Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 186 of 310
Found at i:60881070 original size:81 final size:81
Alignment explanation
Indices: 60880935--60881097 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
60880925 GGGCCAAAGT
60880935 ATAAAATCAACACGGCCTGGACCCCCTCACACGGGTAGATCACATGGCCGTGTCAATTTGGCAGG
1 ATAAAATCAACACGGCCTGGACCCCCTCACACGGGTAGATCACATGGCCGTGTCAATTTGGCAGG
60881000 CTTAAGAATGGCCTGA
66 CTTAAGAATGGCCTGA
60881016 ATAAAATCAACACGGCCTGGACCCCCTCACACGGGTAGATCACATGGCCGTGTCAATTTGGCAGG
1 ATAAAATCAACACGGCCTGGACCCCCTCACACGGGTAGATCACATGGCCGTGTCAATTTGGCAGG
60881081 CTTAAGAATGGCCTGA
66 CTTAAGAATGGCCTGA
60881097 A
1 A
60881098 GTAATCACAC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.20
Consensus pattern (81 bp):
ATAAAATCAACACGGCCTGGACCCCCTCACACGGGTAGATCACATGGCCGTGTCAATTTGGCAGG
CTTAAGAATGGCCTGA
Found at i:60885305 original size:22 final size:22
Alignment explanation
Indices: 60885279--60885336 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
60885269 GATAATAGTA
60885279 AAAAAAATACGAAAGA-AAAAAT
1 AAAAAAATA-GAAAGAGAAAAAT
*
60885301 AAAAAAATAGAAATAGAAAAAT
1 AAAAAAATAGAAAGAGAAAAAT
60885323 AAAAATAATA-AAAG
1 AAAAA-AATAGAAAG
60885337 TATATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.16
22 23 0.72
23 4 0.12
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.12
Consensus pattern (22 bp):
AAAAAAATAGAAAGAGAAAAAT
Found at i:60885307 original size:8 final size:8
Alignment explanation
Indices: 60885294--60885362 Score: 52
Period size: 8 Copynumber: 8.8 Consensus size: 8
60885284 AATACGAAAG
60885294 AAAAAATA
1 AAAAAATA
60885302 AAAAAAT-
1 AAAAAATA
*
60885309 -AGAAATA
1 AAAAAATA
*
60885316 GAAAAATA
1 AAAAAATA
60885324 AAAATAATA
1 AAAA-AATA
**
60885333 AAAGTATA
1 AAAAAATA
* *
60885341 TAAAAATT
1 AAAAAATA
*
60885349 AAAATATA
1 AAAAAATA
60885357 AAAAAA
1 AAAAAA
60885363 AATATAAGTA
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
6 5 0.11
8 33 0.73
9 7 0.16
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (8 bp):
AAAAAATA
Found at i:60885357 original size:14 final size:12
Alignment explanation
Indices: 60885278--60885369 Score: 60
Period size: 14 Copynumber: 7.1 Consensus size: 12
60885268 TGATAATAGT
*
60885278 AAAAAAAATACGA
1 AAAAAAAATA-TA
*
60885291 AAGAAAAAATAAA
1 AA-AAAAAATATA
*
60885304 AAAATAGAAATAGA
1 AAAA-A-AAATATA
60885318 AAAATAAAA-ATA
1 AAAA-AAAATATA
**
60885330 ATAAAAGTATATA
1 A-AAAAAAATATA
60885343 AAAATTAAAATATA
1 AAAA--AAAATATA
60885357 AAAAAAAATATA
1 AAAAAAAATATA
60885369 A
1 A
60885370 GTATAAGAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
12 19 0.29
13 16 0.25
14 30 0.46
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.17
Consensus pattern (12 bp):
AAAAAAAATATA
Found at i:60885361 original size:16 final size:15
Alignment explanation
Indices: 60885294--60885362 Score: 52
Period size: 17 Copynumber: 4.4 Consensus size: 15
60885284 AATACGAAAG
60885294 AAAAAATAAAA-A-A
1 AAAAAATAAAATATA
* *
60885307 ATAGAAATAGAAAAATA
1 A-AAAAATA-AAATATA
60885324 AAAATAATAAAAGTATA
1 AAAA-AATAAAA-TATA
*
60885341 TAAAAATTAAAATATA
1 -AAAAAATAAAATATA
60885357 AAAAAA
1 AAAAAA
60885363 AATATAAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
13 1 0.02
14 6 0.14
15 8 0.18
16 10 0.23
17 15 0.34
18 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (15 bp):
AAAAAATAAAATATA
Found at i:60888539 original size:5 final size:6
Alignment explanation
Indices: 60888517--60888558 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
60888507 GTTAGTAAAT
*
60888517 TAAAAG TAAAACA -AAAAA T-AAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAA-A TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
60888559 GGCTAAAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
5 6 0.19
6 26 0.81
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:60888543 original size:23 final size:23
Alignment explanation
Indices: 60888512--60888558 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
60888502 GAAAAGTTAG
* *
60888512 TAAATTAAAAGTAAAACA-AAAAA
1 TAAAATAAAAATAAAA-ATAAAAA
60888535 TAAAATAAAAATAAAAATAAAAA
1 TAAAATAAAAATAAAAATAAAAA
60888558 T
1 T
60888559 GGCTAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (23 bp):
TAAAATAAAAATAAAAATAAAAA
Found at i:60888550 original size:17 final size:18
Alignment explanation
Indices: 60888517--60888556 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
60888507 GTTAGTAAAT
60888517 TAAAAGTAAAACAAAAAA
1 TAAAAGTAAAACAAAAAA
60888535 TAAAA-TAAAA-ATAAAAA
1 TAAAAGTAAAACA-AAAAA
60888552 TAAAA
1 TAAAA
60888557 ATGGCTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.71
18 5 0.24
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (18 bp):
TAAAAGTAAAACAAAAAA
Found at i:60895373 original size:32 final size:32
Alignment explanation
Indices: 60895321--60895488 Score: 133
Period size: 32 Copynumber: 5.2 Consensus size: 32
60895311 GTGTGCGTTT
* * **
60895321 CTTTTTGAGTGGTACACACAAAGTATACCTTTC
1 CTTTTCGAGT-GTACACACAAAGTATACATAAC
* *
60895354 CTTTTCGAGTGTACACACAAAGTGTATATAAC
1 CTTTTCGAGTGTACACACAAAGTATACATAAC
* *
60895386 CTTTTCAAGTGTACACACAAAGTGT-CAATAAC
1 CTTTTCGAGTGTACACACAAAGTATAC-ATAAC
* * * * *
60895418 TTTTTCAAGTGTACACACAAACTGTGCATAAC
1 CTTTTCGAGTGTACACACAAAGTATACATAAC
* * *
60895450 ATTTTC-ATGTGGTATACACAAAGTATACCTAAC
1 CTTTTCGA-GT-GTACACACAAAGTATACATAAC
*
60895483 CCTTTC
1 CTTTTC
60895489 ACATTCGATA
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
31 1 0.01
32 81 0.72
33 31 0.27
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (32 bp):
CTTTTCGAGTGTACACACAAAGTATACATAAC
Found at i:60895436 original size:34 final size:32
Alignment explanation
Indices: 60895353--60895473 Score: 145
Period size: 32 Copynumber: 3.8 Consensus size: 32
60895343 GTATACCTTT
*
60895353 CCTTTTCGAGTGTACACACAAAGTGTATATAA
1 CCTTTTCAAGTGTACACACAAAGTGTATATAA
60895385 CCTTTTCAAGTGTACACACAAAGTGTCA-ATAA
1 CCTTTTCAAGTGTACACACAAAGTGT-ATATAA
* * **
60895417 CTTTTTCAAGTGTACACACAAACTGTGCATAA
1 CCTTTTCAAGTGTACACACAAAGTGTATATAA
* * *
60895449 CATTTTCATGTGGTATACACAAAGT
1 CCTTTTCAAGT-GTACACACAAAGT
60895474 ATACCTAACC
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
32 66 0.85
33 12 0.15
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (32 bp):
CCTTTTCAAGTGTACACACAAAGTGTATATAA
Found at i:60895523 original size:29 final size:29
Alignment explanation
Indices: 60895485--60895611 Score: 173
Period size: 29 Copynumber: 4.3 Consensus size: 29
60895475 TACCTAACCC
60895485 TTTCACATTCGATAGCCAAAGCTATCCCT
1 TTTCACATTCGATAGCCAAAGCTATCCCT
**
60895514 TTTCACATTCGATAGCTGAAGCTATCCCT
1 TTTCACATTCGATAGCCAAAGCTATCCCT
* * *
60895543 TTTCACATTCGATAGTCGAAGCTATCCTTTTT
1 TTTCACATTCGATAGCCAAAGCTATCC---CT
*
60895575 TTTTACATTCGATAGCCAAAGCTATCCCT
1 TTTCACATTCGATAGCCAAAGCTATCCCT
60895604 TTTCACAT
1 TTTCACAT
60895612 GGTACACACA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
29 60 0.71
32 25 0.29
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (29 bp):
TTTCACATTCGATAGCCAAAGCTATCCCT
Found at i:60895604 original size:61 final size:58
Alignment explanation
Indices: 60895485--60895611 Score: 173
Period size: 61 Copynumber: 2.1 Consensus size: 58
60895475 TACCTAACCC
**
60895485 TTTCACATTCGATAGCCAAAGCTATCCCTTTTCACATTCGATAGCTGAAGCTATCCCT
1 TTTCACATTCGATAGCCAAAGCTATCCCTTTTCACATTCGATAGCCAAAGCTATCCCT
* * * *
60895543 TTTCACATTCGATAGTCGAAGCTATCCTTTTTTTTTACATTCGATAGCCAAAGCTATCCCT
1 TTTCACATTCGATAGCCAAAGCTATCC---CTTTTCACATTCGATAGCCAAAGCTATCCCT
60895604 TTTCACAT
1 TTTCACAT
60895612 GGTACACACA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 25 0.42
61 35 0.58
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (58 bp):
TTTCACATTCGATAGCCAAAGCTATCCCTTTTCACATTCGATAGCCAAAGCTATCCCT
Found at i:60898255 original size:33 final size:33
Alignment explanation
Indices: 60898212--60898340 Score: 127
Period size: 33 Copynumber: 3.9 Consensus size: 33
60898202 TCTTTCTGAG
*
60898212 TGGTACACACAAAGTATACTTTTCCTTTTCATA
1 TGGTACACACAAAGTATACCTTTCCTTTTCATA
*
60898245 TGGTATACACAAAGTATACCTTTCCTTTTCA-A
1 TGGTACACACAAAGTATACCTTTCCTTTTCATA
* * ** * *
60898277 -GTGTACACACAAAGTGTACGTAACCATTTCATG
1 TG-GTACACACAAAGTATACCTTTCCTTTTCATA
* * **
60898310 TGGTATACAAAAAGTATACCTAACCTTTTCA
1 TGGTACACACAAAGTATACCTTTCCTTTTCA
60898341 CATTCGATAT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
31 1 0.01
32 24 0.30
33 53 0.67
34 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (33 bp):
TGGTACACACAAAGTATACCTTTCCTTTTCATA
Found at i:60898283 original size:65 final size:65
Alignment explanation
Indices: 60898214--60898340 Score: 173
Period size: 65 Copynumber: 2.0 Consensus size: 65
60898204 TTTCTGAGTG
* ** * * **
60898214 GTACACACAAAGTATACTTTTCCTTTTCATATGGTATACACAAAGTATACCTTTCCTTTTCAAGT
1 GTACACACAAAGTATACGTAACCATTTCATATGGTATACAAAAAGTATACCTAACCTTTTCAAGT
* *
60898279 GTACACACAAAGTGTACGTAACCATTTCATGTGGTATACAAAAAGTATACCTAACCTTTTCA
1 GTACACACAAAGTATACGTAACCATTTCATATGGTATACAAAAAGTATACCTAACCTTTTCA
60898341 CATTCGATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (65 bp):
GTACACACAAAGTATACGTAACCATTTCATATGGTATACAAAAAGTATACCTAACCTTTTCAAGT
Found at i:60898375 original size:29 final size:29
Alignment explanation
Indices: 60898333--60898460 Score: 177
Period size: 29 Copynumber: 4.4 Consensus size: 29
60898323 GTATACCTAA
* *
60898333 CCTTTTCACATTCGATATCCAAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
60898362 CCTTTTCACATTCGATAGCTGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
60898391 CGTTTTCACA-TCTGATAGCCGAAGCTATC
1 CCTTTTCACATTC-GATAGCCGAAGCTATC
* *
60898420 CTTTTTTTACATTCGATAGCCGAAGCTATC
1 C-CTTTTCACATTCGATAGCCGAAGCTATC
60898450 CCTTTTCACAT
1 CCTTTTCACAT
60898461 GGTACACACA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.02
29 59 0.68
30 24 0.28
31 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCGAAGCTATC
Found at i:60898446 original size:59 final size:58
Alignment explanation
Indices: 60898333--60898460 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 58
60898323 GTATACCTAA
* *
60898333 CCTTTTCACATTCGATATCCAAAGCTATCCCTTTTCACATTCGATAGCTGAAGCTATC
1 CCTTTTCACATTCGATAGCCAAAGCTATCCCTTTTCACATTCGATAGCCGAAGCTATC
* * * *
60898391 CGTTTTCACA-TCTGATAGCCGAAGCTATCCTTTTTTTACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTC-GATAGCCAAAGCTATCC-CTTTTCACATTCGATAGCCGAAGCTATC
60898450 CCTTTTCACAT
1 CCTTTTCACAT
60898461 GGTACACACA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
57 2 0.03
58 24 0.40
59 34 0.57
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (58 bp):
CCTTTTCACATTCGATAGCCAAAGCTATCCCTTTTCACATTCGATAGCCGAAGCTATC
Found at i:60902463 original size:18 final size:18
Alignment explanation
Indices: 60902440--60902475 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
60902430 TCAAAGTTTC
60902440 AAACATTCCAAGTTGAGA
1 AAACATTCCAAGTTGAGA
60902458 AAACATTCCAAGTTGAGA
1 AAACATTCCAAGTTGAGA
60902476 TCCCCTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (18 bp):
AAACATTCCAAGTTGAGA
Found at i:60911257 original size:15 final size:14
Alignment explanation
Indices: 60911226--60911264 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
60911216 CATTTAGAGC
*
60911226 TTTTTTTAAATATA
1 TTTTTTTAAATAAA
*
60911240 TTTTTTTAATTTAAA
1 TTTTTTTAA-ATAAA
60911255 TTTTTTTAAA
1 TTTTTTTAAA
60911265 AATAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTTAAATAAA
Found at i:60913482 original size:13 final size:12
Alignment explanation
Indices: 60913464--60913495 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
60913454 AAATATTATA
60913464 TTTTTTTCTTCT
1 TTTTTTTCTTCT
60913476 TTTTTTTCTTTCT
1 TTTTTTTC-TTCT
60913489 TTTTTTT
1 TTTTTTT
60913496 TCTTTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTTCTTCT
Found at i:60913492 original size:14 final size:13
Alignment explanation
Indices: 60913464--60913500 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
60913454 AAATATTATA
60913464 TTTTTTTC-TTCT
1 TTTTTTTCTTTCT
60913476 TTTTTTTCTTTCTT
1 TTTTTTTCTTTC-T
60913490 TTTTTTTCTTT
1 TTTTTTTCTTT
60913501 TTGACTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 12 0.52
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTCTTTCT
Found at i:60914469 original size:6 final size:6
Alignment explanation
Indices: 60914458--60914531 Score: 80
Period size: 6 Copynumber: 12.7 Consensus size: 6
60914448 CATAATAGAC
* *
60914458 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT-AAA A-GAAG ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * * *
60914504 ATAAAA GTAAAC ATAAAC GTAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
60914532 TCGGACTCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
5 7 0.12
6 50 0.88
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:60916653 original size:21 final size:22
Alignment explanation
Indices: 60916629--60916669 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
60916619 AGAGAAGGGA
*
60916629 AAAAGAGAAGGAA-AAGGAAAG
1 AAAAGAGAAGAAATAAGGAAAG
*
60916650 AAAAGGGAAGAAATAAGGAA
1 AAAAGAGAAGAAATAAGGAA
60916670 GGGGGAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (22 bp):
AAAAGAGAAGAAATAAGGAAAG
Found at i:60920105 original size:22 final size:22
Alignment explanation
Indices: 60920080--60920123 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
60920070 GATAAGTTAG
60920080 TAAATT-ATAATAAAAATAAAAA
1 TAAATTGAT-ATAAAAATAAAAA
*
60920102 TAAATTGCTATAAAAATAAAAA
1 TAAATTGATATAAAAATAAAAA
60920124 AATGGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTGATATAAAAATAAAAA
Found at i:60920131 original size:20 final size:22
Alignment explanation
Indices: 60920089--60920144 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
60920079 GTAAATTATA
*
60920089 ATAAAAATAAAAATAAATTGCT
1 ATAAAAATAAAAATAAATGGCT
60920111 ATAAAAAT-AAAA-AAATGGCT
1 ATAAAAATAAAAATAAATGGCT
*
60920131 A-AAGTAATAAAAAT
1 ATAA-AAATAAAAAT
60920145 TAAGCGTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 8 0.28
22 8 0.28
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.23
Consensus pattern (22 bp):
ATAAAAATAAAAATAAATGGCT
Found at i:60923653 original size:12 final size:12
Alignment explanation
Indices: 60923636--60923660 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60923626 GGGCCAGTTT
60923636 ATGGATTTTTCA
1 ATGGATTTTTCA
60923648 ATGGATTTTTCA
1 ATGGATTTTTCA
60923660 A
1 A
60923661 CCATCTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (12 bp):
ATGGATTTTTCA
Found at i:60924979 original size:18 final size:19
Alignment explanation
Indices: 60924946--60924992 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
60924936 TTTGCACAAT
60924946 TGCGAGCTC-CTACAAA-A
1 TGCGAGCTCACTACAAAGA
*
60924963 CTGTGAGCTCACT-CAAAGA
1 -TGCGAGCTCACTACAAAGA
60924982 TGCGAGCTCAC
1 TGCGAGCTCAC
60924993 CATATCTGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (19 bp):
TGCGAGCTCACTACAAAGA
Found at i:60925093 original size:16 final size:17
Alignment explanation
Indices: 60925061--60925107 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
60925051 GTGGGCTTGC
*
60925061 CCAAGACTGCGAGCTCA
1 CCAAGACTGCAAGCTCA
60925078 CCAAGACT-CAAGCTCA
1 CCAAGACTGCAAGCTCA
* *
60925094 TCAAGATTGCAAGC
1 CCAAGACTGCAAGC
60925108 CCTCTAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (17 bp):
CCAAGACTGCAAGCTCA
Found at i:60928244 original size:16 final size:17
Alignment explanation
Indices: 60928217--60928249 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
60928207 CAAAATTGAG
*
60928217 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
60928234 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
60928250 ATAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:60930779 original size:33 final size:34
Alignment explanation
Indices: 60930740--60930806 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 34
60930730 AATAAAATAT
*
60930740 CTCATATG-GCCAAATATACAAATTCAATATAAG
1 CTCATATGAACCAAATATACAAATTCAATATAAG
* *
60930773 CTCATATGAAATCAAATATACAAGTTCAATATAA
1 CTCATATG-AACCAAATATACAAATTCAATATAA
60930807 CTTCACAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 8 0.28
35 21 0.72
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.28
Consensus pattern (34 bp):
CTCATATGAACCAAATATACAAATTCAATATAAG
Found at i:60938608 original size:35 final size:35
Alignment explanation
Indices: 60938530--60938630 Score: 105
Period size: 35 Copynumber: 2.9 Consensus size: 35
60938520 ATCTCATATG
* * *
60938530 GCCGAATATACAAATTCAATATAACCTCATATGAA
1 GCCGAATATACAAGTTCAATATAACCTCACAAGAA
** * * *
60938565 ATCAAATATACAAGTTCAATATAACTTCACAAGCA
1 GCCGAATATACAAGTTCAATATAACCTCACAAGAA
*
60938600 GCCGAATATACAAAG-TCAATATGACCTCACA
1 GCCGAATATAC-AAGTTCAATATAACCTCACA
60938631 TGTACATACT
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 49 0.94
36 3 0.06
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (35 bp):
GCCGAATATACAAGTTCAATATAACCTCACAAGAA
Found at i:60949673 original size:20 final size:19
Alignment explanation
Indices: 60949627--60949664 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
60949617 CATCCAAACA
60949627 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
60949646 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
60949665 TCTGGAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:60953537 original size:54 final size:55
Alignment explanation
Indices: 60953423--60953539 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 55
60953413 GATAAGTTTT
* ** *
60953423 AGAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTCGACTTGTA
1 AGAATTACCAAAATACCCCTGACTTGTAAAATTACCAAAATACCCCCGACTTGTA
*
60953478 A-AATTACCAAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCCCCGA-TT-TA
1 AGAATTACCAAAATACCCCT-GACTTGTAAAATTACCAAAATACCCCCGACTTGTA
60953530 CAGAATTACC
1 -AGAATTACC
60953540 GTTTTACCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
52 2 0.04
53 7 0.13
54 44 0.81
55 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.26
Consensus pattern (55 bp):
AGAATTACCAAAATACCCCTGACTTGTAAAATTACCAAAATACCCCCGACTTGTA
Found at i:60953539 original size:27 final size:27
Alignment explanation
Indices: 60953446--60953521 Score: 143
Period size: 27 Copynumber: 2.8 Consensus size: 27
60953436 TACCCCTGGT
60953446 TTGTAAAATTACCAAAATACCCTCGAC
1 TTGTAAAATTACCAAAATACCCTCGAC
60953473 TTGTAAAATTACCAAAATACCCTCGAC
1 TTGTAAAATTACCAAAATACCCTCGAC
*
60953500 TTGTAAAATTACCAAAGTACCC
1 TTGTAAAATTACCAAAATACCC
60953522 CCGATTTACA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (27 bp):
TTGTAAAATTACCAAAATACCCTCGAC
Found at i:60953574 original size:27 final size:27
Alignment explanation
Indices: 60953450--60953576 Score: 128
Period size: 27 Copynumber: 4.7 Consensus size: 27
60953440 CCTGGTTTGT
**
60953450 AAAATTACCAAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCTCGACTTAC
**
60953477 AAAATTACCAAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCTCGACTTAC
* * *
60953504 AAAATTACCAAAGTACCCCCGATTTAC
1 AAAATTACCAAAATACCCTCGACTTAC
* **** *
60953531 AGAATTACCGTTTTACCCTCGATTTAC
1 AAAATTACCAAAATACCCTCGACTTAC
*
60953558 AAAATTACCGAAATACCCT
1 AAAATTACCAAAATACCCT
60953577 TGTAGGGTAG
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 85 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.27
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGACTTAC
Found at i:60953678 original size:27 final size:27
Alignment explanation
Indices: 60953618--60953679 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
60953608 GGGTAGGACT
* *
60953618 ACCAATTTACCCCTAGAGGGTAAAATG
1 ACCATTTTGCCCCTAGAGGGTAAAATG
*
60953645 ACCATTTTGCCCCTAG-GGTGTTAAATG
1 ACCATTTTGCCCCTAGAGG-GTAAAATG
*
60953672 ACTATTTT
1 ACCATTTT
60953680 TCCCTTCGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (27 bp):
ACCATTTTGCCCCTAGAGGGTAAAATG
Found at i:60959913 original size:27 final size:28
Alignment explanation
Indices: 60959883--60959980 Score: 130
Period size: 27 Copynumber: 3.6 Consensus size: 28
60959873 TAAGTTTTAG
* **
60959883 AATTACTAAAATACCCCT-GGTTTGTAA
1 AATTACCAAAATACCCCTCGACTTGTAA
60959910 AATTACCAAAATA-CCCTCGACTTGTAA
1 AATTACCAAAATACCCCTCGACTTGTAA
60959937 AATTACCAAAATA-CCCTCGACTTGTAA
1 AATTACCAAAATACCCCTCGACTTGTAA
* *
60959964 AACTACCAAAGTACCCC
1 AATTACCAAAATACCCC
60959981 CGAGTTACAG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.06
27 57 0.89
28 3 0.05
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (28 bp):
AATTACCAAAATACCCCTCGACTTGTAA
Found at i:60959995 original size:54 final size:54
Alignment explanation
Indices: 60959881--60959997 Score: 128
Period size: 54 Copynumber: 2.2 Consensus size: 54
60959871 GATAAGTTTT
* ** * * **
60959881 AGAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTCGACTTGT
1 AGAATTACCAAAATACCCCTGACTTGTAAAACTACCAAAATACCCCCGACTTAC
* * *
60959935 AAAATTACCAAAATA-CCCTCGACTTGTAAAACTACCAAAGTACCCCCGAGTTAC
1 AGAATTACCAAAATACCCCT-GACTTGTAAAACTACCAAAATACCCCCGACTTAC
60959989 AGAATTACC
1 AGAATTACC
60959998 GTTTTACCCT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
53 4 0.08
54 47 0.92
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.25
Consensus pattern (54 bp):
AGAATTACCAAAATACCCCTGACTTGTAAAACTACCAAAATACCCCCGACTTAC
Found at i:60960051 original size:27 final size:27
Alignment explanation
Indices: 60960021--60960101 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
60960011 TTTACAAAAT
* *
60960021 TACCGAAATATCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
* *
60960048 TACCGAAATACCCCTGTAGGGTAGGAC
1 TACCGAAATACCCCTGTAGGGTAGAAA
**
60960075 TACCGATTTACCCCTAG-AGGGTA-AAA
1 TACCGAAATACCCCT-GTAGGGTAGAAA
60960101 T
1 T
60960102 GACCATTTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
26 2 0.04
27 42 0.93
28 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (27 bp):
TACCGAAATACCCCTGTAGGGTAGAAA
Found at i:60960115 original size:27 final size:27
Alignment explanation
Indices: 60960085--60960141 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
60960075 TACCGATTTA
60960085 CCCCTAGAGG-GTAAAATGACCATTTTG
1 CCCCTAG-GGTGTAAAATGACCATTTTG
* *
60960112 CCCCTAGGGTGTTAAATGACTATTTTG
1 CCCCTAGGGTGTAAAATGACCATTTTG
60960139 CCC
1 CCC
60960142 TTCGTGCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (27 bp):
CCCCTAGGGTGTAAAATGACCATTTTG
Found at i:60969337 original size:14 final size:13
Alignment explanation
Indices: 60969313--60969352 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
60969303 CTAACCTCTA
60969313 TTTTATATTTTAT
1 TTTTATATTTTAT
60969326 TTTTATTATTTTA-
1 TTTTA-TATTTTAT
60969339 TTTTAT-TTTTAT
1 TTTTATATTTTAT
60969351 TT
1 TT
60969353 GCTATCAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.20
12 3 0.12
13 10 0.40
14 7 0.28
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATATTTTAT
Found at i:60969941 original size:7 final size:7
Alignment explanation
Indices: 60969929--60969976 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
60969919 CATTAATTAA
60969929 CTAAACC
1 CTAAACC
60969936 CTAAACTC
1 CTAAAC-C
* *
60969944 TTAATCC
1 CTAAACC
60969951 CTAAACC
1 CTAAACC
*
60969958 CTAAATC
1 CTAAACC
*
60969965 CTAAATC
1 CTAAACC
60969972 CTAAA
1 CTAAA
60969977 ATATAAACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 30 0.86
8 5 0.14
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (7 bp):
CTAAACC
Found at i:60969954 original size:22 final size:22
Alignment explanation
Indices: 60969929--60969993 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
60969919 CATTAATTAA
60969929 CTAAACCCTAAACTCTTAATCC
1 CTAAACCCTAAACTCTTAATCC
*
60969951 CTAAACCCTAAA-TCCTAAAT-C
1 CTAAACCCTAAACT-CTTAATCC
***
60969972 CTAAAATATAAACTCTTAATCC
1 CTAAACCCTAAACTCTTAATCC
60969994 TAGACCCCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.28
Consensus pattern (22 bp):
CTAAACCCTAAACTCTTAATCC
Found at i:60969992 original size:21 final size:21
Alignment explanation
Indices: 60969937--60969995 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
60969927 AACTAAACCC
* *
60969937 TAAACTCTTAATCCCTAAACCC
1 TAAACTCTTAAT-CCTAAAACA
* *
60969959 TAAA-TCCTAAATCCTAAAATA
1 TAAACT-CTTAATCCTAAAACA
60969980 TAAACTCTTAATCCTA
1 TAAACTCTTAATCCTA
60969996 GACCCCTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAACTCTTAATCCTAAAACA
Found at i:60970266 original size:23 final size:23
Alignment explanation
Indices: 60970224--60970287 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
60970214 AGGGGTTATA
60970224 GTTTAGG-GTTTAAGAT-TTTTAAG
1 GTTTAGGAGTTT-AG-TGTTTTAAG
60970247 GTTTAGGAGTTTAGTGTTTTAAG
1 GTTTAGGAGTTTAGTGTTTTAAG
* * *
60970270 GATTA-CAGATTAGTGTTT
1 GTTTAGGAGTTTAGTGTTT
60970288 ATGATTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 12 0.33
23 20 0.56
24 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.47
Consensus pattern (23 bp):
GTTTAGGAGTTTAGTGTTTTAAG
Found at i:60970425 original size:40 final size:40
Alignment explanation
Indices: 60970329--60970465 Score: 202
Period size: 41 Copynumber: 3.4 Consensus size: 40
60970319 GTTATATGAC
* *
60970329 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGC
1 TTTTAGCGGCGTTTTACCAAAAGAGCCGCTAATGCTCT-GT
*
60970370 TTTTAGCGGCGTTTTACCAAAAGAGCCGCTAATGCTCTAT
1 TTTTAGCGGCGTTTTACCAAAAGAGCCGCTAATGCTCTGT
* * *
60970410 TTTTAGCGGCGTTTTAACAAAAAATGCCGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTACCAAAAGA-GCCGCTAATGCTCTGT
60970451 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
60970466 TGGTCAAATG
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 22 0.25
41 66 0.75
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAGAGCCGCTAATGCTCTGT
Found at i:60970496 original size:41 final size:41
Alignment explanation
Indices: 60970329--60970496 Score: 162
Period size: 41 Copynumber: 4.1 Consensus size: 41
60970319 GTTATATGAC
* ** * **
60970329 TTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTGGC
1 TTTTAGCGGCGTTTTAACAAAAAATGCCGCTATTGCTCT-AT
* * *
60970370 TTTTAGCGGCGTTTTACCAAAAGA-GCCGCTAATGCTCTAT
1 TTTTAGCGGCGTTTTAACAAAAAATGCCGCTATTGCTCTAT
*
60970410 TTTTAGCGGCGTTTTAACAAAAAATGCCGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTAACAAAAAATGCCGCTATTGCTCTAT
*****
60970451 TTTTAGCGGCGTTTT-TGGTCAAATGCCGCTATTGCTCTAT
1 TTTTAGCGGCGTTTTAACAAAAAATGCCGCTATTGCTCTAT
60970491 GTTTTA
1 -TTTTA
60970497 CAATTTTTGT
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
40 41 0.38
41 63 0.58
42 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTAACAAAAAATGCCGCTATTGCTCTAT
Found at i:60970604 original size:20 final size:20
Alignment explanation
Indices: 60970581--60970618 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
60970571 TTTGGTATGA
60970581 TATTAAAAATTTTAATATAG
1 TATTAAAAATTTTAATATAG
*
60970601 TATTAGAAATTTTAATAT
1 TATTAAAAATTTTAATAT
60970619 CACCTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TATTAAAAATTTTAATATAG
Found at i:60970651 original size:20 final size:20
Alignment explanation
Indices: 60970582--60970651 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
60970572 TTGGTATGAT
* * **
60970582 ATTAAAAATTTTAATATAGT
1 ATTAGAAATTTCAATATAAC
* *
60970602 ATTAGAAATTTTAATATCAC
1 ATTAGAAATTTCAATATAAC
* *
60970622 CTTA-AAATTTCGATATAAC
1 ATTAGAAATTTCAATATAAC
60970641 ATTAGAAATTT
1 ATTAGAAATTT
60970652 TACATTAGTC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 15 0.38
20 25 0.62
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (20 bp):
ATTAGAAATTTCAATATAAC
Found at i:60983837 original size:41 final size:40
Alignment explanation
Indices: 60983790--60983902 Score: 106
Period size: 41 Copynumber: 2.9 Consensus size: 40
60983780 TTGACCTAGA
*
60983790 GCCGATGAGACACTGGGTGTCACTATATTTCTTCGGATAG
1 GCCGATGAGACACTGGGTGTCACTATATTACTTCGGATAG
** ** ** *
60983830 ATTCGATGAGGTACTGGGTACCAC--T-TTACTTCGGTTAG
1 -GCCGATGAGACACTGGGTGTCACTATATTACTTCGGATAG
* *
60983868 GCCGATGAGACACTGGCTGTCACTATATTGCTTCG
1 GCCGATGAGACACTGGGTGTCACTATATTACTTCG
60983903 AACTATCTGA
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
37 16 0.30
38 11 0.21
39 2 0.04
40 7 0.13
41 17 0.32
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (40 bp):
GCCGATGAGACACTGGGTGTCACTATATTACTTCGGATAG
Found at i:60984331 original size:52 final size:52
Alignment explanation
Indices: 60984269--60984371 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
60984259 ATTGTTTAAT
*
60984269 GACTTGTGAATAAATCGTGGAAAGTTATATAGGTTAGTAAGTGAAATGAATA
1 GACTTGTGAATAAATCGTGGAAAGTTATATAGGCTAGTAAGTGAAATGAATA
60984321 GACTTGTGAATAAATCGTGGAAAGTTATATAGGCTAGTAAGTGAAATGAAT
1 GACTTGTGAATAAATCGTGGAAAGTTATATAGGCTAGTAAGTGAAATGAAT
60984372 GAAATAAGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (52 bp):
GACTTGTGAATAAATCGTGGAAAGTTATATAGGCTAGTAAGTGAAATGAATA
Found at i:60991196 original size:26 final size:26
Alignment explanation
Indices: 60991165--60991272 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
60991155 TGAAATGTCC
*
60991165 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
60991191 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
60991217 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
60991243 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
60991269 ATCA
1 ATCA
60991273 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:60992125 original size:8 final size:8
Alignment explanation
Indices: 60992112--60992136 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
60992102 TTTTCACATT
60992112 ATAAACAA
1 ATAAACAA
60992120 ATAAACAA
1 ATAAACAA
60992128 ATAAACAA
1 ATAAACAA
60992136 A
1 A
60992137 ACAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
ATAAACAA
Found at i:60992948 original size:13 final size:14
Alignment explanation
Indices: 60992925--60992968 Score: 65
Period size: 13 Copynumber: 3.3 Consensus size: 14
60992915 TTATTCAAAC
60992925 ATAATTAAATATTA
1 ATAATTAAATATTA
*
60992939 ATCA-TAAATATT-
1 ATAATTAAATATTA
60992951 ATAATTAAATATTA
1 ATAATTAAATATTA
60992965 ATAA
1 ATAA
60992969 CTCTCGGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 3 0.12
13 16 0.62
14 7 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATTAAATATTA
Found at i:60993074 original size:17 final size:16
Alignment explanation
Indices: 60993036--60993078 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
60993026 AGTTTTAACA
60993036 TTTATTTATAATTAATT
1 TTTATTTA-AATTAATT
* *
60993053 ATTATTTAAATATATTT
1 TTTATTTAAAT-TAATT
60993070 TTTATTTAA
1 TTTATTTAA
60993079 TGATGAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATTTAAATTAATT
Found at i:60993565 original size:6 final size:6
Alignment explanation
Indices: 60993556--60993582 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
60993546 TATTTTTATT
60993556 TTTCTC TTTCTC TTTCTC TTTCTC TTT
1 TTTCTC TTTCTC TTTCTC TTTCTC TTT
60993583 TATGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCTC
Found at i:60995571 original size:14 final size:14
Alignment explanation
Indices: 60995554--60995596 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
60995544 CATTTCTTAA
60995554 TTTTTATTTTTTTC
1 TTTTTATTTTTTTC
* *
60995568 TTTTTCTTCTTTTC
1 TTTTTATTTTTTTC
60995582 TTTATCTATTTTTTT
1 TTT-T-TATTTTTTT
60995597 TCTTAGCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 15 0.65
15 1 0.04
16 7 0.30
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTATTTTTTTC
Found at i:60998245 original size:6 final size:6
Alignment explanation
Indices: 60998234--60998270 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
60998224 CAACTATCTG
60998234 TTTCTT TTTCTT TGTTCTT TTTC-T TTTC-T TTTCTT TT
1 TTTCTT TTTCTT T-TTCTT TTTCTT TTTCTT TTTCTT TT
60998271 ATTTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 13 0.45
7 6 0.21
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:60998253 original size:13 final size:13
Alignment explanation
Indices: 60998235--60998259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60998225 AACTATCTGT
60998235 TTCTTTTTCTTTG
1 TTCTTTTTCTTTG
60998248 TTCTTTTTCTTT
1 TTCTTTTTCTTT
60998260 TCTTTTCTTT
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:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (13 bp):
TTCTTTTTCTTTG
Found at i:60998398 original size:23 final size:25
Alignment explanation
Indices: 60998351--60998399 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
60998341 AAAATATAAG
**
60998351 TAAATACATATATATTACATTTGTA
1 TAAATACATATATATTACAAATGTA
60998376 TAAATACA-AT-TATTACAAATGTA
1 TAAATACATATATATTACAAATGTA
60998399 T
1 T
60998400 TAATTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 2 0.09
25 8 0.36
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (25 bp):
TAAATACATATATATTACAAATGTA
Found at i:61001925 original size:5 final size:5
Alignment explanation
Indices: 61001910--61001951 Score: 75
Period size: 5 Copynumber: 8.2 Consensus size: 5
61001900 AATTTAAGTA
61001910 ATTATT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
1 ATTA-T ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
61001952 ATAATTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 32 0.89
6 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:61002668 original size:13 final size:13
Alignment explanation
Indices: 61002650--61002674 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61002640 TAAATGTTAT
61002650 GGTAAGTAAATAA
1 GGTAAGTAAATAA
61002663 GGTAAGTAAATA
1 GGTAAGTAAATA
61002675 TCATGATGGC
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:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (13 bp):
GGTAAGTAAATAA
Found at i:61008477 original size:35 final size:35
Alignment explanation
Indices: 61008405--61008482 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
61008395 TTAAGTTGAG
*
61008405 AATGTTATTTACCGTTGGCTAAATTTGTATACGAT
1 AATGTTATTTACCGTTGGCTAAATTTGTATACAAT
*
61008440 AATGTTATTTACCGTTGGCTAAATTTGTATATAAT
1 AATGTTATTTACCGTTGGCTAAATTTGTATACAAT
61008475 AATAGTTA
1 AAT-GTTA
61008483 CCAATCAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 36 0.90
36 4 0.10
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (35 bp):
AATGTTATTTACCGTTGGCTAAATTTGTATACAAT
Found at i:61009490 original size:5 final size:5
Alignment explanation
Indices: 61009480--61009509 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
61009470 TTTAAGTAAT
61009480 TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA
61009510 ATTTAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:61009619 original size:86 final size:85
Alignment explanation
Indices: 61009511--61009674 Score: 283
Period size: 86 Copynumber: 1.9 Consensus size: 85
61009501 ATTATATTAA
* * *
61009511 TTTAATAATAAAATAAATAAAAGAAATAAAACGATGGAAAAAAGAAACAGTGAAGCAAACGAAAT
1 TTTAATAATAAAATAAATAAAAGAAATAAAACAATAGAAAAAAGAAACAGAGAAGCAAACGAAAT
61009576 AGGAAAGAAAAAGGAAATAG
66 AGGAAAGAAAAAGGAAATAG
*
61009596 TTTAATAATAAAAATGAATAAAAGAAATAAAACAATAGAAAAAAGAAACAGAGAAGCAAACGAAA
1 TTTAATAAT-AAAATAAATAAAAGAAATAAAACAATAGAAAAAAGAAACAGAGAAGCAAACGAAA
61009661 TAGGAAAGAAAAAG
65 TAGGAAAGAAAAAG
61009675 AAAGCAAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 9 0.12
86 65 0.88
ACGTcount: A:0.65, C:0.05, G:0.16, T:0.13
Consensus pattern (85 bp):
TTTAATAATAAAATAAATAAAAGAAATAAAACAATAGAAAAAAGAAACAGAGAAGCAAACGAAAT
AGGAAAGAAAAAGGAAATAG
Found at i:61010194 original size:19 final size:20
Alignment explanation
Indices: 61010151--61010194 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
61010141 AAATACATTT
*
61010151 AAAAACATAAAAACAAATAT
1 AAAAACATAAAAACAAATAA
* *
61010171 TAAAACA-AGAAACAAATAA
1 AAAAACATAAAAACAAATAA
61010190 AAAAA
1 AAAAA
61010195 TGAGACAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAACATAAAAACAAATAA
Found at i:61011274 original size:10 final size:10
Alignment explanation
Indices: 61011259--61011284 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
61011249 AATAAGATTC
61011259 ATATTGAATG
1 ATATTGAATG
61011269 ATATTGAATG
1 ATATTGAATG
61011279 ATATTG
1 ATATTG
61011285 TATGTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.42
Consensus pattern (10 bp):
ATATTGAATG
Found at i:61015199 original size:53 final size:53
Alignment explanation
Indices: 61015043--61015208 Score: 212
Period size: 53 Copynumber: 3.1 Consensus size: 53
61015033 GACGAAAAAT
* **
61015043 ATGTGATAAGTGCG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGCGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
*
61015095 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGCGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
61015148 ATGTGATAATGCGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGCGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
61015202 TATGTGA
1 -ATGTGA
61015209 ACCGTGTAAG
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
51 3 0.03
52 11 0.11
53 80 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (53 bp):
ATGTGATAATGCGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:61023236 original size:13 final size:13
Alignment explanation
Indices: 61023220--61023272 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
61023210 TTTAAATTAA
61023220 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
61023233 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
* *
61023246 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
61023259 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
61023272 A
1 A
61023273 TTTCCAAACT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:61027983 original size:17 final size:17
Alignment explanation
Indices: 61027957--61027990 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
61027947 TATATATTTG
*
61027957 AAATATGTTATAATATA
1 AAATAAGTTATAATATA
61027974 AAATAAGTTATAATATA
1 AAATAAGTTATAATATA
61027991 TTAAGTGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAATAAGTTATAATATA
Found at i:61029337 original size:24 final size:24
Alignment explanation
Indices: 61029305--61029445 Score: 176
Period size: 24 Copynumber: 5.9 Consensus size: 24
61029295 GAAATGACAT
61029305 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
*
61029329 TGGCACTATGTGTGCAGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
*
61029353 TGACACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
* * *
61029377 TGGCACTACGTGTGTGGATTAGCAA
1 TGGCACTATGTGTGCGGATTTG-AA
** * *
61029402 -GGCACTATGTGTGCGGGCTAGCA
1 TGGCACTATGTGTGCGGATTTGAA
*
61029425 TGGCACTATGTGTGCGAATTT
1 TGGCACTATGTGTGCGGATTT
61029446 CCTTGACCGA
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
23 1 0.01
24 96 0.97
25 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.31
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:61040972 original size:24 final size:24
Alignment explanation
Indices: 61040945--61041015 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 24
61040935 GGATGCTCTA
61040945 AAGAGCTATTAACGGGAAGCTCAT
1 AAGAGCTATTAACGGGAAGCTCAT
* * * *
61040969 AAGAACCATATAATGGGAAGCTCGT
1 AAGAGCTAT-TAACGGGAAGCTCAT
* * * *
61040994 GAGAGCTACTATCGGGACGCTC
1 AAGAGCTATTAACGGGAAGCTC
61041016 TTTCGAGCTG
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
24 17 0.49
25 18 0.51
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (24 bp):
AAGAGCTATTAACGGGAAGCTCAT
Found at i:61046040 original size:5 final size:5
Alignment explanation
Indices: 61046020--61046062 Score: 59
Period size: 5 Copynumber: 8.0 Consensus size: 5
61046010 GTGTTACTTT
61046020 TTTTA TTTTA GGTTTTA TTTTA TTTTA TTTTTA TTTTA TTTTA
1 TTTTA TTTTA --TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
61046063 ATTATTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 25 0.71
6 5 0.14
7 5 0.14
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:61046053 original size:11 final size:11
Alignment explanation
Indices: 61046032--61046061 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
61046022 TTATTTTAGG
61046032 TTTTA-TTTTA
1 TTTTATTTTTA
61046042 TTTTATTTTTA
1 TTTTATTTTTA
61046053 TTTTATTTT
1 TTTTATTTT
61046062 AATTATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:61046053 original size:16 final size:17
Alignment explanation
Indices: 61046020--61046062 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
61046010 GTGTTACTTT
61046020 TTTTATTTTAGGTTTTA
1 TTTTATTTTAGGTTTTA
*
61046037 TTTTATTTTA-TTTTTA
1 TTTTATTTTAGGTTTTA
61046053 TTTTATTTTA
1 TTTTATTTTA
61046063 ATTATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTTATTTTAGGTTTTA
Found at i:61047736 original size:6 final size:6
Alignment explanation
Indices: 61047725--61047761 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
61047715 GTATTATTAC
61047725 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT T
61047762 CTTTTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:61058228 original size:13 final size:13
Alignment explanation
Indices: 61058210--61058234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61058200 AAGTAATCGC
61058210 ACATGGGCATGTT
1 ACATGGGCATGTT
61058223 ACATGGGCATGT
1 ACATGGGCATGT
61058235 CCCTGTCAAG
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:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (13 bp):
ACATGGGCATGTT
Found at i:61063116 original size:6 final size:6
Alignment explanation
Indices: 61063092--61063135 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
61063082 CCAGTACCTA
*
61063092 AACAGT AATCAGT AACAGT AGCAGT AACAGT AACAGT AACAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
61063136 TTCAACACAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (6 bp):
AACAGT
Found at i:61063167 original size:45 final size:45
Alignment explanation
Indices: 61063116--61063225 Score: 168
Period size: 45 Copynumber: 2.4 Consensus size: 45
61063106 ACAGTAGCAG
* *
61063116 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCT-A
1 TAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAAT-TGA
* *
61063161 TAACAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATTGG
1 TAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATTGA
61063206 TAACAGTAACGGTAACAGTA
1 TAACAGTAACGGTAACAGTA
61063226 ACAGTAGTCG
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
44 1 0.02
45 59 0.98
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (45 bp):
TAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATTGA
Found at i:61063490 original size:41 final size:40
Alignment explanation
Indices: 61063438--61063516 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
61063428 TTTCATCAAA
**
61063438 AATTTTACAGTTCAATGCAGTATACGTAACAATATTCAGT
1 AATTTTACAGTTCAATGCAGTATACAAAACAATATTCAGT
* *
61063478 AATTTTCACAGTTCAATTCAGTATTCAAAACAATATTCA
1 AATTTT-ACAGTTCAATGCAGTATACAAAACAATATTCA
61063517 ATATCCCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 6 0.18
41 28 0.82
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.35
Consensus pattern (40 bp):
AATTTTACAGTTCAATGCAGTATACAAAACAATATTCAGT
Found at i:61070009 original size:21 final size:21
Alignment explanation
Indices: 61069985--61070181 Score: 145
Period size: 21 Copynumber: 9.6 Consensus size: 21
61069975 AAAGCCAGAA
*
61069985 AGCTGAACAGAAGCTCGTGAG
1 AGCTGAACAGAAGCTCGTAAG
* * * *
61070006 AGCTAAACAGAAACCCATAATG
1 AGCTGAACAGAAGCTCGTAA-G
* *
61070028 -GTTGAACAAAAGCTCG-AA-
1 AGCTGAACAGAAGCTCGTAAG
* *
61070046 AGCTAAAAAGAAGCTCG-AA-
1 AGCTGAACAGAAGCTCGTAAG
* *
61070065 ATCTGAACAGAAGCTCGTGAG
1 AGCTGAACAGAAGCTCGTAAG
* * * *
61070086 AACTTAACAGAAACTCTTAAG
1 AGCTGAACAGAAGCTCGTAAG
61070107 AG-TAGAACAGAAGCTCGTAAG
1 AGCT-GAACAGAAGCTCGTAAG
* * *
61070128 AGCTGAACAAAAACTCATAAG
1 AGCTGAACAGAAGCTCGTAAG
* *
61070149 AGTTAAACAGAAGCTCGTAAG
1 AGCTGAACAGAAGCTCGTAAG
*
61070170 AGCTAAACAGAA
1 AGCTGAACAGAA
61070182 AGTAAAACAC
Statistics
Matches: 133, Mismatches: 37, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
19 28 0.21
20 4 0.03
21 99 0.74
22 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCGTAAG
Found at i:61070061 original size:19 final size:19
Alignment explanation
Indices: 61070037--61070081 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
61070027 GGTTGAACAA
61070037 AAGCTCGAAAGCTAAAAAG
1 AAGCTCGAAAGCTAAAAAG
* * *
61070056 AAGCTCGAAATCTGAACAG
1 AAGCTCGAAAGCTAAAAAG
61070075 AAGCTCG
1 AAGCTCG
61070082 TGAGAACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
AAGCTCGAAAGCTAAAAAG
Found at i:61070117 original size:42 final size:43
Alignment explanation
Indices: 61069989--61070182 Score: 192
Period size: 42 Copynumber: 4.7 Consensus size: 43
61069979 CCAGAAAGCT
* *
61069989 GAACAGAAGCTCGTGAGAGCTAAACAGAAACCCATAATG-GTT-
1 GAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAA-GAGTTA
* * * *
61070031 GAACAAAAGCTCG-AA-AGCTAAAAAGAAGCTC-GAA-A-TCT-
1 GAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGT-TA
* * * *
61070069 GAACAGAAGCTCGTGAGAACTTAACAGAAACTCTTAAGAG-TA
1 GAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTA
* *
61070111 GAACAGAAGCTCGTAAGAGCTGAACAAAAACTCATAAGAGTTA
1 GAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTA
61070154 -AACAGAAGCTCGTAAGAGCTAAACAGAAA
1 GAACAGAAGCTCGTAAGAGCTAAACAGAAA
61070183 GTAAAACACG
Statistics
Matches: 123, Mismatches: 20, Indels: 18
0.76 0.12 0.11
Matches are distributed among these distances:
37 1 0.01
38 13 0.11
39 3 0.02
40 25 0.20
41 4 0.03
42 75 0.61
43 2 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (43 bp):
GAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTA
Found at i:61071766 original size:15 final size:15
Alignment explanation
Indices: 61071744--61071784 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
61071734 TTTGGTAACC
61071744 TCGA-ACCACTATTT
1 TCGACACCACTATTT
61071758 TCGACACCACTATTT
1 TCGACACCACTATTT
*
61071773 TTGACACCACTA
1 TCGACACCACTA
61071785 AAAATTGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.32
Consensus pattern (15 bp):
TCGACACCACTATTT
Found at i:61072586 original size:19 final size:19
Alignment explanation
Indices: 61072562--61072598 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
61072552 AAATCTCAAA
61072562 AAAATCTTTGAACAAATTG
1 AAAATCTTTGAACAAATTG
*
61072581 AAAATCTTTGAAGAAATT
1 AAAATCTTTGAACAAATT
61072599 TTGATGAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (19 bp):
AAAATCTTTGAACAAATTG
Found at i:61074897 original size:11 final size:11
Alignment explanation
Indices: 61074873--61074915 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
61074863 TTCTAATACG
*
61074873 TATATATATTA
1 TATATATTTTA
*
61074884 TATGTATTTTA
1 TATATATTTTA
* *
61074895 TATATATTATG
1 TATATATTTTA
61074906 TATATATTTT
1 TATATATTTT
61074916 TAATGCCATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Found at i:61075023 original size:33 final size:34
Alignment explanation
Indices: 61074962--61075026 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
61074952 TGTATGTATT
*
61074962 TTATATCATCTTATGTTTATATTCTTAAATACTA
1 TTATATCATATTATGTTTATATTCTTAAATACTA
* * *
61074996 TTATAT-ATATTATTTTTATTTTTTTAAATAC
1 TTATATCATATTATGTTTATATTCTTAAATAC
61075027 CATGTTGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (34 bp):
TTATATCATATTATGTTTATATTCTTAAATACTA
Found at i:61075048 original size:3 final size:3
Alignment explanation
Indices: 61075040--61075091 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
61075030 GTTGTGTATA
* ** * *
61075040 TAT TAT TAT TACT AAT TAT TAT TAT TGC TAG TAT TAT TAT AAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61075086 TAT TAT
1 TAT TAT
61075092 GTTAGTGTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:61075061 original size:16 final size:15
Alignment explanation
Indices: 61075040--61075079 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
61075030 GTTGTGTATA
*
61075040 TATTATTATTACTAAT
1 TATTATTATTACT-AG
*
61075056 TATTATTATTGCTAG
1 TATTATTATTACTAG
61075071 TATTATTAT
1 TATTATTAT
61075080 AATTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (15 bp):
TATTATTATTACTAG
Found at i:61075214 original size:26 final size:25
Alignment explanation
Indices: 61075185--61075255 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
61075175 TATATTTTAA
*
61075185 TATTGTTATTATTATATCATTACTAT
1 TATTATTATTATTATATCA-TACTAT
*
61075211 TATTTTTTATATATTAT-TCATACTAT
1 TA-TTATTAT-TATTATATCATACTAT
*
61075237 CATTATTA-TATTATTATCA
1 TATTATTATTATTA-TATCA
61075256 CTATTACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 5 0.13
24 1 0.03
25 8 0.21
26 9 0.24
27 9 0.24
28 6 0.16
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (25 bp):
TATTATTATTATTATATCATACTAT
Found at i:61075246 original size:23 final size:26
Alignment explanation
Indices: 61075216--61075275 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 26
61075206 ACTATTATTT
61075216 TTTA-TATATTATTCAT-ACTA-T-CA
1 TTTATTATATTATT-ATCACTATTACA
61075239 -TTATTATATTATTATCACTATTACA
1 TTTATTATATTATTATCACTATTACA
61075264 TTTATTATATTA
1 TTTATTATATTA
61075276 GTATTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 5 0.16
23 13 0.41
24 1 0.03
25 2 0.06
26 11 0.34
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTATTATATTATTATCACTATTACA
Found at i:61075260 original size:17 final size:18
Alignment explanation
Indices: 61075234--61075271 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
61075224 TTATTCATAC
* *
61075234 TATCATTATTATA-TTAT
1 TATCACTATTACATTTAT
61075251 TATCACTATTACATTTAT
1 TATCACTATTACATTTAT
61075269 TAT
1 TAT
61075272 ATTAGTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (18 bp):
TATCACTATTACATTTAT
Found at i:61077329 original size:15 final size:16
Alignment explanation
Indices: 61077309--61077341 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
61077299 TTTTTTTATT
61077309 TTTTAAAAATA-ATAA
1 TTTTAAAAATATATAA
*
61077324 TTTTAAATATATATAA
1 TTTTAAAAATATATAA
61077340 TT
1 TT
61077342 ATTATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAAAAATATATAA
Found at i:61080476 original size:18 final size:18
Alignment explanation
Indices: 61080453--61080495 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
61080443 GAATATATTT
61080453 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
61080471 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
61080489 TTAATTA
1 TTAATTA
61080496 CACCTTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:61082621 original size:169 final size:168
Alignment explanation
Indices: 61082343--61082669 Score: 505
Period size: 169 Copynumber: 1.9 Consensus size: 168
61082333 ATACTTCCTT
* * *
61082343 TCTAATTCATAAATAGAAAAAAATATATTTCAATGCACTCAAACATACGTCCTCCTATATTAATA
1 TCTAATTCATAAATAGAAAAAAATATAATTCAATGCACTCAAACATACATCCTCCTATATTAACA
*
61082408 ATAATAGTCAAACCAATTAAATCAAGACTCAATCGACACTTATTACTTATTTCTTGTTTAAATAG
66 ATAATAGTCAAACCAATTAAATCAAGACTCAATCGACACTTATTACTTATTTCATGTTTAAATAG
61082473 CTATAATCTTTTGCATTTTA-TTTCATAAATAGTTCCGC
131 CTATAATCTTTTGCATTTTACTTT-ATAAATAGTTCCGC
* * * *
61082511 TCTAATTCATAAATAGGAAGATAATGTAATTCAATGCACTCAAACATACATCCTCCTATATTGAC
1 TCTAATTCATAAATA-GAAAAAAATATAATTCAATGCACTCAAACATACATCCTCCTATATTAAC
* * *
61082576 AATAATAGTTATACCAATTAAA-CTAAGATTCAATCGACACTTATTACTTATTTCATGTTTAAAT
65 AATAATAGTCAAACCAATTAAATC-AAGACTCAATCGACACTTATTACTTATTTCATGTTTAAAT
*
61082640 TGCTATAATCTTTTGCATTTTACTTTATAA
129 AGCTATAATCTTTTGCATTTTACTTTATAA
61082670 TTAAATATTT
Statistics
Matches: 144, Mismatches: 12, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
168 16 0.11
169 125 0.87
170 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (168 bp):
TCTAATTCATAAATAGAAAAAAATATAATTCAATGCACTCAAACATACATCCTCCTATATTAACA
ATAATAGTCAAACCAATTAAATCAAGACTCAATCGACACTTATTACTTATTTCATGTTTAAATAG
CTATAATCTTTTGCATTTTACTTTATAAATAGTTCCGC
Found at i:61092831 original size:62 final size:60
Alignment explanation
Indices: 61092750--61092880 Score: 156
Period size: 63 Copynumber: 2.1 Consensus size: 60
61092740 AACAAAAAAA
61092750 GTATCAAATTAGGCC-AAAAAAATTTAGATACCAAATTTAAAAAGAAAAAGTGTCAAATTCAG
1 GTATCAAATTAGGCCAAAAAAAATTTAGATACCAAA-TTAAAAA-AAAAA-TGTCAAATTCAG
* * * * * * *
61092812 GTATTAAATTGGGCTAAAAAAAATTTAGCTACCAAATTAGAAAAAAAATGTCAAGTTCAA
1 GTATCAAATTAGGCCAAAAAAAATTTAGATACCAAATTAAAAAAAAAATGTCAAATTCAG
*
61092872 ATATCAAAT
1 GTATCAAAT
61092881 ATTATATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 17 0.29
61 5 0.08
62 18 0.31
63 19 0.32
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (60 bp):
GTATCAAATTAGGCCAAAAAAAATTTAGATACCAAATTAAAAAAAAAATGTCAAATTCAG
Found at i:61093151 original size:24 final size:24
Alignment explanation
Indices: 61093121--61093172 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
61093111 TTAATATCAC
* *
61093121 AAATAAATCACATTATTTAAT-TAA
1 AAATAAATAACATT-TTAAATCTAA
61093145 AAATAAATAACATTTTAAATCTAA
1 AAATAAATAACATTTTAAATCTAA
61093169 AAAT
1 AAAT
61093173 TTATGTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAAATAACATTTTAAATCTAA
Found at i:61094095 original size:22 final size:20
Alignment explanation
Indices: 61094063--61094103 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
61094053 TTTTAATGAT
*
61094063 TTTTAATTTTTGAAAATAATTA
1 TTTTAAATTTT-AAAA-AATTA
61094085 TTTTAAATTTTAAAAAATT
1 TTTTAAATTTTAAAAAATT
61094104 TAAAATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTAAATTTTAAAAAATTA
Found at i:61094101 original size:23 final size:23
Alignment explanation
Indices: 61094056--61094102 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
61094046 TAAATAATTT
* **
61094056 TAATGATTTTTAATTTTTGAAAA
1 TAATGATTTTAAATTTTAAAAAA
*
61094079 TAATTATTTTAAATTTTAAAAAA
1 TAATGATTTTAAATTTTAAAAAA
61094102 T
1 T
61094103 TTAAAATGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TAATGATTTTAAATTTTAAAAAA
Found at i:61095172 original size:21 final size:21
Alignment explanation
Indices: 61095148--61095189 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
61095138 ATATTAGAAT
61095148 AAAATTAAT-ATTTATGGTTTA
1 AAAATT-ATCATTTATGGTTTA
*
61095169 AAAATTATCATTTATTGTTTA
1 AAAATTATCATTTATGGTTTA
61095190 TTAAACTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (21 bp):
AAAATTATCATTTATGGTTTA
Found at i:61096787 original size:31 final size:31
Alignment explanation
Indices: 61096752--61096813 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
61096742 CGATTGTGGC
61096752 AATTTGTGTGTCTTATTGAAGTG-TTGTAGTA
1 AATTTGTGTGTCTTATTGAAG-GCTTGTAGTA
* * *
61096783 AATTTTTGTGTTTTGTTGAAGGCTTGTAGTA
1 AATTTGTGTGTCTTATTGAAGGCTTGTAGTA
61096814 GTTTTGTAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.50
Consensus pattern (31 bp):
AATTTGTGTGTCTTATTGAAGGCTTGTAGTA
Found at i:61111936 original size:22 final size:23
Alignment explanation
Indices: 61111908--61111962 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
61111898 TATGATTTGT
*
61111908 ATATTTAAATTAAGTCT-TACAA
1 ATATTTAAATTAAGTATGTACAA
* *
61111930 ATATTTATATTAATTATGTACAA
1 ATATTTAAATTAAGTATGTACAA
61111953 AGTATTTAAA
1 A-TATTTAAA
61111963 ATTATATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 14 0.52
23 6 0.22
24 7 0.26
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (23 bp):
ATATTTAAATTAAGTATGTACAA
Found at i:61112175 original size:9 final size:10
Alignment explanation
Indices: 61112149--61112201 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
61112139 AATAAATTAT
*
61112149 TTTTAATATT
1 TTTTAATATA
61112159 TTTATAATA-A
1 TTT-TAATATA
*
61112169 TTTTAATTTA
1 TTTTAATATA
61112179 TATTTAATATA
1 T-TTTAATATA
*
61112190 TTATAATATA
1 TTTTAATATA
61112200 TT
1 TT
61112202 AAAAAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 4 0.11
10 18 0.50
11 14 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTAATATA
Found at i:61113200 original size:14 final size:14
Alignment explanation
Indices: 61113181--61113207 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
61113171 TAAACAATAA
61113181 CAACATAATAGTAG
1 CAACATAATAGTAG
61113195 CAACATAATAGTA
1 CAACATAATAGTA
61113208 AAATGGTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
CAACATAATAGTAG
Found at i:61115540 original size:32 final size:32
Alignment explanation
Indices: 61115499--61115560 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
61115489 GATAATTAAA
61115499 TGTCGATTGACTCAATATTAATTCTACAACCC
1 TGTCGATTGACTCAATATTAATTCTACAACCC
61115531 TGTCGATTGACTCAATATTAATTCTACAAC
1 TGTCGATTGACTCAATATTAATTCTACAAC
61115561 TCTTCGACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (32 bp):
TGTCGATTGACTCAATATTAATTCTACAACCC
Found at i:61116981 original size:34 final size:34
Alignment explanation
Indices: 61116936--61117010 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
61116926 CAGTATCAAA
61116936 TATGCAGTAGGGCCTTAGCCCATCACAGTATTAG
1 TATGCAGTAGGGCCTTAGCCCATCACAGTATTAG
*
61116970 TATGCATTAGGGCCTTAGCCCATCACAGTATTAG
1 TATGCAGTAGGGCCTTAGCCCATCACAGTATTAG
61117004 TA-GCAGT
1 TATGCAGT
61117011 CATGCAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 4 0.10
34 35 0.90
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (34 bp):
TATGCAGTAGGGCCTTAGCCCATCACAGTATTAG
Found at i:61119068 original size:16 final size:17
Alignment explanation
Indices: 61119036--61119070 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
61119026 ATTAAACAAG
*
61119036 AATTTTACAATATTTAT
1 AATTTTACAACATTTAT
61119053 AATTTTA-AACATTTAT
1 AATTTTACAACATTTAT
61119069 AA
1 AA
61119071 CAAAAATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTTACAACATTTAT
Found at i:61119664 original size:15 final size:15
Alignment explanation
Indices: 61119644--61119677 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
61119634 CATATACTCA
61119644 TAATTCAATTCAATT
1 TAATTCAATTCAATT
61119659 TAATTCAATTCAATT
1 TAATTCAATTCAATT
61119674 TAAT
1 TAAT
61119678 ACCAATACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTCAATTCAATT
Found at i:61119979 original size:20 final size:20
Alignment explanation
Indices: 61119939--61119979 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
61119929 AGTCCTTAAA
** *
61119939 TCCAAACTAATTCTTTTTCT
1 TCCAAACTAATTCCATATCT
61119959 TCCAAACTAATTCCATATCT
1 TCCAAACTAATTCCATATCT
61119979 T
1 T
61119980 ATCCAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (20 bp):
TCCAAACTAATTCCATATCT
Found at i:61126537 original size:63 final size:63
Alignment explanation
Indices: 61126438--61126560 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 63
61126428 GGAATCGGCT
*
61126438 CTGGATGCTGATTCAACAATCTCACTTTGATCTAACCTGCGCACAAAAACAAACCGTACGCTG
1 CTGGATGCTGATTCAACAATCTCACTTTGACCTAACCTGCGCACAAAAACAAACCGTACGCTG
* * ***
61126501 CTGGATGTTGATTCAACAATCTGACTTTGACCTAACCTGCGCATGGAAACAAACCGTACG
1 CTGGATGCTGATTCAACAATCTCACTTTGACCTAACCTGCGCACAAAAACAAACCGTACG
61126561 TTAAGTATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (63 bp):
CTGGATGCTGATTCAACAATCTCACTTTGACCTAACCTGCGCACAAAAACAAACCGTACGCTG
Found at i:61126644 original size:16 final size:17
Alignment explanation
Indices: 61126612--61126646 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
61126602 ATTAAACAAG
*
61126612 AATTTTACAATATTTAT
1 AATTTTACAACATTTAT
61126629 AATTTTA-AACATTTAT
1 AATTTTACAACATTTAT
61126645 AA
1 AA
61126647 CAAAAATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTTACAACATTTAT
Found at i:61143635 original size:43 final size:43
Alignment explanation
Indices: 61143588--61143687 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 43
61143578 CCGCAAATGA
* *
61143588 TCATGACTTTTAGCGGCGTTTATGGGAAAA--TTGCTGCTAAAAG
1 TCATGGCTTTTAGCGACGTTTATGGGAAAAGCTT-C-GCTAAAAG
* *
61143631 TCATGGCTTTTAGCGACGTTTGTGGGAGAAGCTTCGCTAAAAG
1 TCATGGCTTTTAGCGACGTTTATGGGAAAAGCTTCGCTAAAAG
*
61143674 TCGTGGCTTTTAGC
1 TCATGGCTTTTAGC
61143688 AGTGCTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
43 47 0.94
44 1 0.02
45 2 0.04
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (43 bp):
TCATGGCTTTTAGCGACGTTTATGGGAAAAGCTTCGCTAAAAG
Found at i:61143887 original size:33 final size:31
Alignment explanation
Indices: 61143804--61143889 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
61143794 AACCCTTCCT
* * *
61143804 GCATTAAATGCAACCAAAAACAGCAAATATG
1 GCATAAAATACAACCAAAAACAGCAAATATA
* * *
61143835 GCATGAAATCCAACCAAAAACAGCAAATGTA
1 GCATAAAATACAACCAAAAACAGCAAATATA
61143866 GCATAAAAAATACAACCAAAAACA
1 GCAT--AAAATACAACCAAAAACA
61143890 TTAAATCTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 31 0.66
33 16 0.34
ACGTcount: A:0.56, C:0.21, G:0.10, T:0.13
Consensus pattern (31 bp):
GCATAAAATACAACCAAAAACAGCAAATATA
Found at i:61146122 original size:21 final size:21
Alignment explanation
Indices: 61146098--61146140 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
61146088 GCATAACTTG
61146098 TAATTGAAGAATTAACAACTA
1 TAATTGAAGAATTAACAACTA
61146119 TAATTGAAGAATTAACAACTA
1 TAATTGAAGAATTAACAACTA
61146140 T
1 T
61146141 TCCACAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (21 bp):
TAATTGAAGAATTAACAACTA
Found at i:61147659 original size:12 final size:12
Alignment explanation
Indices: 61147644--61147669 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61147634 ATCATCCTCT
61147644 TCATCAGATTCA
1 TCATCAGATTCA
61147656 TCATCAGATTCA
1 TCATCAGATTCA
61147668 TC
1 TC
61147670 CCTCGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:61149403 original size:9 final size:9
Alignment explanation
Indices: 61149389--61149503 Score: 59
Period size: 9 Copynumber: 13.7 Consensus size: 9
61149379 TAAGTATAAT
61149389 TAAGTTATG
1 TAAGTTATG
61149398 TAAGTTATG
1 TAAGTTATG
* * *
61149407 ATATGATATA
1 -TAAGTTATG
*
61149417 T-ATTTATG
1 TAAGTTATG
*
61149425 TAAATTATG
1 TAAGTTATG
61149434 TAAGTTATG
1 TAAGTTATG
*
61149443 -AAATT-TG
1 TAAGTTATG
61149450 -AA--TAT-
1 TAAGTTATG
* *
61149455 TAAATTATA
1 TAAGTTATG
61149464 TAAGTTATG
1 TAAGTTATG
61149473 T-A-TTATG
1 TAAGTTATG
*
61149480 TAAATTATG
1 TAAGTTATG
*
61149489 TAAATTATG
1 TAAGTTATG
*
61149498 TGAGTT
1 TAAGTT
61149504 GCTGGTGAAC
Statistics
Matches: 83, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 10 0.12
8 13 0.16
9 50 0.60
10 6 0.07
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:61149496 original size:25 final size:25
Alignment explanation
Indices: 61149428--61149498 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
61149418 ATTTATGTAA
*
61149428 ATTATGTAAGTTATG-AAATT-TG-
1 ATTATGTAAATTATGTAAATTATGT
* * *
61149450 AATAT-TAAATTATATAAGTTATGT
1 ATTATGTAAATTATGTAAATTATGT
61149474 ATTATGTAAATTATGTAAATTATGT
1 ATTATGTAAATTATGTAAATTATGT
61149499 GAGTTGCTGG
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 7 0.18
22 8 0.21
23 2 0.05
24 4 0.11
25 17 0.45
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (25 bp):
ATTATGTAAATTATGTAAATTATGT
Found at i:61154907 original size:14 final size:14
Alignment explanation
Indices: 61154888--61154932 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
61154878 CCAAAATTAT
61154888 ACCCTAAACCTTAA
1 ACCCTAAACCTTAA
* *
61154902 ACCCTAAATCTTGA
1 ACCCTAAACCTTAA
**
61154916 ATTCTAAACCTTAA
1 ACCCTAAACCTTAA
61154930 ACC
1 ACC
61154933 ACAAAACACC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.40, C:0.31, G:0.02, T:0.27
Consensus pattern (14 bp):
ACCCTAAACCTTAA
Found at i:61155482 original size:27 final size:29
Alignment explanation
Indices: 61155429--61155484 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 29
61155419 AGACCCTAAT
61155429 CTCTAAAACAATAAACCCCAAAACCCAAA
1 CTCTAAAACAATAAACCCCAAAACCCAAA
*
61155458 CTCTAAAAC-ATAAA-CCCATAACCCAAA
1 CTCTAAAACAATAAACCCCAAAACCCAAA
61155485 ATAATAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 12 0.46
28 5 0.19
29 9 0.35
ACGTcount: A:0.54, C:0.34, G:0.00, T:0.12
Consensus pattern (29 bp):
CTCTAAAACAATAAACCCCAAAACCCAAA
Found at i:61155492 original size:28 final size:29
Alignment explanation
Indices: 61155432--61155492 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 29
61155422 CCCTAATCTC
* *
61155432 TAAAACAATAAACCCCAAAACCCAAACTC
1 TAAAACAATAAACCCCAAAACCCAAAATA
*
61155461 TAAAAC-ATAAA-CCCATAACCCAAAATAA
1 TAAAACAATAAACCCCAAAACCCAAAAT-A
61155489 TAAA
1 TAAA
61155493 CATTATATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.46
28 9 0.32
29 6 0.21
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.13
Consensus pattern (29 bp):
TAAAACAATAAACCCCAAAACCCAAAATA
Found at i:61162789 original size:5 final size:5
Alignment explanation
Indices: 61162779--61162807 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
61162769 TGATTTCCAA
61162779 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
61162808 ATCTACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Done.