972742 -TTTA---A-AATCAAATATAAAAAAATT--AT
1 TTTTATTTATAATTAAATAT-AAATAATTAAAT
* * * *
972768 TTTTATTAAATAAATAAATTTAAATAATTTAAT
1 TTTTATT-TATAATTAAATATAAATAATTAAAT
* *
972801 TTTTATTT-TAAATCAAATTTAAAT-ATTAAA
1 TTTTATTTAT-AATTAAATATAAATAATTAAA
972831 AATAAAACTC
Statistics
Matches: 94, Mismatches: 13, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
25 1 0.01
26 8 0.09
27 12 0.13
30 4 0.04
31 14 0.15
32 37 0.39
33 18 0.19
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
TTTTATTTATAATTAAATATAAATAATTAAAT
Found at i:972895 original size:22 final size:23
Alignment explanation
Indices: 972868--972910 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
972858 ATTTTTAAAA
*
972868 TTTAAA-TCAAATTTAACTTTTT
1 TTTAAATTAAAATTTAACTTTTT
*
972890 TTTAAATTAAAATTTGACTTT
1 TTTAAATTAAAATTTAACTTT
972911 ACTTACAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTAAATTAAAATTTAACTTTTT
Found at i:974625 original size:71 final size:74
Alignment explanation
Indices: 974448--974644 Score: 230
Period size: 71 Copynumber: 2.7 Consensus size: 74
974438 TTTAAGTTTT
*
974448 ATAATTAAATTAAAAAATAAATCTTAAATTTTTACAAATAAAAATAAATTATACCATTAAAAATT
1 ATAATCAAA-TAAAAAATAAAT-TTAAATTTTTACAAATAAAAATAAATTATACCA-TAAAAATT
974513 TAAACTCGTATC
63 TAAACTCGTATC
* * *
974525 AT-ATC---TAAAAATATATATTTAAATTTTTACAAATCAATATAAATTATATCC-TAAAAATTT
1 ATAATCAAATAAAAA-ATAAATTTAAATTTTTACAAATAAAAATAAATTATA-CCATAAAAATTT
*
974585 -AA-TCTTA-C
64 AAACTCGTATC
* *
974593 ATAATCAAATAAAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATAC
1 ATAATCAAATAAAAAATAAATTTAAATTTTTACAAATAAAAATAAATTATAC
974645 ATCTAATCAA
Statistics
Matches: 104, Mismatches: 10, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
68 3 0.03
69 7 0.07
70 3 0.03
71 40 0.38
72 40 0.38
73 7 0.07
76 2 0.02
77 2 0.02
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.36
Consensus pattern (74 bp):
ATAATCAAATAAAAAATAAATTTAAATTTTTACAAATAAAAATAAATTATACCATAAAAATTTAA
ACTCGTATC
Found at i:974832 original size:15 final size:16
Alignment explanation
Indices: 974807--974836 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
974797 TGATAATTTT
974807 TTTTAAAATATTAAAA
1 TTTTAAAATATTAAAA
974823 TTTT-AAATATTAAA
1 TTTTAAAATATTAAA
974837 GAGCTCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTAAAATATTAAAA
Found at i:975148 original size:76 final size:73
Alignment explanation
Indices: 975017--975161 Score: 168
Period size: 76 Copynumber: 1.9 Consensus size: 73
975007 AATTTAAAAT
* * * *
975017 TTTTTATTTTTTAAAAATATAATAATTAATATTTTAATTTATTAATTTAATTTTTTTAAAATTTG
1 TTTTTATTTTTTAAAAATATAATAATTAATATCTTAATTTAATAA--TAAATTTTTT-AAATTTA
975082 ATTAAATATCA
63 ATTAAATATCA
*
975093 TTTTTATTTTATTAAATAATAATAATAATTAATA-CTTGATTTCAATAA-AAATTTTTTAAATTT
1 TTTTTATTTT-TTAAA-AAT-ATAATAATTAATATCTTAATTT-AATAATAAATTTTTTAAATTT
975156 AATTAA
62 AATTAA
975162 TTTATTTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
75 11 0.18
76 18 0.30
77 5 0.08
78 9 0.15
79 17 0.28
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (73 bp):
TTTTTATTTTTTAAAAATATAATAATTAATATCTTAATTTAATAATAAATTTTTTAAATTTAATT
AAATATCA
Found at i:975298 original size:14 final size:13
Alignment explanation
Indices: 975271--975317 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
975261 AATTAATACA
*
975271 TAAAAAATTATTT
1 TAAAAAATTTTTT
975284 TAAAAAATATTTTT
1 TAAAAAAT-TTTTT
975298 T-AAAAATTTTATT
1 TAAAAAATTTT-TT
975311 TAAAAAA
1 TAAAAAA
975318 ATTTATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 3 0.10
13 17 0.57
14 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAAAATTTTTT
Found at i:975322 original size:14 final size:14
Alignment explanation
Indices: 975272--975323 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
975262 ATTAATACAT
975272 AAAAAA-TTATTTTA
1 AAAAAATTTA-TTTA
975286 AAAAATATTT-TTT-
1 AAAAA-ATTTATTTA
*
975299 AAAAATTTTATTTA
1 AAAAAATTTATTTA
975313 AAAAAATTTAT
1 AAAAAATTTAT
975324 ATAATTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 3 0.09
13 8 0.25
14 18 0.56
15 1 0.03
16 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AAAAAATTTATTTA
Found at i:975379 original size:2 final size:2
Alignment explanation
Indices: 975372--975408 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
975362 ATAATATTAC
975372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
975409 AGTAGAAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:975546 original size:12 final size:13
Alignment explanation
Indices: 975528--975561 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
975518 GAAAGAATGG
975528 GAGAAAAAAAAGA
1 GAGAAAAAAAAGA
975541 GA-AAAAAAAAGA
1 GAGAAAAAAAAGA
975553 GAGAAAAAA
1 GAGAAAAAA
975562 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
GAGAAAAAAAAGA
Found at i:975550 original size:14 final size:14
Alignment explanation
Indices: 975531--975567 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
975521 AGAATGGGAG
975531 AAAAAAAAGAGAAA
1 AAAAAAAAGAGAAA
*
975545 AAAAAAGAGAGAAA
1 AAAAAAAAGAGAAA
975559 AAATAAAAA
1 AAA-AAAAA
975568 ATTATGCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAAAAAGAGAAA
Found at i:976338 original size:15 final size:15
Alignment explanation
Indices: 976320--976377 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
976310 TTTTCATAAT
976320 TAAAATTTAAAAAAA
1 TAAAATTTAAAAAAA
976335 TAAAAATTTAAATAATAA
1 T-AAAATTTAAA-AA-AA
* * *
976353 TTATAACTTAATAAAA
1 -TAAAATTTAAAAAAA
976369 TAAAATTTA
1 TAAAATTTA
976378 TAATTAATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 8 0.24
16 12 0.35
17 4 0.12
18 9 0.26
19 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATTTAAAAAAA
Found at i:976378 original size:22 final size:21
Alignment explanation
Indices: 976344--976385 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
976334 ATAAAAATTT
976344 AAATAATAATTATAACTTAATA
1 AAATAATAATTATAA-TTAATA
976366 AAATAA-AATTTATAATTAAT
1 AAATAATAA-TTATAATTAAT
976386 TCTTATACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAATAATTATAATTAATA
Found at i:976396 original size:34 final size:34
Alignment explanation
Indices: 976315--976414 Score: 96
Period size: 34 Copynumber: 2.9 Consensus size: 34
976305 TTTAATTTTC
* * *
976315 ATAATTAAAATTTAAAAAAATAAAAATTTA-AATA
1 ATAATTATAACTTAATAAAAT-AAAATTTATAATA
976349 ATAATTATAACTTAATAAAATAAAATTTATAATTA
1 ATAATTATAACTTAATAAAATAAAATTTATAA-TA
** * * *
976384 ATTCTTAT-ACTTAATTAATTAAAACTTATAA
1 ATAATTATAACTTAATAAAATAAAATTTATAA
976415 AAAATTTTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
33 8 0.14
34 40 0.71
35 8 0.14
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (34 bp):
ATAATTATAACTTAATAAAATAAAATTTATAATA
Found at i:976577 original size:15 final size:15
Alignment explanation
Indices: 976557--976609 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
976547 AATAATTAAA
976557 TTAAATAAAATATAT
1 TTAAATAAAATATAT
*
976572 TTAAATATGAATA-AT
1 TTAAATA-AAATATAT
*
976587 TTATATAAAAT-TAT
1 TTAAATAAAATATAT
*
976601 ATAAATAAA
1 TTAAATAAA
976610 TATCGATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.39
15 15 0.48
16 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
TTAAATAAAATATAT
Found at i:976890 original size:34 final size:34
Alignment explanation
Indices: 976852--976921 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
976842 ACCAATGCGA
*
976852 TTATGCACTTATTTCTCGCACATTCCATATAAAG
1 TTATGCACTAATTTCTCGCACATTCCATATAAAG
* * *
976886 TTATGCACTAATTTCTCTCACATTGCATGTAAAG
1 TTATGCACTAATTTCTCGCACATTCCATATAAAG
976920 TT
1 TT
976922 GTACTTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (34 bp):
TTATGCACTAATTTCTCGCACATTCCATATAAAG
Found at i:977032 original size:3 final size:3
Alignment explanation
Indices: 977024--977054 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
977014 TGCTACAGTG
*
977024 ACA ACA ACA ACA ACA ACA ACA ACA GCA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
977055 TTGATGTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.32, G:0.03, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:977958 original size:18 final size:18
Alignment explanation
Indices: 977915--977961 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
977905 AATTATCTGT
977915 TATTTAAAT-TCAGATAAA
1 TATTTAAATAT-AGATAAA
*
977933 TA-TTAAATATAGATACA
1 TATTTAAATATAGATAAA
977950 TATTTAAATATA
1 TATTTAAATATA
977962 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
TATTTAAATATAGATAAA
Found at i:977981 original size:16 final size:17
Alignment explanation
Indices: 977952--977983 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
977942 TAGATACATA
977952 TTTAAATATATTTTATT
1 TTTAAATATATTTTATT
977969 TTTAAAT-TATTTTAT
1 TTTAAATATATTTTAT
977984 ATATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAAATATATTTTATT
Found at i:977990 original size:17 final size:17
Alignment explanation
Indices: 977949--977991 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
977939 ATATAGATAC
977949 ATATTTAAATATATTTT
1 ATATTTAAATATATTTT
*
977966 ATTTTTAAAT-TATTTT
1 ATATTTAAATATATTTT
977982 ATATATTAAA
1 ATAT-TTAAA
977992 AAAATCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTAAATATATTTT
Found at i:982706 original size:16 final size:16
Alignment explanation
Indices: 982685--982724 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
982675 CATAAAGATC
982685 TTATAATTGTAACTCA
1 TTATAATTGTAACTCA
*
982701 TTATAATTGTAACTTA
1 TTATAATTGTAACTCA
982717 TTATAATT
1 TTATAATT
982725 CCATTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (16 bp):
TTATAATTGTAACTCA
Found at i:982835 original size:50 final size:50
Alignment explanation
Indices: 982760--982996 Score: 359
Period size: 50 Copynumber: 4.8 Consensus size: 50
982750 TGTGAAAAGT
* *
982760 ACCTTTGACAATAGAGAGAGGTGGTCACAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* * *
982810 ACCTTTGATAATAGAGAGAGGTGGTCGTAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
982860 ACCTTTGACAATAGAGGGAGGTGACCATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
982910 ACATTTGACAATAGAG-GGGGTGGCCATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* * *
982959 ACCTTTGACAATAGAGAAATGTGACCATAATTGTTGAC
1 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
982997 TCTAAGTATA
Statistics
Matches: 170, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
49 46 0.27
50 124 0.73
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (50 bp):
ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
Found at i:982983 original size:99 final size:100
Alignment explanation
Indices: 982760--982996 Score: 368
Period size: 99 Copynumber: 2.4 Consensus size: 100
982750 TGTGAAAAGT
** * * *
982760 ACCTTTGACAATAGAGAGAGGTGGTCACAATTGTTGACGATTCTTCACCAACCTTTGATAATAGA
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAACATTTGACAATAGA
* *
982825 GAGAGGTGGTCGTAATTGTTGACGATTCTTCACCA
66 GAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
*
982860 ACCTTTGACAATAGAGGGAGGTGACCATAATTGTTGACGATTCTTCACCAACATTTGACAATAGA
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAACATTTGACAATAGA
*
982925 G-GGGGTGGCCATAATTGTTGACGATTCTTCACCA
66 GAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
982959 ACCTTTGACAATAGAGAAATGTGACCATAATTGTTGAC
1 ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGAC
982997 TCTAAGTATA
Statistics
Matches: 125, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
99 65 0.52
100 60 0.48
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (100 bp):
ACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAACATTTGACAATAGA
GAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
Found at i:983290 original size:19 final size:19
Alignment explanation
Indices: 983248--983291 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
983238 CTTGTCGAGG
**
983248 TACTGTTCATGTATACAGA
1 TACTGTTCATACATACAGA
* *
983267 CACTGTTCATACATACAGT
1 TACTGTTCATACATACAGA
983286 TACTGT
1 TACTGT
983292 ACACGTGAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (19 bp):
TACTGTTCATACATACAGA
Found at i:986029 original size:51 final size:50
Alignment explanation
Indices: 985867--986037 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 50
985857 GAAATAACGA
* * *
985867 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCG
* * * * *
985918 GAGTTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 G-GTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATC-G
* * * *
985972 GGTTGGAGTATCCCCGATTTTGAAAAATCGATATTTTGAAAATAAAGTCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATC-G
986023 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
986038 TCAGAAATAA
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
51 38 0.39
52 17 0.17
53 31 0.32
54 12 0.12
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCG
Found at i:986083 original size:27 final size:28
Alignment explanation
Indices: 986022--986095 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
986012 AATAAAGTCA
*
986022 GGGTTGGAGTATCCCCTCA-GAAATAACG
1 GGGTTGGAGTATCCCC-GATGAAATAACG
*
986050 GGGTTGGAGTATCCCCGATG-ATTAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
*
986077 GGGTTGGAGTGTCCCCGAT
1 GGGTTGGAGTATCCCCGAT
986096 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACG
Found at i:988587 original size:13 final size:13
Alignment explanation
Indices: 988569--988594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
988559 ACAAAGATCC
988569 ATGTATCGATACA
1 ATGTATCGATACA
988582 ATGTATCGATACA
1 ATGTATCGATACA
988595 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:988590 original size:33 final size:33
Alignment explanation
Indices: 988548--988614 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
988538 AAAATTTCCA
***
988548 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
988581 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
988614 A
1 A
988615 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:988658 original size:19 final size:18
Alignment explanation
Indices: 988634--988701 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
988624 CAGTAGCTAA
988634 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
988653 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
988668 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
988685 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
988702 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:988674 original size:13 final size:13
Alignment explanation
Indices: 988656--988680 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
988646 ACAATACTTA
988656 TGTATCGATACAT
1 TGTATCGATACAT
988669 TGTATCGATACA
1 TGTATCGATACA
988681 AAACTTATGT
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:988678 original size:32 final size:32
Alignment explanation
Indices: 988637--988699 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
988627 TAGCTAATTA
*
988637 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
988669 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
988700 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:988781 original size:21 final size:21
Alignment explanation
Indices: 988757--988813 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
988747 CATTTGTAGG
988757 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
988778 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
988799 ATGTATCGATACATT
1 ATGTATCGATACATT
988814 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:988841 original size:12 final size:12
Alignment explanation
Indices: 988824--988856 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
988814 TAAATTTTTT
988824 TTTTTTTTTCAA
1 TTTTTTTTTCAA
988836 TTTTTTTTTCAA
1 TTTTTTTTTCAA
988848 TTTTTTTTT
1 TTTTTTTTT
988857 TTTCAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:988841 original size:15 final size:15
Alignment explanation
Indices: 988821--988862 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 15
988811 ATTTAAATTT
988821 TTTTTTTTTTTTCAA
1 TTTTTTTTTTTTCAA
988836 ---TTTTTTTTTCAA
1 TTTTTTTTTTTTCAA
988848 TTTTTTTTTTTTCAA
1 TTTTTTTTTTTTCAA
988863 ACACTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.50
15 12 0.50
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTTTTTTCAA
Found at i:989539 original size:55 final size:54
Alignment explanation
Indices: 989455--990027 Score: 837
Period size: 55 Copynumber: 10.4 Consensus size: 54
989445 ATAAATTGTA
* * * * *
989455 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
989510 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
989565 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
989620 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
989675 TCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
989730 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
989785 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
989840 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
989895 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
989950 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
990005 TCCTGCTCTTTGAGGACTGAAAG
1 TCCTGCTCTTTGAGGACTGAAAG
990028 GCGGAAGGAG
Statistics
Matches: 484, Mismatches: 26, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
54 15 0.03
55 457 0.94
56 12 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:989750 original size:26 final size:26
Alignment explanation
Indices: 989721--989810 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
989711 GTGTGGGCTT
989721 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
989747 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
* *
989774 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
989802 TGAAAGGTG
1 TGAAAGGTG
989811 CCACCAACTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:989839 original size:29 final size:29
Alignment explanation
Indices: 989751--989839 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
989741 GAGGACTGAA
989751 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
989780 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
989806 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
989835 AGGTG
1 AGGTG
989840 TCCTGCTCGT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:991034 original size:11 final size:11
Alignment explanation
Indices: 991018--991047 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
991008 CTTTGTTTTG
*
991018 TTTTTTTTGTT
1 TTTTTTTTCTT
991029 TTTTTTTTCTT
1 TTTTTTTTCTT
991040 TTTTTTTT
1 TTTTTTTT
991048 TTGAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.93
Consensus pattern (11 bp):
TTTTTTTTCTT
Done.