Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1050
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: 23443
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Found at i:2436 original size:51 final size:53
Alignment explanation
Indices: 2321--2441 Score: 201
Period size: 53 Copynumber: 2.3 Consensus size: 53
2311 TAAAATTTAT
* *
2321 CTGCATGTATCGATACATTAATAGTGTATCGATACATTCCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTAATAATGTATCAATACATTCCTGGGCAAATTTGC
*
2374 CTGCATGTATCGATACATTTATAATGTATCAATACA-T-CTGGGCAAATTTGC
1 CTGCATGTATCGATACATTAATAATGTATCAATACATTCCTGGGCAAATTTGC
2425 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
2442 AAGATCATGT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
51 31 0.48
52 1 0.02
53 33 0.51
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (53 bp):
CTGCATGTATCGATACATTAATAATGTATCAATACATTCCTGGGCAAATTTGC
Found at i:2452 original size:51 final size:51
Alignment explanation
Indices: 2321--2460 Score: 185
Period size: 51 Copynumber: 2.7 Consensus size: 51
2311 TAAAATTTAT
2321 CTGCATGTATCGATACATTAATAGTGTATCGATACATTCCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAATA-TGTATCGATACATTCCTGGGCAAATTTGC
* *
2374 CTGCATGTATCGATACATTTATAATGTATCAATACA-T-CTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAT-ATGTATCGATACATTCCTGGGCAAATTTGC
*
2425 CTGCATGTATCGATACAAAGATCATGTATCGATACA
1 CTGCATGTATCGATACATA-AT-ATGTATCGATACA
2461 AATGTATCGA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 45 0.57
52 1 0.01
53 32 0.41
54 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATAATATGTATCGATACATTCCTGGGCAAATTTGC
Found at i:2561 original size:13 final size:13
Alignment explanation
Indices: 2543--2567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2533 CAAAAAAATA
2543 TGTATCGATACAT
1 TGTATCGATACAT
2556 TGTATCGATACA
1 TGTATCGATACA
2568 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2565 original size:33 final size:32
Alignment explanation
Indices: 2519--2587 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
2509 GGCAGTAGCT
2519 TACATTGATCGATACAAAAAAATATGTATCGA
1 TACATTGATCGATACAAAAAAATATGTATCGA
* ***
2551 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTG-ATCGATACAAAAAAATATGTATCGA
2584 TACA
1 TACA
2588 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (32 bp):
TACATTGATCGATACAAAAAAATATGTATCGA
Found at i:3471 original size:27 final size:27
Alignment explanation
Indices: 3392--3654 Score: 210
Period size: 27 Copynumber: 9.2 Consensus size: 27
3382 CCAGCTATAT
* *
3392 TGGGCTTAGAAGGGTT-CCACCGACTTGTG
1 TGGGCTTTGAA-GGTTGCCACTGAC-T-TG
* *
3421 TGGGCTTTGGAAAAGGGTGCCACTGATTTG
1 TGGGCTTT-G--AAGGTTGCCACTGACTTG
3451 TGGGCTTTGAAGGTTGCCACTGACTT-
1 TGGGCTTTGAAGGTTGCCACTGACTTG
*
3477 TGGGCTTTTAAAGGTTGCCACTGACTT-
1 TGGGC-TTTGAAGGTTGCCACTGACTTG
**
3504 TGGGCTTTGAAAAATATGCCACTGACTTG
1 TGGGCTTTG-AAGGT-TGCCACTGACTTG
* *
3533 TGGGCTTTTGAACAGGGTGCCACTAACTTG
1 TGGGC-TTTG-A-AGGTTGCCACTGACTTG
*
3563 TGGGCTTTAAAGGTTGCCACTGACTTG
1 TGGGCTTTGAAGGTTGCCACTGACTTG
**
3590 TGGGCTTTTGAAAAATATGCCACTGAC-TG
1 TGGGC-TTTG-AAGGT-TGCCACTGACTTG
* *
3619 TGGGCTCTTGAAAAGGGTGCCACTAACTTG
1 TGGGCT-TTG--AAGGTTGCCACTGACTTG
3649 TGGGCT
1 TGGGCT
3655 GAAAAGAGTG
Statistics
Matches: 194, Mismatches: 24, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
26 8 0.04
27 63 0.32
28 17 0.09
29 38 0.20
30 55 0.28
31 5 0.03
32 8 0.04
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (27 bp):
TGGGCTTTGAAGGTTGCCACTGACTTG
Found at i:3588 original size:112 final size:116
Alignment explanation
Indices: 3419--3654 Score: 336
Period size: 112 Copynumber: 2.1 Consensus size: 116
3409 CACCGACTTG
* * *
3419 TGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTT-TGGGCT
1 TGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCT
** * * *
3483 TTT-AAAGGT-TGCCACTGACTTTGGGCT-TTGAAAAATATGCCACTGACT
66 TTTGAAAAATATGCCACTGACTGTGGGCTCTTGAAAAAGATGCCACTAACT
* *
3531 TGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCT
* *
3596 TTTGAAAAATATGCCACTGACTGTGGGCTCTTGAAAAGGGTGCCACTAACT
66 TTTGAAAAATATGCCACTGACTGTGGGCTCTTGAAAAAGATGCCACTAACT
3647 TGTGGGCT
1 TGTGGGCT
3655 GAAAAGAGTG
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
112 53 0.49
113 9 0.08
114 4 0.04
115 17 0.16
116 25 0.23
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.32
Consensus pattern (116 bp):
TGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCT
TTTGAAAAATATGCCACTGACTGTGGGCTCTTGAAAAAGATGCCACTAACT
Found at i:3630 original size:86 final size:84
Alignment explanation
Indices: 3419--3654 Score: 318
Period size: 86 Copynumber: 2.8 Consensus size: 84
3409 CACCGACTTG
* *** * * *
3419 TGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGCTTTG-AAGGTTGCCACTGACTT-TGGGC
1 TGTGGGCTTTTGAAAAATATGCCACTGA-CTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
3482 TTTTAAAGGTTGCCACTGACT
65 -TTTAAAGGTTGCCACTGACT
3503 T-TGGGC-TTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGG
1 TGTGGGCTTTTGAAAAATATGCCACTGAC-TGTGGGC-TTTGAA-AGGGTGCCACTAACTTGTGG
3566 GCTTTAAAGGTTGCCACTGACT
63 GCTTTAAAGGTTGCCACTGACT
3588 TGTGGGCTTTTGAAAAATATGCCACTGACTGTGGGCTCTTGAAAAGGGTGCCACTAACTTGTGGG
1 TGTGGGCTTTTGAAAAATATGCCACTGACTGTGGGCT-TTG-AAAGGGTGCCACTAACTTGTGGG
3653 CT
64 CT
3655 GAAAAGAGTG
Statistics
Matches: 136, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
82 23 0.17
83 9 0.07
84 2 0.01
85 36 0.26
86 43 0.32
87 23 0.17
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.32
Consensus pattern (84 bp):
TGTGGGCTTTTGAAAAATATGCCACTGACTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
TTAAAGGTTGCCACTGACT
Found at i:3748 original size:29 final size:29
Alignment explanation
Indices: 3714--3852 Score: 131
Period size: 29 Copynumber: 4.8 Consensus size: 29
3704 GTTGGACTTT
*
3714 GGAAAAGATGCCACCGACTTGTGGGCTTC
1 GGAAAAGATGCCACTGACTTGTGGGCTTC
* *
3743 GGAAAAGGGTGCCACTGATTTGTGGGCTT-
1 GGAAAA-GATGCCACTGACTTGTGGGCTTC
* * *
3772 TG-AAGGTTGCCACTGACTTGTGGGCTTTC
1 GGAAAAGATGCCACTGACTTGTGGGC-TTC
* * * *
3801 GAAAAAAATGCC-CCGACTTGTGGGCTTT
1 GGAAAAGATGCCACTGACTTGTGGGCTTC
* *
3829 GAAAAAAATGCCACTGACTTGTGG
1 GGAAAAGATGCCACTGACTTGTGG
3853 ACTTTGAAGG
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
27 18 0.20
28 18 0.20
29 29 0.32
30 25 0.28
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (29 bp):
GGAAAAGATGCCACTGACTTGTGGGCTTC
Found at i:3857 original size:29 final size:29
Alignment explanation
Indices: 3419--3860 Score: 301
Period size: 27 Copynumber: 15.4 Consensus size: 29
3409 CACCGACTTG
* * *
3419 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
* *
3449 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * *
3476 T-TGGGCTTT-TAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
3503 T-TGGGCTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * * *
3531 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* *
3561 TGTGGGCTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
3588 TGTGGGCTTTTGAAAAATATGCCACTGAC-
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* * *
3617 TGTGGGCTCTTGAAAAGGGTGCCACTAACT
1 TGTGGGCT-TTGAAAAAGATGCCACTGACT
* *
3647 TGTGGGC--TG-AAAAGAGTGCTA-TAGAGT
1 TGTGGGCTTTGAAAAAGA-TGCCACT-GACT
* * *
3674 TGTGAGCTTACAAAAGAAAAAG-TGCCAC-GA-G
1 TGTGGGCTT-----TGAAAAAGATGCCACTGACT
* * *
3705 T-TGGACTTTGGAAAAGATGCCACCGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * * *
3733 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTT-TGAAAAAGATGCCACTGACT
* *
3763 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* *
3790 TGTGGGCTTTCGAAAAAAATGCC-CCGACT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
*
3819 TGTGGGCTTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
3848 TGTGGACTTTGAA
1 TGTGGGCTTTGAA
3861 GGGTGATGAA
Statistics
Matches: 331, Mismatches: 51, Indels: 61
0.75 0.12 0.14
Matches are distributed among these distances:
25 6 0.02
26 19 0.06
27 101 0.31
28 33 0.10
29 71 0.21
30 88 0.27
31 1 0.00
32 2 0.01
33 4 0.01
34 1 0.00
35 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAAGATGCCACTGACT
Found at i:5278 original size:1 final size:1
Alignment explanation
Indices: 5274--5456 Score: 87
Period size: 1 Copynumber: 183.0 Consensus size: 1
5264 CCGGACCCCC
* * * * * * ** * **
5274 TTTTTTGTTTGTTTTTTTATTATTTTTTGTTGTTTTTTTTTCCTTTTGTTTTTTTTTTTTTTGGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * ** ** ** **
5339 TTTTTTTTTGGTTTTTTTTTTGTTTTTTGGTTTTTTCATTTTTTTCGTTTTTTTTTTTTTGGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * ** ** **
5404 TTCATTTTTTGTTTTTTTTTTTTTTGGTTTTTCATTTTTTTCGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5457 GGAGGACGCC
Statistics
Matches: 137, Mismatches: 45, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 137 1.00
ACGTcount: A:0.03, C:0.04, G:0.10, T:0.83
Consensus pattern (1 bp):
T
Found at i:5325 original size:15 final size:13
Alignment explanation
Indices: 5274--5456 Score: 113
Period size: 14 Copynumber: 13.3 Consensus size: 13
5264 CCGGACCCCC
5274 TTTTTTGTTTGTTT
1 TTTTTTGTTT-TTT
*
5288 TTTTATTATTTTTT
1 TTTT-TTGTTTTTT
*
5302 GTTGTTT-TTTTTT
1 -TTTTTTGTTTTTT
**
5315 CCTTTTGTTTTTT
1 TTTTTTGTTTTTT
5328 TTTTTT-TTGGTTTT
1 TTTTTTGTT--TTTT
*
5342 TTTTTTG-GTTTT
1 TTTTTTGTTTTTT
5354 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
**
5367 GGTTTTTTCATTTTT
1 --TTTTTTGTTTTTT
**
5382 TTCGTT-TTTTTT
1 TTTTTTGTTTTTT
*
5394 TTTTTGGTTTTTCAT
1 TTTTTTGTTTTT--T
*
5409 TTTTTGTTTTTTTT
1 TTTTT-TGTTTTTT
5423 TTTTTTGGTTTTTCAT
1 TTTTTT-GTTTTT--T
5439 TTTTTTCGTTTTTT
1 TTTTTT-GTTTTTT
5453 TTTT
1 TTTT
5457 GGAGGACGCC
Statistics
Matches: 132, Mismatches: 21, Indels: 32
0.71 0.11 0.17
Matches are distributed among these distances:
12 24 0.18
13 30 0.23
14 35 0.27
15 25 0.19
16 18 0.14
ACGTcount: A:0.03, C:0.04, G:0.10, T:0.83
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:5333 original size:19 final size:17
Alignment explanation
Indices: 5274--5456 Score: 115
Period size: 17 Copynumber: 10.2 Consensus size: 17
5264 CCGGACCCCC
*
5274 TTTTTTGTTTGTTTTTT
1 TTTTTTTTTTGTTTTTT
*
5291 TATTATTTTTTGTTGTTTT
1 T-TTTTTTTTTGTT-TTTT
*
5310 TTTTTCCTTTTG-TTTTT
1 TTTTT-TTTTTGTTTTTT
*
5327 TTTTTTTTTGGTTTTTT
1 TTTTTTTTTTGTTTTTT
5344 TTTTGGTTTTTT-TTTTGTT
1 TTTT--TTTTTTGTTTT-TT
*
5363 TTTTGGTTTTTTCATTTTTT
1 TTTT--TTTTTT-GTTTTTT
5383 TCGTTTTTTTTT-TTTTGGTT
1 T--TTTTTTTTTGTTTT--TT
*
5403 TTTCATTTTTTG--TTTT
1 TTT-TTTTTTTGTTTTTT
*
5419 TTTTTTTTTTGGTTTTT
1 TTTTTTTTTTGTTTTTT
** *
5436 CATTTTTTTCGTTTTTT
1 TTTTTTTTTTGTTTTTT
5453 TTTT
1 TTTT
5457 GGAGGACGCC
Statistics
Matches: 134, Mismatches: 15, Indels: 34
0.73 0.08 0.19
Matches are distributed among these distances:
15 7 0.05
16 9 0.07
17 38 0.28
18 26 0.19
19 35 0.26
20 12 0.09
21 4 0.03
22 3 0.02
ACGTcount: A:0.03, C:0.04, G:0.10, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTTGTTTTTT
Found at i:5368 original size:31 final size:28
Alignment explanation
Indices: 5274--5458 Score: 163
Period size: 31 Copynumber: 6.0 Consensus size: 28
5264 CCGGACCCCC
*
5274 TTTTTTGTTTGTTTTTTTATTATTTTTTGTTGT
1 TTTTTT-TTT-TTTTTTT-TT-TTTTTT-TTGG
5307 TTTTTTTTCCTTTTGTTTTTTTTTTTTTTGG
1 TTTTTTTT--TTTT-TTTTTTTTTTTTTTGG
5338 TTTTTTTTTTGGTTTTTTTTTTGTTTTTTGG
1 TTTTTTTTTT--TTTTTTTTTT-TTTTTTGG
5369 TTTTTTCATTTTTTTCGTTTTTTTTTTTTTGG
1 TTTTTT--TTTTTTT--TTTTTTTTTTTTTGG
*
5401 TTTTTCATTTTTTGTTTTTTTTTTTTTTGG
1 TTTTT--TTTTTTTTTTTTTTTTTTTTTGG
** **
5431 TTTTTCATTTTTTTCGTTTTTTTTTTGG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTGG
5459 AGGACGCCGT
Statistics
Matches: 133, Mismatches: 7, Indels: 29
0.79 0.04 0.17
Matches are distributed among these distances:
28 18 0.14
29 2 0.02
30 28 0.21
31 30 0.23
32 27 0.20
33 22 0.17
34 6 0.05
ACGTcount: A:0.03, C:0.04, G:0.11, T:0.82
Consensus pattern (28 bp):
TTTTTTTTTTTTTTTTTTTTTTTTTTGG
Found at i:5436 original size:30 final size:30
Alignment explanation
Indices: 5317--5456 Score: 178
Period size: 30 Copynumber: 4.5 Consensus size: 30
5307 TTTTTTTTCC
5317 TTTTGTTTTTTTTTTTTTTGGTTTTT--TT
1 TTTTGTTTTTTTTTTTTTTGGTTTTTCATT
*
5345 TTTGGTTTTTTTTTTGTTTTTTGGTTTTTTCATT
1 TTT--TGTTTTTTTT-TTTTTTGG-TTTTTCATT
5379 TTTT-TCGTTTTTTTTTTTTTGGTTTTTCATT
1 TTTTGT--TTTTTTTTTTTTTGGTTTTTCATT
5410 TTTTGTTTTTTTTTTTTTTGGTTTTTCATTT
1 TTTTGTTTTTTTTTTTTTTGGTTTTTCA-TT
5441 TTTTCGTTTTTTTTTT
1 TTTT-GTTTTTTTTTT
5457 GGAGGACGCC
Statistics
Matches: 100, Mismatches: 1, Indels: 18
0.84 0.01 0.15
Matches are distributed among these distances:
28 3 0.03
30 31 0.31
31 28 0.28
32 26 0.26
33 7 0.07
34 5 0.05
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.84
Consensus pattern (30 bp):
TTTTGTTTTTTTTTTTTTTGGTTTTTCATT
Found at i:19330 original size:51 final size:51
Alignment explanation
Indices: 19261--19379 Score: 204
Period size: 51 Copynumber: 2.3 Consensus size: 51
19251 GAAAATTTAT
* *
19261 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC-AATTTGC
1 CTGCATGTATCGATACATTT-ATAATGTATCAATACATCTGGGCAAATTTGC
19312 CTGCATGTATCGATACATTTATAATGTATCAATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTATAATGTATCAATACATCTGGGCAAATTTGC
19363 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
19380 AAGATCAATG
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
50 21 0.32
51 44 0.68
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
CTGCATGTATCGATACATTTATAATGTATCAATACATCTGGGCAAATTTGC
Found at i:19403 original size:13 final size:13
Alignment explanation
Indices: 19385--19412 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19375 ATACAAAGAT
19385 CAATGTATCGATA
1 CAATGTATCGATA
19398 CAATGTATCGATA
1 CAATGTATCGATA
19411 CA
1 CA
19413 TGTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:19494 original size:13 final size:13
Alignment explanation
Indices: 19476--19500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19466 CAAAAAAATA
19476 TGTATCGATACAT
1 TGTATCGATACAT
19489 TGTATCGATACA
1 TGTATCGATACA
19501 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:19495 original size:33 final size:32
Alignment explanation
Indices: 19452--19520 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
19442 GGCAGTAGCT
19452 TACATGTATCGATACAAAAAAATATGTATCGA
1 TACATGTATCGATACAAAAAAATATGTATCGA
* ***
19484 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACA-TGTATCGATACAAAAAAATATGTATCGA
19517 TACA
1 TACA
19521 AAACGTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 4 0.12
33 28 0.88
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (32 bp):
TACATGTATCGATACAAAAAAATATGTATCGA
Found at i:21636 original size:48 final size:52
Alignment explanation
Indices: 21523--21647 Score: 195
Period size: 48 Copynumber: 2.5 Consensus size: 52
21513 CGAAATATGA
* * *
21523 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTCTCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
21575 AAATTTGCCTACATGTATCGATACA-TT-ATAGT-TATCAAT-CATCTGGGC
1 AAATTTGCCTACATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
21623 AAATTTGCCTACATGTATCGATACA
1 AAATTTGCCTACATGTATCGATACA
21648 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
48 34 0.49
49 5 0.07
50 5 0.07
51 2 0.03
52 24 0.34
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTACATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
Found at i:21673 original size:12 final size:12
Alignment explanation
Indices: 21656--21701 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
21646 CAAAGATCAG
21656 TGTATCGATACA
1 TGTATCGATACA
21668 TGTATCGATACA
1 TGTATCGATACA
21680 T-T-T-GAGTA-A
1 TGTATCGA-TACA
21689 TGTATCGATACA
1 TGTATCGATACA
21701 T
1 T
21702 TTTTGGCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.14
10 4 0.14
11 4 0.14
12 17 0.59
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:21758 original size:13 final size:13
Alignment explanation
Indices: 21740--21795 Score: 67
Period size: 13 Copynumber: 3.9 Consensus size: 13
21730 ACAAAACTTA
21740 TGTATCGATACAT
1 TGTATCGATACAT
21753 TGTATCGATACAACACT
1 TGTATCGAT---ACA-T
21770 ATGTATCGATACAT
1 -TGTATCGATACAT
21784 TGTATCGATACA
1 TGTATCGATACA
21796 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
15 3 0.08
16 3 0.08
17 1 0.03
18 9 0.24
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:21773 original size:31 final size:32
Alignment explanation
Indices: 21724--21810 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 32
21714 CTTATATGTA
* *
21724 ATCGGTACAAAACTTATGTATCGATACATTGT
1 ATCGATACAACACTTATGTATCGATACATTGT
21756 ATCGATACAACAC-TATGTATCGATACATTGT
1 ATCGATACAACACTTATGTATCGATACATTGT
21787 ATCGATACAACACTTATGTATCGA
1 ATCGATACAACACTTATGTATCGA
21811 GACAAAATCG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
31 31 0.60
32 21 0.40
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (32 bp):
ATCGATACAACACTTATGTATCGATACATTGT
Found at i:22650 original size:112 final size:111
Alignment explanation
Indices: 22383--22731 Score: 348
Period size: 112 Copynumber: 3.0 Consensus size: 111
22373 GCTTTGAAAG
* * * * * *
22383 AAAGGCGTCCTGCCCTTTGAG-ATTGGAAGGTGCCACCAACTTGTGT-GGCTTTGCAAAAAGAAA
1 AAAGGCATCCTGCTCTTTGAGAACTGAAAAGTGCCACCAACTTGTGTGGGCTTT--AAAAGGAAA
* * *
22446 GCATCTGCTCTTTGAGGATTGAAAAGTGCCACCGACTTGTGTGGGCTTTTGCAA
64 GCGTCTGCTCTTTGAGGACTG-AAGGTGCCACCG-CTTGTGTGGGC-TTT---A
*
22500 AAAGAAACATCCTGCTCTTTGAGAACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
1 AAAG--GCATCCTGCTCTTTGAGAACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
*
22565 GACGTCCTGCTCTTTGAGGACTGAAGGTGCCACCGCTTATGTGGGCTTTA
64 G-CGT-CTGCTCTTTGAGGACTGAAGGTGCCACCGCTTGTGTGGGCTTTA
* * * * * *
22615 AAAGGCGTCC-GCTTTTTGAGGACTGAATAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGAAG
1 AAAGGCATCCTGCTCTTTGAGAACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAA
* *
22679 GCGTTCTACTCTTT-AGG-CTAAAGGTGCCACCAGCTTGTGTGGGCTTTA
64 GCG-TCTGCTCTTTGAGGACTGAAGGTGCCACC-GCTTGTGTGGGCTTTA
22727 AAAGG
1 AAAGG
22732 AAAGGCGTCC
Statistics
Matches: 201, Mismatches: 21, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
111 13 0.06
112 63 0.31
113 18 0.09
114 5 0.02
115 5 0.02
117 4 0.02
118 3 0.01
119 33 0.16
120 35 0.17
121 22 0.11
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (111 bp):
AAAGGCATCCTGCTCTTTGAGAACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGC
GTCTGCTCTTTGAGGACTGAAGGTGCCACCGCTTGTGTGGGCTTTA
Found at i:22719 original size:58 final size:59
Alignment explanation
Indices: 22335--22761 Score: 296
Period size: 58 Copynumber: 7.3 Consensus size: 59
22325 AAGTGTGTCT
* ** * * * *
22335 TACTCTTTGAGAACTGAAAAATGCCA-CAAATCGTGTAGGCTTTGAAA-GAAAGGCGTCC
1 TACTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCC
* * * * * *
22393 TGCCCTTTGA-GATTGGAAGGTGCCACCAACTTGTGT-GGCTTTGCAAAAAGAAA-GCAT-C
1 TACTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT--AAAAGGAAAGGCGTCC
* * * * * *
22451 TGCTCTTTGAGGATTGAAAAGTGCCACCGACTTGTGTGGGCTTTTGCAAAAAGAAA--CATCC
1 TACTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGC-TTT--AAAAGGAAAGGCGTCC
* * * *
22512 TGCTCTTTGAGAACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGACGTCC
1 TACTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCC
* * * *
22572 TGCTCTTTGAGGACTGAAGGTGCCACC-GCTTATGTGGGCTTT---A--AAAGGCGTCC
1 TACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCC
* * * * *
22625 -GCTTTTTGAGGACTGAATA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGCGAAGGCGTTC
1 TACTCTTTGAGGACT-AA-AGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGCGTCC
*
22685 TACTCTTT-AGG-CTAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAGGCGTCC
1 TACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCC
* * *
22742 TACTTTTTTAGGACTGAAGG
1 TACTCTTTGAGGACTAAAGG
22762 GCTAAAGAGG
Statistics
Matches: 306, Mismatches: 40, Indels: 45
0.78 0.10 0.12
Matches are distributed among these distances:
52 13 0.04
53 18 0.06
54 14 0.05
55 1 0.00
57 33 0.11
58 80 0.26
59 47 0.15
60 42 0.14
61 58 0.19
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (59 bp):
TACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCC
Done.