Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1747
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: 62252
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:524 original size:31 final size:33
Alignment explanation
Indices: 459--526 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 33
449 GCCATTTGGG
*
459 ACAATGTATCGATACAATTTCTCATGTATCGAT
1 ACAATGTATCGATACAATTGCTCATGTATCGAT
*
492 ACAATGTATCGA-A-AATATGC-CATGTATTGAT
1 ACAATGTATCGATACAAT-TGCTCATGTATCGAT
523 ACAA
1 ACAA
527 ATAGTGGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 17 0.53
32 3 0.09
33 12 0.38
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (33 bp):
ACAATGTATCGATACAATTGCTCATGTATCGAT
Found at i:1762 original size:50 final size:50
Alignment explanation
Indices: 1690--1839 Score: 219
Period size: 50 Copynumber: 2.9 Consensus size: 50
1680 CTAGATTACA
* * *
1690 TACATTGAAGAATGGTATCGATACATTGGGTCAAAACCCAGAATGTATAAT
1 TACAATGAAGAAT-GTATCGATACATTTGGACAAAACCCAGAATGTATAAT
* *
1741 TACAATGAAGAATGTATCGATACATTTGGACAAAACCTAGAATGTATCAT
1 TACAATGAAGAATGTATCGATACATTTGGACAAAACCCAGAATGTATAAT
*
1791 TACAATGAAGAATGTATCGATATATTTTGGACAAAAACCCAGAATGTAT
1 TACAATGAAGAATGTATCGATACA-TTTGGAC-AAAACCCAGAATGTAT
1840 CAATACATTT
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
50 56 0.62
51 19 0.21
52 15 0.17
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (50 bp):
TACAATGAAGAATGTATCGATACATTTGGACAAAACCCAGAATGTATAAT
Found at i:2270 original size:38 final size:40
Alignment explanation
Indices: 2190--2292 Score: 129
Period size: 39 Copynumber: 2.6 Consensus size: 40
2180 CAAAACTAAT
* * ** *
2190 AAGTCAACAAGTTAAAAAGGTTGACCAAGATGAAATTTAC
1 AAGTAAACAAGTTAAAGAGGTTGATAAAGATGAAATTGAC
*
2230 AAGTAAATAAGTT-AAGAGGTTGATAAAGA-GAAATTGAC
1 AAGTAAACAAGTTAAAGAGGTTGATAAAGATGAAATTGAC
*
2268 AAGTCAACAAGTTAAAGAGGTTGAT
1 AAGTAAACAAGTTAAAGAGGTTGAT
2293 TGGGATGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 19 0.35
39 24 0.44
40 11 0.20
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (40 bp):
AAGTAAACAAGTTAAAGAGGTTGATAAAGATGAAATTGAC
Found at i:2286 original size:39 final size:40
Alignment explanation
Indices: 2190--2317 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
2180 CAAAACTAAT
* ** *
2190 AAGTCAACAAGTTAAAAAGGTTGACCAAGATGAAATTTAC
1 AAGTCAACAAGTTAAAGAGGTTGATAAAGATGAAATTGAC
* *
2230 AAGTAAATAAGTT-AAGAGGTTGATAAAGA-GAAATTGAC
1 AAGTCAACAAGTTAAAGAGGTTGATAAAGATGAAATTGAC
*** *
2268 AAGTCAACAAGTTAAAGAGGTTGATTGGGATGAAATCGAC
1 AAGTCAACAAGTTAAAGAGGTTGATAAAGATGAAATTGAC
*
2308 ATGTCAACAA
1 AAGTCAACAA
2318 AGAGTTTAAG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
38 19 0.26
39 26 0.36
40 28 0.38
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (40 bp):
AAGTCAACAAGTTAAAGAGGTTGATAAAGATGAAATTGAC
Found at i:2494 original size:105 final size:105
Alignment explanation
Indices: 2268--2525 Score: 288
Period size: 105 Copynumber: 2.4 Consensus size: 105
2258 AGAAATTGAC
* * * *
2268 AAGTCAACAAGTTAAAGAGGTTGATTGGGATGAAATCGACATGTCAACAAAGAGTTTAAGAGGGT
1 AAGTCAACAAGTTAAAAAGGTTGACTGGGATGAAAT-GACAAGTCAACAAAGAGTTGAAGAGGGT
* * * **
2333 AAAATCCAAGTCAGAATAGGGTTGACTAAGGTGAAACCAAT
65 AAAACCCAAGTCAGAAAAAGGTTGACTAAGGCAAAACCAAT
* * * * *
2374 AAGTCAACAACTTAAAAAGGTTAAGTGGGATGAAACTGACAAGTCAACAAAGAG-TGACTG-GTG
1 AAGTCAACAAGTTAAAAAGGTTGACTGGGATGAAA-TGACAAGTCAACAAAGAGTTGA-AGAGGG
* **
2437 TAAAACCCATG-CTAGAAAAAGGTTGACTAAGGCAAAACTGAT
64 TAAAACCCAAGTC-AGAAAAAGGTTGACTAAGGCAAAACCAAT
*
2479 AAGTTAACAAGTTAAAAAGGTTGACTGGGATGAAATTGACAAGTCAA
1 AAGTCAACAAGTTAAAAAGGTTGACTGGGATGAAA-TGACAAGTCAA
2526 TAAGTTAAAA
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
104 1 0.01
105 78 0.61
106 48 0.38
107 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (105 bp):
AAGTCAACAAGTTAAAAAGGTTGACTGGGATGAAATGACAAGTCAACAAAGAGTTGAAGAGGGTA
AAACCCAAGTCAGAAAAAGGTTGACTAAGGCAAAACCAAT
Found at i:3218 original size:40 final size:40
Alignment explanation
Indices: 3132--3221 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
3122 TAAAACTGAT
* *
3132 AAGTCAACAAGTTAAAGAGGTTAACCAGGATGAAATCAAT
1 AAGTCAACAAGTTAAAGAGGTTAACCAAGATGAAATCAAC
* * * **
3172 AGGTCAACAAGTTAAAGAGGTTGACTAAGATGAAATTGAC
1 AAGTCAACAAGTTAAAGAGGTTAACCAAGATGAAATCAAC
3212 AAGTCAACAA
1 AAGTCAACAA
3222 AGAGTGACTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.20
Consensus pattern (40 bp):
AAGTCAACAAGTTAAAGAGGTTAACCAAGATGAAATCAAC
Found at i:7177 original size:83 final size:83
Alignment explanation
Indices: 7023--7179 Score: 183
Period size: 83 Copynumber: 1.9 Consensus size: 83
7013 AAATAGTTTG
* ** * * *
7023 ACCAGGTCCTAACGCCAATATAATCAAACGAAGGTGGAAAGAGTTTGATTAGTATTAATGCTAAT
1 ACCAGGTCCTAACGCCAATATAATCAAACGAAGGTGGAAAAAGTTTGACAAGTACTAACGCCAAT
7088 ACAGCCAAACAAAGGAAA
66 ACAGCCAAACAAAGGAAA
* * * *
7106 ACCAGGTCTTAATGCCAATATAGTCAAACGAGGGT-GAAAAACGTTTGACCAAG-ACTAACGCCA
1 ACCAGGTCCTAACGCCAATATAATCAAACGAAGGTGGAAAAA-GTTTGA-CAAGTACTAACGCCA
*
7169 ATATAGCCAAA
64 ATACAGCCAAA
7180 TGAAGAAAGA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
82 5 0.08
83 54 0.89
84 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (83 bp):
ACCAGGTCCTAACGCCAATATAATCAAACGAAGGTGGAAAAAGTTTGACAAGTACTAACGCCAAT
ACAGCCAAACAAAGGAAA
Found at i:8518 original size:18 final size:18
Alignment explanation
Indices: 8495--8531 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
8485 GTTATAACAT
8495 CCTTTTAATCTTTGAATA
1 CCTTTTAATCTTTGAATA
8513 CCTTTTAATCTTTGAATA
1 CCTTTTAATCTTTGAATA
8531 C
1 C
8532 AATAGCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (18 bp):
CCTTTTAATCTTTGAATA
Found at i:9327 original size:13 final size:14
Alignment explanation
Indices: 9311--9352 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
9301 TTTCATTCTT
9311 TTCTTTTT-TTTTC
1 TTCTTTTTCTTTTC
9324 TTCTTTTTCTTTT-
1 TTCTTTTTCTTTTC
9337 TTCCATTTTTCTTTTC
1 TT-C-TTTTTCTTTTC
9353 ACAAAGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.40
14 5 0.20
15 10 0.40
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:9327 original size:18 final size:20
Alignment explanation
Indices: 9301--9338 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
9291 TTTTAATTCC
9301 TTTCATTC-TTTTCTTTTTT
1 TTTCATTCTTTTTCTTTTTT
9320 TTTC-TTCTTTTTCTTTTTT
1 TTTCATTCTTTTTCTTTTTT
9339 CCATTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTCATTCTTTTTCTTTTTT
Found at i:11275 original size:13 final size:13
Alignment explanation
Indices: 11234--11282 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
11224 CGTTACAAGC
11234 CAATGTATCGATA
1 CAATGTATCGATA
*
11247 CAAT-T-T-GGT-
1 CAATGTATCGATA
11256 C-ATGTATCGATA
1 CAATGTATCGATA
11268 CAATGTATCGATA
1 CAATGTATCGATA
11281 CA
1 CA
11283 TCTTGTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 3 0.10
11 3 0.10
12 2 0.07
13 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:11277 original size:34 final size:32
Alignment explanation
Indices: 11234--11302 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
11224 CGTTACAAGC
11234 CAATGTATCGATACAAT-TTGGTCATGTATCGATA
1 CAATGTATCGATAC-ATCTT-GT-ATGTATCGATA
11268 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
11300 CAA
1 CAA
11303 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 14 0.41
33 4 0.12
34 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:11400 original size:13 final size:13
Alignment explanation
Indices: 11382--11406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11372 TACAGTGGTC
11382 ATGTATCGATACA
1 ATGTATCGATACA
11395 ATGTATCGATAC
1 ATGTATCGATAC
11407 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:12116 original size:94 final size:92
Alignment explanation
Indices: 11948--12135 Score: 317
Period size: 94 Copynumber: 2.0 Consensus size: 92
11938 AAGATTTTTC
*
11948 ATTTTCCTTTTCTCTCCCCCTTAATCAAATAAAAAATTTCTCCTTCTTAATAAAACAATTTCCTT
1 ATTTTCCTTTTCTCTCCCCCTTAATCAAATAAAAAATTTCTCCTCCTTAATAAAACAATTTCCTT
12013 TAATCACATGTTTCTTTTTCCCCCTTA
66 TAATCACATGTTTCTTTTTCCCCCTTA
12040 ATTTTCCTTTTCTCTCCCCCTTAATCAAATAAAAAAAAAATTTC-CC-CCTTAATAAAACAATTT
1 ATTTTCCTTTTCTCTCCCCCTTAATCAAAT----AAAAAATTTCTCCTCCTTAATAAAACAATTT
12103 CCTTTAATCACATGTTTCTTTTTCCCCCTTA
62 CCTTTAATCACATGTTTCTTTTTCCCCCTTA
12134 AT
1 AT
12136 CATAAATTTA
Statistics
Matches: 91, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
92 30 0.33
94 49 0.54
95 2 0.02
96 10 0.11
ACGTcount: A:0.29, C:0.27, G:0.01, T:0.43
Consensus pattern (92 bp):
ATTTTCCTTTTCTCTCCCCCTTAATCAAATAAAAAATTTCTCCTCCTTAATAAAACAATTTCCTT
TAATCACATGTTTCTTTTTCCCCCTTA
Found at i:13499 original size:20 final size:20
Alignment explanation
Indices: 13474--13547 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
13464 CTGCCCGGTT
13474 GCGACCTGGGAGTACCGATC
1 GCGACCTGGGAGTACCGATC
13494 GCGACCTGGGAGTACCGATC
1 GCGACCTGGGAGTACCGATC
* *
13514 GCGACCTGGGAGTGCCGGTC
1 GCGACCTGGGAGTACCGATC
*
13534 GTGACCTGGTGAGT
1 GCGACCTGG-GAGT
13548 GCTGCCTAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
20 46 0.92
21 4 0.08
ACGTcount: A:0.16, C:0.27, G:0.39, T:0.18
Consensus pattern (20 bp):
GCGACCTGGGAGTACCGATC
Found at i:20152 original size:13 final size:13
Alignment explanation
Indices: 20111--20159 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
20101 CGTTACAAGC
20111 CAATGTATCGATA
1 CAATGTATCGATA
*
20124 CAAT-T-T-GGT-
1 CAATGTATCGATA
20133 C-ATGTATCGATA
1 CAATGTATCGATA
20145 CAATGTATCGATA
1 CAATGTATCGATA
20158 CA
1 CA
20160 TCTTGTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 3 0.10
11 3 0.10
12 2 0.07
13 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:20154 original size:34 final size:32
Alignment explanation
Indices: 20111--20179 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
20101 CGTTACAAGC
20111 CAATGTATCGATACAAT-TTGGTCATGTATCGATA
1 CAATGTATCGATAC-ATCTT-GT-ATGTATCGATA
20145 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
20177 CAA
1 CAA
20180 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 14 0.41
33 4 0.12
34 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:24343 original size:13 final size:13
Alignment explanation
Indices: 24325--24350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24315 CAATTTTTTG
24325 TGTATCGATACAT
1 TGTATCGATACAT
24338 TGTATCGATACAT
1 TGTATCGATACAT
24351 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:26895 original size:13 final size:13
Alignment explanation
Indices: 26877--26914 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
26867 ATAATCACCT
26877 TGTATCGATACAG
1 TGTATCGATACAG
*
26890 TGTATCGATACAT
1 TGTATCGATACAG
26903 TGTATCGATACA
1 TGTATCGATACA
26915 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:28997 original size:15 final size:15
Alignment explanation
Indices: 28977--29007 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28967 ATTTCGTTTG
*
28977 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
28992 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
29007 G
1 G
29008 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:30838 original size:21 final size:21
Alignment explanation
Indices: 30809--30853 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
30799 AAGTTTTTAT
*
30809 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
30829 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
30851 TTT
1 TTT
30854 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:36291 original size:11 final size:11
Alignment explanation
Indices: 36275--36314 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
36265 TTAATTTTTC
36275 TTTTTCTCTCT
1 TTTTTCTCTCT
*
36286 TTTTTCTTTCTTT
1 TTTTTC--TCTCT
36299 TTTTTCTCTCT
1 TTTTTCTCTCT
36310 TTTTT
1 TTTTT
36315 TTCTACTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 15 0.60
13 10 0.40
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCTCTCT
Found at i:36303 original size:13 final size:13
Alignment explanation
Indices: 36275--36318 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
36265 TTAATTTTTC
36275 TTTTTCTCTC--T
1 TTTTTCTCTCTTT
*
36286 TTTTTCTTTCTTT
1 TTTTTCTCTCTTT
36299 TTTTTCTCTCTTT
1 TTTTTCTCTCTTT
36312 TTTTTCT
1 TTTTTCT
36319 ACTTGCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 9 0.31
13 20 0.69
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTCTCTTT
Found at i:36680 original size:13 final size:13
Alignment explanation
Indices: 36640--36681 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 13
36630 TAGAAAAAAT
36640 AAATAAAATTAAA
1 AAATAAAATTAAA
36653 TTAAATAAAATTAAA
1 --AAATAAAATTAAA
36668 AAATCAAAA-TAAA
1 AAAT-AAAATTAAA
36681 A
1 A
36682 TTATAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.35
14 4 0.15
15 13 0.50
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAATTAAA
Found at i:37500 original size:166 final size:164
Alignment explanation
Indices: 36883--37500 Score: 570
Period size: 167 Copynumber: 3.7 Consensus size: 164
36873 AGAATATTAT
* ** * * * * **
36883 ATGAATTTTAAAAATTTTAAACTGAGAAAAAT-CTCCATAAAACATTTACGGAGTAGAAAACTTG
1 ATGAATTTTAAAAATTAT-AACCAATAAAAATCCCCCA-AAAATATTTACGGAGTAGCAAACTCC
* * * *
36947 GTTTTTCGAAAATA-AGAGAATTTCAAAGAAAAAATGAAAAACTTATGAAAATAAATAAATTTTT
64 ATATTTCAAAAATAGGGA-AATTTCAAAGAAAAAATGAAAAACTTATGAAAATAAATAAATTTTT
* * * * *
37011 CAAAACTAATTTACTATGAATTAAATTATGATGTTTA
128 TAAAACAAATTTACTATGAATTAAATAATGATATTTG
* *
37048 ATGAATTTTAAAAATTATAAACCAAGAAAAATCCCCCCAAAAATATTTACGGAGTAGCAAATTCC
1 ATGAATTTTAAAAATTAT-AACCAATAAAAAT-CCCCCAAAAATATTTACGGAGTAGCAAACTCC
* * ** * ** **
37113 ATATTTGAGAAACCGGGGAA-TTCTAAA-AAAAAGAACAAAAAGCTTACAAAAATAAATAAATTT
64 ATATTTCAAAAATAGGGAAATTTC-AAAGAAAAA-ATGAAAAA-CTTATGAAAATAAATAAATTT
37176 TTTAAAA-ATAATTTACTATGAATTAAATAATGATATTTG
126 TTTAAAACA-AATTTACTATGAATTAAATAATGATATTTG
* * * * * *
37215 GTGAATATTAAAAATTTTGAACCTATAAAAA-CCCCTTCAAAAATATTTACAGAATAGCAAACTC
1 ATGAATTTTAAAAATTAT-AACCAATAAAAATCCCC--CAAAAATATTTACGGAGTAGCAAACTC
* * *
37279 CATATTTCGAAAATAGGGAGATTTCAAAGAAAAAATGAAAAACTTATGAAAATAAATGAATTTTT
63 CATATTTCAAAAATAGGGAAATTTCAAAGAAAAAATGAAAAACTTATGAAAATAAATAAATTTTT
* *
37344 TAAAACAAATTTACCATGAATTAAATGATGATATTTG
128 TAAAACAAATTTACTATGAATTAAATAATGATATTTG
* * * * *
37381 ATGATTTTTAGAAATTATAAGCCAATAAAAATCCCCCAAAAAACATTTACGGAGCTTTGC-TACT
1 ATGAATTTTAAAAATTATAA-CCAATAAAAATCCCCC-AAAAATATTTACGGAG--TAGCAAACT
* ** * *
37445 CCGTATTTCAAAAATAGAAAAATTTTAAGGAAAAAATGAAAAA-TTCATG-AAATAAA
62 CCATATTTCAAAAATAGGGAAATTTCAAAGAAAAAATGAAAAACTT-ATGAAAATAAA
37501 AGGAAATTGT
Statistics
Matches: 367, Mismatches: 68, Indels: 35
0.78 0.14 0.07
Matches are distributed among these distances:
165 44 0.12
166 136 0.37
167 176 0.48
168 11 0.03
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (164 bp):
ATGAATTTTAAAAATTATAACCAATAAAAATCCCCCAAAAATATTTACGGAGTAGCAAACTCCAT
ATTTCAAAAATAGGGAAATTTCAAAGAAAAAATGAAAAACTTATGAAAATAAATAAATTTTTTAA
AACAAATTTACTATGAATTAAATAATGATATTTG
Found at i:40137 original size:97 final size:97
Alignment explanation
Indices: 39937--40134 Score: 256
Period size: 97 Copynumber: 2.1 Consensus size: 97
39927 CAACGATGAT
* * *
39937 AATTTAGGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATAGAGTTAGAGTATCCCCTCGG
1 AATTTAAGCAAAAATAAGATTTAAATCTTGACAAATTTAAAAACAGAGTTAGAGTATCCCCTCGG
* * **
40002 AAGAATGGAGTTTAAGTTTCTCCGATGCTAAC
66 AAGAATGGAGTTGAAGTATCTCCGATAATAAC
* * *
40034 AATTTAAGCAAAAGTAAGATTTAAATCTTGACAAATTTAAAAACAGGGTTGGAGTATCCCCTCGG
1 AATTTAAGCAAAAATAAGATTTAAATCTTGACAAATTTAAAAACAGAGTTAGAGTATCCCCTCGG
* * *
40099 AAGAATGGGGTTGGAGTATC-CTGATAAATAA-
66 AAGAATGGAGTTGAAGTATCTCCGAT-AATAAC
40130 AATTT
1 AATTT
40135 TAATTTTTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
96 9 0.10
97 78 0.90
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (97 bp):
AATTTAAGCAAAAATAAGATTTAAATCTTGACAAATTTAAAAACAGAGTTAGAGTATCCCCTCGG
AAGAATGGAGTTGAAGTATCTCCGATAATAAC
Found at i:42832 original size:20 final size:21
Alignment explanation
Indices: 42807--42856 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
42797 CAACAACGTA
*
42807 TATCGATACAATAAG-GTATG
1 TATCGATACAATAAGTGAATG
*
42827 TATCGATA-TATAAGTGAATG
1 TATCGATACAATAAGTGAATG
*
42847 TATCAATACA
1 TATCGATACA
42857 TGCTTGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (21 bp):
TATCGATACAATAAGTGAATG
Found at i:42974 original size:52 final size:52
Alignment explanation
Indices: 42913--43049 Score: 190
Period size: 52 Copynumber: 2.7 Consensus size: 52
42903 TCTAGAAAGA
* *
42913 AAATGTATCAATATATTTTTCATTGTATCGATACATTTTGGGTTTTTGACCC
1 AAATGTATCAATATATTTTTCATTGTATCGATACATTTTAGGTTTTGGACCC
*
42965 AAATGTATCAATACT-TTTTTCATTGTATCGATATATTTTAGGTTTTGGACCC
1 AAATGTATCAATA-TATTTTTCATTGTATCGATACATTTTAGGTTTTGGACCC
* * *
43017 AAAT-TATCGATA-ATTCTTCAATGTATCGATACA
1 AAATGTATCAATATATTTTTCATTGTATCGATACA
43050 AATAAGTAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
50 17 0.22
51 7 0.09
52 51 0.67
53 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (52 bp):
AAATGTATCAATATATTTTTCATTGTATCGATACATTTTAGGTTTTGGACCC
Found at i:57835 original size:21 final size:21
Alignment explanation
Indices: 57806--57846 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
57796 AAAGGTCACA
57806 ACCCTAGAAAGTATCGATACAG
1 ACCCTAG-AAGTATCGATACAG
57828 ACCC-AGAAGTATCGATACA
1 ACCCTAGAAGTATCGATACA
57847 TATTGCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 2 0.11
22 4 0.21
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (21 bp):
ACCCTAGAAGTATCGATACAG
Found at i:58725 original size:1 final size:1
Alignment explanation
Indices: 58719--58768 Score: 73
Period size: 1 Copynumber: 50.0 Consensus size: 1
58709 AAAGTGTTTG
***
58719 AAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
58769 TTTAAATGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.94, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:58741 original size:20 final size:20
Alignment explanation
Indices: 58716--58768 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
58706 GATAAAGTGT
58716 TTGAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAA
58736 TTGAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAA
58756 ---AAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
58769 TTTAAATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.39
20 20 0.61
ACGTcount: A:0.89, C:0.00, G:0.04, T:0.08
Consensus pattern (20 bp):
TTGAAAAAAAAAAAAAAAAA
Found at i:58797 original size:21 final size:21
Alignment explanation
Indices: 58773--58829 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
58763 AAAAAATTTA
58773 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
58794 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
58815 AATGTATCGATACAT
1 AATGTATCGATACAT
58830 CCTACAAATG
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:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:58909 original size:19 final size:19
Alignment explanation
Indices: 58885--58952 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
58875 AATTCAACAA
58885 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
58904 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
58919 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
58936 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
58953 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:58924 original size:13 final size:13
Alignment explanation
Indices: 58906--58930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58896 ACATAAGTTT
58906 TGTATCGATACAA
1 TGTATCGATACAA
58919 TGTATCGATACA
1 TGTATCGATACA
58931 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:58928 original size:32 final size:32
Alignment explanation
Indices: 58887--58949 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
58877 TTCAACAATT
*
58887 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
58919 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
58950 TAATTAGCTA
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:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:59010 original size:13 final size:13
Alignment explanation
Indices: 58992--59017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58982 CATTTTTCTG
58992 TGTATCGATACAT
1 TGTATCGATACAT
59005 TGTATCGATACAT
1 TGTATCGATACAT
59018 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:59014 original size:33 final size:33
Alignment explanation
Indices: 58972--59038 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
58962 GCCAAGGAAA
***
58972 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
59005 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
59038 T
1 T
59039 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:61676 original size:28 final size:30
Alignment explanation
Indices: 61640--61712 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 30
61630 ATTTTTCACA
* *
61640 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
61668 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
61698 A--GGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
61713 TCTGGTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:61754 original size:212 final size:213
Alignment explanation
Indices: 61372--61784 Score: 722
Period size: 212 Copynumber: 1.9 Consensus size: 213
61362 AATTCTCCAC
* *
61372 AATCGAGGATATTCCAACTCCGATTTTATTTCCAAAAAAAATACCAATTTCTTCACAATCGGGGA
1 AATCGAGGATACTCCAACTCCGATTTTATTTCC--AAAAAATACCAATTTCTTCACAATCGAGGA
*
61437 TACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACT
64 TACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACT
61502 CCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTT
129 CCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTT
61567 CAAAACGCCAATTTTCCTTT
194 CAAAACGCCAATTTTCCTTT
*
61587 AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATA
1 AATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATA
* *
61650 CTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTC
66 CTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTC
*
61715 TGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTC
130 CGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTC
61780 AAAAC
195 AAAAC
61785 CATTTTTCGA
Statistics
Matches: 190, Mismatches: 7, Indels: 5
0.94 0.03 0.02
Matches are distributed among these distances:
211 28 0.15
212 131 0.69
215 31 0.16
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (213 bp):
AATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATA
CTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCC
GGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCA
AAACGCCAATTTTCCTTT
Found at i:61784 original size:52 final size:52
Alignment explanation
Indices: 61487--61784 Score: 188
Period size: 52 Copynumber: 5.7 Consensus size: 52
61477 TTATTTTCGA
* *
61487 GGGGATACTCCAACTCC-GGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAA-TCCTGGTTTTAT-TTTCAAAACACCAATTTTTCCACAATC
* **
61539 GGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAATCCTGGTTTTATTTTCAAAACACCAATTTTTCC-ACAATC
* * *
61591 GGGGATACTCCAACTCC-GATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACACCAATTTTTCCACAATC
* * * * * *** **
61643 GAGGATACTCCAA-CCTCG--TTATTTCATCGGGGATACTCCAACCCCGTT--ACTTTC
1 GGGGATACTCCAATCCTGGTTTTATTT--TC---AAAACACCAA--TTTTTCCACAATC
* *
61697 GAGGGGATACTCCAA-CTCTGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 --GGGGATACTCCAATC-CTGGTTTTAT-TTTCAAAACACCAATTTTTCCACAATC
61751 GGGGATACTCCAATCCTGGTTTTATTTTCAAAAC
1 GGGGATACTCCAATCCTGGTTTTATTTTCAAAAC
61785 CATTTTTCGA
Statistics
Matches: 185, Mismatches: 38, Indels: 46
0.69 0.14 0.17
Matches are distributed among these distances:
49 6 0.03
50 2 0.01
51 14 0.08
52 102 0.55
53 19 0.10
54 18 0.10
55 2 0.01
56 13 0.07
57 3 0.02
58 1 0.01
59 4 0.02
60 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (52 bp):
GGGGATACTCCAATCCTGGTTTTATTTTCAAAACACCAATTTTTCCACAATC
Done.