Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010937.1 Corchorus capsularis cultivar CVL-1 contig10958, whole genome shotgun sequence
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: 78571
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:3548 original size:36 final size:33
Alignment explanation
Indices: 3505--3604 Score: 116
Period size: 30 Copynumber: 3.0 Consensus size: 33
3495 GATCAGTCAG
**
3505 AAAAGTAAAAAGGGTAATCAGAGTAATTAAGTTCCA
1 AAAAGTAAAAAGGCAAATC--AGTAATTAAGTT-CA
3541 AAAAGTAAAAAGGCAAATCAGTAATTAAGTTCA
1 AAAAGTAAAAAGGCAAATCAGTAATTAAGTTCA
* *
3574 ATAAG-AAAAA-G-AAATCAGTGATTAAGTTCA
1 AAAAGTAAAAAGGCAAATCAGTAATTAAGTTCA
3604 A
1 A
3605 TAAGAAAGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
30 19 0.32
31 1 0.02
32 5 0.08
33 6 0.10
34 12 0.20
36 17 0.28
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (33 bp):
AAAAGTAAAAAGGCAAATCAGTAATTAAGTTCA
Found at i:3590 original size:30 final size:32
Alignment explanation
Indices: 3526--3611 Score: 122
Period size: 30 Copynumber: 2.7 Consensus size: 32
3516 GGGTAATCAG
*
3526 AGTAATTAAGTTCCAAAAAGTAAAAAGGCAAATC
1 AGTAATTAAGTT-CAATAAG-AAAAAGGCAAATC
3560 AGTAATTAAGTTCAATAAGAAAAA-G-AAATC
1 AGTAATTAAGTTCAATAAGAAAAAGGCAAATC
*
3590 AGTGATTAAGTTCAATAAGAAA
1 AGTAATTAAGTTCAATAAGAAA
3612 GATATAATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
30 26 0.52
31 1 0.02
32 5 0.10
33 6 0.12
34 12 0.24
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.23
Consensus pattern (32 bp):
AGTAATTAAGTTCAATAAGAAAAAGGCAAATC
Found at i:3654 original size:22 final size:21
Alignment explanation
Indices: 3620--3676 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
3610 AAGATATAAT
3620 TAGTAAA-AGGTAAAATGACAA
1 TAGTAAAGA-GTAAAATGACAA
* *
3641 CTAGTAAAGAGTAAAGTGATAA
1 -TAGTAAAGAGTAAAATGACAA
3663 TCAGTAAAGAGTAA
1 T-AGTAAAGAGTAA
3677 TAGAAATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (21 bp):
TAGTAAAGAGTAAAATGACAA
Found at i:3686 original size:20 final size:21
Alignment explanation
Indices: 3643--3690 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3633 AATGACAACT
3643 AGTAAAGAGTAAAGTGATAATC
1 AGTAAAGAGTAAAG-GATAATC
3665 AGTAAAGAGTAATA-GA-AATC
1 AGTAAAGAGTAA-AGGATAATC
3685 AGTAAA
1 AGTAAA
3691 TCAGTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.40
21 2 0.08
22 12 0.48
23 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTAAAGAGTAAAGGATAATC
Found at i:3742 original size:55 final size:55
Alignment explanation
Indices: 3672--4030 Score: 558
Period size: 55 Copynumber: 6.5 Consensus size: 55
3662 ATCAGTAAAG
* * *
3672 AGTAATAGAAATCAGTAAATCAGTAATTAAGTGAAAAGAAATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* * *
3727 AGTAGTAGTAATCAGTAAATTAATAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
3782 AGTAGTAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* * *
3837 AGTAGTAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAAATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* * *
3892 GGTAATAGTAATCCGTAAATCAGTAATTAAGCAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* *
3947 AGTAAAAATAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
4002 GGTAATAGTAATCAGTAAATC-GATAATTA
1 AGTAATAGTAATCAGTAAATCAG-TAATTA
4031 GGAGTTAAAA
Statistics
Matches: 279, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
54 1 0.00
55 278 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (55 bp):
AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
Found at i:3784 original size:26 final size:26
Alignment explanation
Indices: 3755--3840 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
3745 ATTAATAATT
3755 AAGTAAAAAGAGATTAATCAGAGTCA
1 AAGTAAAAAGAGATTAATCAGAGTCA
** * * *
3781 AAGTAGTAGTAATCAG-TAAATCAGTAAT-T
1 AAGTA--A--AAAGAGATTAATCAG-AGTCA
3810 AAGTAAAAAGAGATTAATCAGAGTCA
1 AAGTAAAAAGAGATTAATCAGAGTCA
3836 AAGTA
1 AAGTA
3841 GTAGTAATCA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 6 0.14
26 17 0.40
27 1 0.02
28 1 0.02
29 12 0.28
30 6 0.14
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (26 bp):
AAGTAAAAAGAGATTAATCAGAGTCA
Found at i:3794 original size:21 final size:21
Alignment explanation
Indices: 3714--3796 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 21
3704 GAAAAGAAAT
3714 TAATCAGAGTCAAAGTAGTAG
1 TAATCAGAGTCAAAGTAGTAG
*
3735 TAATC--AGT-AAA-T--TAA
1 TAATCAGAGTCAAAGTAGTAG
* * *
3750 TAATTA-AGTAAAAAG-AG-AT
1 TAATCAGAGT-CAAAGTAGTAG
3769 TAATCAGAGTCAAAGTAGTAG
1 TAATCAGAGTCAAAGTAGTAG
3790 TAATCAG
1 TAATCAG
3797 TAAATCAGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 18
0.66 0.08 0.25
Matches are distributed among these distances:
15 6 0.13
16 3 0.06
17 1 0.02
18 6 0.13
19 13 0.28
20 5 0.11
21 13 0.28
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (21 bp):
TAATCAGAGTCAAAGTAGTAG
Found at i:3802 original size:29 final size:29
Alignment explanation
Indices: 3715--3859 Score: 85
Period size: 29 Copynumber: 5.2 Consensus size: 29
3705 AAAAGAAATT
3715 AATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGAGTCAAAGTAGTAGTAATCAGTA
* * * ** *
3744 AATTA-A-T--AATTAAGTA-AAAAGAGATT
1 AATCAGAGTCAAAGT-AGTAGTAATCAG-TA
3770 AATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGAGTCAAAGTAGTAGTAATCAGTA
* * ** *
3799 AATC--AGT--AATTAAGTA-AAAAGAGATT
1 AATCAGAGTCAAAGT-AGTAGTAATCAG-TA
3825 AATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGAGTCAAAGTAGTAGTAATCAGTA
3854 AATCAG
1 AATCAG
3860 TAATTAAGTG
Statistics
Matches: 80, Mismatches: 22, Indels: 28
0.62 0.17 0.22
Matches are distributed among these distances:
25 14 0.17
26 18 0.22
27 5 0.06
28 5 0.06
29 24 0.30
30 14 0.17
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (29 bp):
AATCAGAGTCAAAGTAGTAGTAATCAGTA
Found at i:3940 original size:26 final size:26
Alignment explanation
Indices: 3909--3995 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 26
3899 GTAATCCGTA
*
3909 AATCAGTAATTAAGCAAAAAGAGATT
1 AATCAGTAATTAAGTAAAAAGAGATT
* * *
3935 AATCAG-AGTCAAAGTAAAAATA-ATCAGT
1 AATCAGTAAT-TAAGTAAAAAGAGAT---T
3963 AAATCAGTAATTAAGTAAAAAGAGATT
1 -AATCAGTAATTAAGTAAAAAGAGATT
3990 AATCAG
1 AATCAG
3996 AGTCAAGGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
25 4 0.09
26 21 0.45
27 1 0.02
28 1 0.02
29 16 0.34
30 4 0.09
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (26 bp):
AATCAGTAATTAAGTAAAAAGAGATT
Found at i:4006 original size:26 final size:25
Alignment explanation
Indices: 3924--4002 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 25
3914 GTAATTAAGC
3924 AAAAAGAGATTAATCAGAGTCAAAGT
1 AAAAAGAGATTAATCAGAGTC-AAGT
* * *
3950 AAAAATA-ATCAGTAAATCAGTAATTAAGT
1 AAAAAGAGAT---T-AATCAG-AGTCAAGT
3979 AAAAAGAGATTAATCAGAGTCAAG
1 AAAAAGAGATTAATCAGAGTCAAG
4003 GTAATAGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
25 7 0.17
26 12 0.29
27 1 0.02
28 1 0.02
29 16 0.39
30 4 0.10
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.22
Consensus pattern (25 bp):
AAAAAGAGATTAATCAGAGTCAAGT
Found at i:4261 original size:35 final size:36
Alignment explanation
Indices: 4221--4296 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
4211 ACATGTAATC
* *
4221 AGTAAAAAGTGCAAAGGT-ATCTG-AAAGGGTAAAAT
1 AGTAAAAAGT-AAAAGGTAATCAGTAAAGGGTAAAAT
*
4256 GGTAAAAAGTAAAAGGTAATCAGTAAAGGGTAAAAT
1 AGTAAAAAGTAAAAGGTAATCAGTAAAGGGTAAAAT
4292 AGTAA
1 AGTAA
4297 TTAGAAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 6 0.17
35 13 0.37
36 16 0.46
ACGTcount: A:0.51, C:0.04, G:0.25, T:0.20
Consensus pattern (36 bp):
AGTAAAAAGTAAAAGGTAATCAGTAAAGGGTAAAAT
Found at i:4280 original size:14 final size:14
Alignment explanation
Indices: 4249--4340 Score: 53
Period size: 14 Copynumber: 6.3 Consensus size: 14
4239 ATCTGAAAGG
4249 GTAAAATGGTAAAAA
1 GTAAAA-GGTAAAAA
**
4264 GTAAAAGGTAATCA
1 GTAAAAGGTAAAAA
*
4278 GTAAAGGGTAAAATA
1 GTAAAAGGTAAAA-A
*
4293 GTAATTA-G-AAAAGA
1 GTAA-AAGGTAAAA-A
**
4307 GTAAAATGGTAATCA
1 GTAAAA-GGTAAAAA
*
4322 GTAAAAAGTAAAAGA
1 GTAAAAGGTAAAA-A
4337 GTAA
1 GTAA
4341 TCAGTAAAGA
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
13 1 0.02
14 29 0.51
15 25 0.44
16 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.21
Consensus pattern (14 bp):
GTAAAAGGTAAAAA
Found at i:4305 original size:22 final size:22
Alignment explanation
Indices: 4259--4375 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 22
4249 GTAAAATGGT
*
4259 AAAA-AGTAAAA-GGTAATCAG
1 AAAAGAGTAAAATAGTAATCAG
* * *
4279 TAAAGGGTAAAATAGTAATTAG
1 AAAAGAGTAAAATAGTAATCAG
*
4301 AAAAGAGTAAAATGGTAATCAG
1 AAAAGAGTAAAATAGTAATCAG
*
4323 TAAAA-AGTAAAAGAGTAATCAG
1 -AAAAGAGTAAAATAGTAATCAG
* * **
4345 TAAAGA--AAAATGGTAAAAAG
1 AAAAGAGTAAAATAGTAATCAG
*
4365 TAAAGAGTAAA
1 AAAAGAGTAAA
4376 GAGAAGAGTA
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
20 19 0.25
21 9 0.12
22 44 0.58
23 4 0.05
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.19
Consensus pattern (22 bp):
AAAAGAGTAAAATAGTAATCAG
Found at i:4376 original size:7 final size:7
Alignment explanation
Indices: 4321--4552 Score: 91
Period size: 7 Copynumber: 34.1 Consensus size: 7
4311 AATGGTAATC
*
4321 AGTAAAA
1 AGTAAAG
4328 AGTAAAAG
1 AGT-AAAG
**
4336 AGTAATC
1 AGTAAAG
4343 AGTAAAG
1 AGTAAAG
*
4350 A-AAAATG
1 AGTAAA-G
*
4357 -GTAAAA
1 AGTAAAG
4363 AGTAAAG
1 AGTAAAG
4370 AGTAAAG
1 AGTAAAG
4377 AG--AAG
1 AGTAAAG
**
4382 AGTAATC
1 AGTAAAG
4389 AGTAAAG
1 AGTAAAG
*
4396 AGAAAATG
1 AGTAAA-G
4404 -GT--AG
1 AGTAAAG
4408 AGTAAAG
1 AGTAAAG
*
4415 AGTAATCG
1 AGTAA-AG
4423 -GTAAAG
1 AGTAAAG
*
4429 A-AAAATG
1 AGTAAA-G
4436 -GTAAAG
1 AGTAAAG
4442 AGTAAAG
1 AGTAAAG
**
4449 AGTAATC
1 AGTAAAG
*
4456 AG-CAA-
1 AGTAAAG
4461 AGTAAA-
1 AGTAAAG
*
4467 ACGGTAAAA
1 A--GTAAAG
4476 AGTAAAAG
1 AGT-AAAG
**
4484 AGTAATC
1 AGTAAAG
4491 AGTAAAG
1 AGTAAAG
**
4498 AAAAAATG
1 AGTAAA-G
4506 -GTAAAG
1 AGTAAAG
4512 AGTAAAG
1 AGTAAAG
4519 AGTAAAG
1 AGTAAAG
4526 AGT--AG
1 AGTAAAG
4531 AGTAAAG
1 AGTAAAG
**
4538 AGTAATC
1 AGTAAAG
4545 AGTAAAG
1 AGTAAAG
4552 A
1 A
4553 AAAAATGGTA
Statistics
Matches: 164, Mismatches: 37, Indels: 48
0.66 0.15 0.19
Matches are distributed among these distances:
4 1 0.01
5 15 0.09
6 13 0.08
7 114 0.70
8 20 0.12
9 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:4418 original size:26 final size:26
Alignment explanation
Indices: 4357--4419 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
4347 AAGAAAAATG
*
4357 GTAAAAAGTAAAGAGTAAAGAGAAGA
1 GTAAAAAGTAAAGAGAAAAGAGAAGA
** *
4383 GTAATCAGTAAAGAGAAAATG-GTAGA
1 GTAAAAAGTAAAGAGAAAA-GAGAAGA
*
4409 GTAAAGAGTAA
1 GTAAAAAGTAA
4420 TCGGTAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.27, T:0.16
Consensus pattern (26 bp):
GTAAAAAGTAAAGAGAAAAGAGAAGA
Found at i:4491 original size:35 final size:34
Alignment explanation
Indices: 4371--4523 Score: 206
Period size: 34 Copynumber: 4.5 Consensus size: 34
4361 AAAGTAAAGA
4371 GTAAAGAG--AAGAGTAATCAGTAAAGAGAAAATG
1 GTAAAGAGTAAAGAGTAATCAGTAAAGA-AAAATG
*
4404 GT--AGAGTAAAGAGTAATCGGTAAAGAAAAATG
1 GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
* * *
4436 GTAAAGAGTAAAGAGTAATCAGCAAAGTAAAACG
1 GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
*
4470 GTAAAAAGTAAAAGAGTAATCAGTAAAGAAAAAATG
1 GTAAAGAGT-AAAGAGTAATCAGTAAAG-AAAAATG
4506 GTAAAGAGTAAAGAGTAA
1 GTAAAGAGTAAAGAGTAA
4524 AGAGTAGAGT
Statistics
Matches: 104, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
31 4 0.04
32 8 0.08
33 19 0.18
34 34 0.33
35 26 0.25
36 13 0.12
ACGTcount: A:0.55, C:0.04, G:0.25, T:0.16
Consensus pattern (34 bp):
GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
Found at i:4534 original size:12 final size:12
Alignment explanation
Indices: 4506--4541 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
4496 AGAAAAAATG
4506 GTAAAGAGTAAAGA
1 GTAAAGAGT--AGA
4520 GTAAAGAGTAGA
1 GTAAAGAGTAGA
4532 GTAAAGAGTA
1 GTAAAGAGTA
4542 ATCAGTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
14 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.31, T:0.17
Consensus pattern (12 bp):
GTAAAGAGTAGA
Found at i:4541 original size:54 final size:57
Alignment explanation
Indices: 4480--4636 Score: 185
Period size: 54 Copynumber: 2.7 Consensus size: 57
4470 GTAAAAAGTA
4480 AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAG-AGTAAAG-AG-TAGAGT
1 AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGCAGTAAAGAAGATAGAGT
* *
4534 AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTGAAGGGAAGTCAGTAAAGAAGAATGGTGT
1 AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGT--A---AAG-CAGTAAAGAAG-ATAGAGT
**
4598 GGAGAGTAATCCAGTAAAGAAAAAATGGTAAAGAGTAAA
1 AAAGAGTAAT-CAGTAAAGAAAAAATGGTAAAGAGTAAA
4637 ATGTGAATCA
Statistics
Matches: 88, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
54 35 0.40
56 1 0.01
59 3 0.03
60 2 0.02
61 7 0.08
62 2 0.02
63 1 0.01
64 12 0.14
65 25 0.28
ACGTcount: A:0.53, C:0.03, G:0.27, T:0.17
Consensus pattern (57 bp):
AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGCAGTAAAGAAGATAGAGT
Found at i:4548 original size:19 final size:19
Alignment explanation
Indices: 4510--4548 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4500 AAAATGGTAA
*
4510 AGAGTAAAGAGTAAAGAGT
1 AGAGTAAAGAGTAAACAGT
*
4529 AGAGTAAAGAGTAATCAGT
1 AGAGTAAAGAGTAAACAGT
4548 A
1 A
4549 AAGAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.28, T:0.18
Consensus pattern (19 bp):
AGAGTAAAGAGTAAACAGT
Found at i:27487 original size:447 final size:445
Alignment explanation
Indices: 26667--27610 Score: 1294
Period size: 447 Copynumber: 2.1 Consensus size: 445
26657 GTATGAAAAT
* *
26667 CATTTGATAAATAATCCAGCAAAAAAATATTTATTTATGGAGACCAAACATAAAAGTCCATTCTT
1 CATTTGATAAATAATCCAGCAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATCCATTCTT
* * * * *
26732 GAACCCTCCGCAAAATTCATTAATTAAACCCAGCTTTTAGGCCATTAACGAAAGTCGACGTAGAT
66 GAACCCTCCACAAAACTCATTAATCAAACCCAGCTTTCAGGCCATTAACAAAAGTCGAC-TAGAT
* * * *
26797 CACATAATAAGCTTTTAACCGACGCTTGAACAACCTCAATAGAACAAGTGGACAGAAACTTATAC
130 CACACAATAAGCTTTTAACCAACACTTGAACAACCTCAATAGAACAAATGGACAGAAACTTATAC
* * ** * *
26862 AATATTATATAGACCGACAATCGAGAGCACAAAATTTCAGAATTAATTATTTTTTAGAATTAAAA
195 AATATTAGATAGACCGACAATCGAGACCACAAAATTTCAG-A--AAGCATTTTTTAAAATCAAAA
*
26927 CATTAAAATTGGCTTTTGAGTCCTTCATGTAAGTTGTAGATCATGAAATTACCTTTTAATAGACA
257 CATTAAAATTGGCTTTTGAGTCCTTCATGTAAGTTATAGATCATGAAATTACCTTTTAATAGACA
* * *
26992 CTTGAATCATCTTGATCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCAATC
322 CTTGAATCACCTTGATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTCAATC
* *
27057 GTCCAA-CC-T-AGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATA-GGTAT
387 GTCCAATCCATCAAAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATATGG-AC
* ** * *
27113 CTTTTGATAAATAATCCAATAAAAAAATATTTGTTTATGGAGGCCAAACATAAAAATTCATTCTT
1 CATTTGATAAATAATCCAGCAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATCCATTCTT
** *
27178 GAACCCTCCATGAAACTCATTAATCAAATCCCA-CTTTCAGGCCCTTAACAAAAGTC-A-TAGAT
66 GAACCCTCCACAAAACTCATTAATCAAA-CCCAGCTTTCAGGCCATTAACAAAAGTCGACTAGAT
* * *
27240 CACACAATAA-CATTTTAACCAACACTTGAACAACCTCAATCGGACAAATGGACCGAAACTTATA
130 CACACAATAAGC-TTTTAACCAACACTTGAACAACCTCAATAGAACAAATGGACAGAAACTTATA
* *
27304 CAATATTAGATAGACCGGCAATCGAGACCACAAAATTTTAG-AAGCATTTTTTAAAATCAAAACA
194 CAATATTAGATAGACCGACAATCGAGACCACAAAATTTCAGAAAGCATTTTTTAAAATCAAAACA
27368 TTAAAATTGGCTTTTGAGTCCTTCATGGAAGTTATAGTCTTATAGATCATGAAATTACCTTTTAA
259 TTAAAATTGGCTTTTGAGTCCTTCAT----G-TA-AG--TTATAGATCATGAAATTACCTTTTAA
27433 TAGACACTTGAATCACCTTGATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACGT
316 TAGACACTTGAATCACCTTGATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACGT
*
27498 TCAATCGTCCAATCGTCCAATCCAAAATTTGTGATGGACTAAATAGCATAAATTATAAAAGTATA
381 TCAATCGTCCAA---TCC-AT-CAAAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATA
27563 TGGAC
441 TGGAC
* *
27568 CACTTGATAAATAATCCAGCAAAAAAATATTTGTTTATTGAGA
1 CATTTGATAAATAATCCAGCAAAAAAATATTTGTTTATGGAGA
27611 ACGAGACCCA
Statistics
Matches: 436, Mismatches: 43, Indels: 29
0.86 0.08 0.06
Matches are distributed among these distances:
439 45 0.10
442 1 0.00
443 98 0.22
444 2 0.00
445 3 0.01
446 101 0.23
447 103 0.24
451 2 0.00
453 1 0.00
455 78 0.18
456 2 0.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (445 bp):
CATTTGATAAATAATCCAGCAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATCCATTCTT
GAACCCTCCACAAAACTCATTAATCAAACCCAGCTTTCAGGCCATTAACAAAAGTCGACTAGATC
ACACAATAAGCTTTTAACCAACACTTGAACAACCTCAATAGAACAAATGGACAGAAACTTATACA
ATATTAGATAGACCGACAATCGAGACCACAAAATTTCAGAAAGCATTTTTTAAAATCAAAACATT
AAAATTGGCTTTTGAGTCCTTCATGTAAGTTATAGATCATGAAATTACCTTTTAATAGACACTTG
AATCACCTTGATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTCAATCGTCC
AATCCATCAAAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATATGGAC
Found at i:29888 original size:144 final size:145
Alignment explanation
Indices: 29625--29892 Score: 407
Period size: 144 Copynumber: 1.9 Consensus size: 145
29615 CTAGATATTA
**
29625 ATATTATCCCCGTGCATTTGTGTCAAGTTTTTCGGTTTATGATTGGAACTGAGTAATTTCAATTC
1 ATATTATCCCCGTGCATTTGCATCAAGTTTTTCGGTTTATGATTGGAACTGAGTAATTTCAATTC
* * * * *
29690 TGAGTAAAATTTTATCTTAGCAATCAAGTTAAATGGAAGGAAATATTGTTAGAATTATACGATAA
66 TAAATAAAATTTTATCTAAGCAATCAAGTTAAATGGAAGGAAATATTATAAGAATTATACGATAA
29755 TGATAATATAACTAG
131 TGATAATATAACTAG
** *
29770 ATATTAT-CCCGTGCATTTGCATCTGGTTTTTTCGGTTTATGATTGGAATTGAGTAA-TTCAATT
1 ATATTATCCCCGTGCATTTGCATCAAG-TTTTTCGGTTTATGATTGGAACTGAGTAATTTCAATT
29833 CTAAATAAAATTTTATCTAAGCAATCAAGTTAAAT-GAGAGGAAATATTATAAGAATTATA
65 CTAAATAAAATTTTATCTAAGCAATCAAGTTAAATGGA-AGGAAATATTATAAGAATTATA
29893 ATTTCTATTT
Statistics
Matches: 111, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
143 2 0.02
144 74 0.67
145 35 0.32
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (145 bp):
ATATTATCCCCGTGCATTTGCATCAAGTTTTTCGGTTTATGATTGGAACTGAGTAATTTCAATTC
TAAATAAAATTTTATCTAAGCAATCAAGTTAAATGGAAGGAAATATTATAAGAATTATACGATAA
TGATAATATAACTAG
Found at i:31131 original size:149 final size:148
Alignment explanation
Indices: 30904--31180 Score: 407
Period size: 149 Copynumber: 1.9 Consensus size: 148
30894 TTTCATTAAA
* * * *
30904 AAAAAGGGTAATTTGCTCCCTTTTTATAAGTCTGTGTGTGCAAATTGGTGATTTTGGAATTTAAC
1 AAAAAGGGTAATTTGCTCCCTTTTTACAAGTCTGGGTGTGCAAATTGCTAATTTTGGAATTTAAC
*
30969 CACCCATCCAAAAAGGCTAATTTGCTCCTTTTTACAAGT-CTAGGCATGCAATTGGTAATTTTTG
66 CACCCATCCAAAAAGGCTAATTTGCTCATTTTTACAAGTAC-AGGCATGCAATTGGTAATTTTTG
31033 GAATTTAACAGTTCTATCC
130 GAATTTAACAGTTCTATCC
* *
31052 AAAAAGGTTAATTTGCT-CCTTTTTACAAGTTTGGGTGTGC-AATTGCTAATTTTGGAATTTAAC
1 AAAAAGGGTAATTTGCTCCCTTTTTACAAGTCTGGGTGTGCAAATTGCTAATTTTGGAATTTAAC
* * *
31115 CAATTTCCATCTAAAAAGGCTAATTTGCTCATTTTTACAAGTACAGGCGTGCAATTGGTAATTTT
66 C-A--CCCATCCAAAAAGGCTAATTTGCTCATTTTTACAAGTACAGGCATGCAATTGGTAATTTT
31180 T
128 T
31181 TATTCATTTT
Statistics
Matches: 115, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
146 22 0.19
147 21 0.18
148 16 0.14
149 55 0.48
150 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (148 bp):
AAAAAGGGTAATTTGCTCCCTTTTTACAAGTCTGGGTGTGCAAATTGCTAATTTTGGAATTTAAC
CACCCATCCAAAAAGGCTAATTTGCTCATTTTTACAAGTACAGGCATGCAATTGGTAATTTTTGG
AATTTAACAGTTCTATCC
Found at i:31155 original size:75 final size:73
Alignment explanation
Indices: 30904--31179 Score: 326
Period size: 74 Copynumber: 3.7 Consensus size: 73
30894 TTTCATTAAA
* * * *
30904 AAAAAGGGTAATTTGCTCCCTTTTTATAAGTCT-GTGTGTGCAAATTGGTGATTTTGGAATTTAA
1 AAAAAGGCTAATTTGCT-CCTTTTTACAAGTCTAG-GCGTGC-AATTGGTAATTTTGGAATTTAA
*
30968 CCA-CCCATCC
63 CCATTCCATCC
*
30978 AAAAAGGCTAATTTGCTCCTTTTTACAAGTCTAGGCATGCAATTGGTAATTTTTGGAATTTAA-C
1 AAAAAGGCTAATTTGCTCCTTTTTACAAGTCTAGGCGTGCAATTGGTAA-TTTTGGAATTTAACC
*
31042 AGTTCTATCC
65 A-TTCCATCC
* * * * *
31052 AAAAAGGTTAATTTGCTCCTTTTTACAAGTTTGGGTGTGCAATTGCTAATTTTGGAATTTAACCA
1 AAAAAGGCTAATTTGCTCCTTTTTACAAGTCTAGGCGTGCAATTGGTAATTTTGGAATTTAACC-
*
31117 ATTTCCATCT
65 A-TTCCATCC
*
31127 AAAAAGGCTAATTTGCTCATTTTTACAAGTAC-AGGCGTGCAATTGGTAATTTT
1 AAAAAGGCTAATTTGCTCCTTTTTACAAGT-CTAGGCGTGCAATTGGTAATTTT
31180 TTATTCATTT
Statistics
Matches: 173, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
72 10 0.06
73 44 0.25
74 66 0.38
75 53 0.31
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (73 bp):
AAAAAGGCTAATTTGCTCCTTTTTACAAGTCTAGGCGTGCAATTGGTAATTTTGGAATTTAACCA
TTCCATCC
Found at i:32745 original size:31 final size:31
Alignment explanation
Indices: 32676--32838 Score: 164
Period size: 31 Copynumber: 5.5 Consensus size: 31
32666 TCCTTTTGTG
* * * * **
32676 CACGTGGCATGCCAAGTGCCATTTTTTGAAA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
32707 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
32738 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
32769 CACGT---G-G-CAC--G--ACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
*
32791 CATGTGGCGTGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
32822 CACGTGGCGTGCCACGT
1 CACGTGGCGTGCCACGT
32839 CGGACACCGT
Statistics
Matches: 110, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
22 15 0.14
24 1 0.01
25 1 0.01
26 3 0.03
27 4 0.04
28 1 0.01
29 1 0.01
31 84 0.76
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:32798 original size:53 final size:53
Alignment explanation
Indices: 32727--32829 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
32717 GCCACGTGTC
*
32727 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACACGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACGTGTCACTTTTTGGTACACGTGGCACG
* *
32780 ACTTTTTGGTACATGTGGCGTGCCACGTGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACGTGTCACTTTTTGGTACACGTGGC
32830 GTGCCACGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACGTGTCACTTTTTGGTACACGTGGCACG
Found at i:46952 original size:16 final size:16
Alignment explanation
Indices: 46931--46963 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
46921 GCTTGGTTGC
46931 ATCCTGGATGGTTCCA
1 ATCCTGGATGGTTCCA
46947 ATCCTGGATGGTTCCA
1 ATCCTGGATGGTTCCA
46963 A
1 A
46964 GATCTATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (16 bp):
ATCCTGGATGGTTCCA
Found at i:51833 original size:25 final size:26
Alignment explanation
Indices: 51799--51851 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
51789 AATATTCTTA
* *
51799 TTCAATGTTACT-AAAAATGCAGTTG
1 TTCAAGGTTACTAAAAAATGCAATTG
51824 TTCAAGGTTACTAAAAAATGCAATTG
1 TTCAAGGTTACTAAAAAATGCAATTG
51850 TT
1 TT
51852 ATTAAGGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (26 bp):
TTCAAGGTTACTAAAAAATGCAATTG
Found at i:52182 original size:20 final size:22
Alignment explanation
Indices: 52149--52188 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
52139 CAAAAAACTT
52149 ATATATATATATATTATAAATA
1 ATATATATATATATTATAAATA
52171 ATAT-TATA-ATATTATAAA
1 ATATATATATATATTATAAA
52189 CAAATTCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATATATATATATTATAAATA
Found at i:56050 original size:6 final size:6
Alignment explanation
Indices: 56041--56067 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56031 TTTATATAAT
56041 ATAAAG ATAAAG ATAAAG ATAAAG ATA
1 ATAAAG ATAAAG ATAAAG ATAAAG ATA
56068 TATATATATA
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:0.67, C:0.00, G:0.15, T:0.19
Consensus pattern (6 bp):
ATAAAG
Found at i:57302 original size:27 final size:27
Alignment explanation
Indices: 57251--57302 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
57241 TACTCAACTT
* *
57251 TTCCTACTCCTTTACATTACCAAACGA
1 TTCCTACTCCTTAACAATACCAAACGA
*
57278 TTCCTACTCCTTAACAATACTAAAC
1 TTCCTACTCCTTAACAATACCAAAC
57303 TACACCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.33
Consensus pattern (27 bp):
TTCCTACTCCTTAACAATACCAAACGA
Found at i:60587 original size:21 final size:23
Alignment explanation
Indices: 60562--60606 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
60552 CACAACAATA
60562 ATTTAG-TT-AAAAAATAAATTG
1 ATTTAGTTTAAAAAAATAAATTG
*
60583 ATTTAGTTTAAAAAAATGAATTG
1 ATTTAGTTTAAAAAAATAAATTG
60606 A
1 A
60607 ATGACAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 2 0.10
23 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (23 bp):
ATTTAGTTTAAAAAAATAAATTG
Found at i:61614 original size:441 final size:433
Alignment explanation
Indices: 60720--61616 Score: 958
Period size: 446 Copynumber: 2.0 Consensus size: 433
60710 CCAAAGTGAC
* * *
60720 CATTTGATAAATAATTCAAATAAAAATTGTTTGTTGATGAGACGAAATATAAAAATTTCCTCTTA
1 CATTTGATAAATAATCCAAATAAAAAATGTTTGTTGATGAGACGAAACATAAAAATTTCCTCTTA
* * ** **
60785 AACTTTTCATGAAACTCGTCGATCAAATTTAGTATCGGGTCCTTCATGAAAGTTTTAGATCATGC
66 AAC-TTTCATGAAACTCGTCAATCAAATTCAACATCGGGTCCTTCATGAAAGTCGTAGATCATGC
** ** * * * * *
60850 AATAACCTTTTAATTGAACTTGAATAACATCAATCAGATATGTGGATCGAAAGTTATATGATATT
130 AATAACCTTTTAAACGAACTACAATAACATCAATCAGATATATGGATCAAAAATTATATAAAATT
* * * * *
60915 AAATAGATCGGCAATCGAAACCAACAAATTTCAGAGGCATTATTTAGAGTTGAAACATAAAAATT
195 AAATAGACCGGCAATCGAAACCAACAAATTTCAGAAGCATTATATAGAGCTGAAAAATAAAAATT
* * *
60980 GGATTGTGAGTCCTTAATGAAAGTTATAGTCTTGTAGATCATGAAAATACCTTTTAATAGACATT
260 AGATTGTGAGTCCTTAATGAAAG-T-TA----TGTAGATCAAGAAAATACCTTTTAATAGACACT
* * *
61045 TGAATCACCTTAAATGGACAAATATAACAAAAAATATACGAATAAAGCTGAAGAATTTAATCGAT
319 TGAATCACCTTAAATGGAAAAATATAACAAAAAATAAACGAATAAAGCTGAAGAATTAAATCGAT
* * * *
61110 TAAGATAGAATTAATAAAGGACTTAGTATGAAATAGAAAAGTATGAGGGT
384 TAAAACAGAATTAATAAAGGACTTAGCATGAAAGAGAAAAGTATGAGGGT
* **
61160 CAATTGATAAATAATCCAAATAAAAAATGTTTGTTGATTGAGGTGAAACAT-AAAATTTCCTCTT
1 CATTTGATAAATAATCCAAATAAAAAATGTTTGTTGA-TGAGACGAAACATAAAAATTTCCTCTT
* *
61224 GAGTAC-TTCATGAAACTCGTCAATCAAATTCAACATTCGGGTCCTTCATGAAAGTCGTAGGTCA
65 -A-AACTTTCATGAAACTCGTCAATCAAATTCAACA-TCGGGTCCTTCATGAAAGTCGTAGATCA
*
61288 TGCAATAACCTTTTAAACGACACTACAATAACTTCAAT-AGGATATATATATGGATCAAAAATTA
127 TGCAATAACCTTTTAAACGA-ACTACAATAACATCAATCA-G----ATATATGGATCAAAAATTA
* *
61352 TATAAAATTAAATAGACCGGCAATCGAAACCACCAAATTTCGGAAGCATT-TAATAGAGCTGAAA
186 TATAAAATTAAATAGACCGGCAATCGAAACCAACAAATTTCAGAAGCATTAT-ATAGAGCTGAAA
* * * * *
61416 AATAAAAATTAGTTTTTGATTCC-TACATGAAAG-TA-GTAGATCAAGAAATTACCTTTTAATGG
250 AATAAAAATTAGATTGTGAGTCCTTA-ATGAAAGTTATGTAGATCAAGAAAATACCTTTTAATAG
* * * * **
61478 ACACTTGAATTACCTT-AATCGGAAAAATATAA-TAAAAATAAAAC-AATTAAA-ATCGATGCGT
314 ACACTTGAATCACCTTAAAT-GGAAAAATATAACAAAAAAT-AAACGAA-TAAAGCT-GAAGAAT
*
61539 TAAATCGATTAAAACAGAA-TAAGTAAAGGATTGAATAGCAT-AAAGGAGAAAAGTATG-GGGAT
375 TAAATCGATTAAAACAGAATTAA-TAAAGGACT---TAGCATGAAA-GAGAAAAGTATGAGGG-T
61601 CATTTGATAAATAATC
1 CATTTGATAAATAATC
61617 TAAAAAAGTT
Statistics
Matches: 381, Mismatches: 54, Indels: 43
0.80 0.11 0.09
Matches are distributed among these distances:
437 15 0.04
438 84 0.22
440 78 0.20
441 87 0.23
442 17 0.04
443 2 0.01
445 3 0.01
446 95 0.25
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (433 bp):
CATTTGATAAATAATCCAAATAAAAAATGTTTGTTGATGAGACGAAACATAAAAATTTCCTCTTA
AACTTTCATGAAACTCGTCAATCAAATTCAACATCGGGTCCTTCATGAAAGTCGTAGATCATGCA
ATAACCTTTTAAACGAACTACAATAACATCAATCAGATATATGGATCAAAAATTATATAAAATTA
AATAGACCGGCAATCGAAACCAACAAATTTCAGAAGCATTATATAGAGCTGAAAAATAAAAATTA
GATTGTGAGTCCTTAATGAAAGTTATGTAGATCAAGAAAATACCTTTTAATAGACACTTGAATCA
CCTTAAATGGAAAAATATAACAAAAAATAAACGAATAAAGCTGAAGAATTAAATCGATTAAAACA
GAATTAATAAAGGACTTAGCATGAAAGAGAAAAGTATGAGGGT
Found at i:62965 original size:31 final size:31
Alignment explanation
Indices: 62927--62989 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
62917 AGTTTTGTAA
* * *
62927 AACTTTTGAAGTGTTTATTGTACCTTTATTT
1 AACTTTTGAAATGCTTATTATACCTTTATTT
*
62958 AACTTTTGAAATGCTTATTATATCTTTATTT
1 AACTTTTGAAATGCTTATTATACCTTTATTT
62989 A
1 A
62990 TCTAACATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (31 bp):
AACTTTTGAAATGCTTATTATACCTTTATTT
Found at i:70005 original size:32 final size:32
Alignment explanation
Indices: 69969--70036 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
69959 GACCTTGTCT
69969 GCGCACCATGCCCGGCCCT-TGCCAAGCCATCC
1 GCGCACCATGCCCGG-CCTATGCCAAGCCATCC
**
70001 GCGCACCATGCCCGGCCTATGCCGTGCCATCC
1 GCGCACCATGCCCGGCCTATGCCAAGCCATCC
70033 GCGC
1 GCGC
70037 GCCCAACCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 3 0.09
32 30 0.91
ACGTcount: A:0.13, C:0.49, G:0.25, T:0.13
Consensus pattern (32 bp):
GCGCACCATGCCCGGCCTATGCCAAGCCATCC
Found at i:73891 original size:25 final size:24
Alignment explanation
Indices: 73863--73909 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
73853 CCAGCAGATG
73863 TGAGGAAATTGTGGGAAGATTATTT
1 TGAGGAAA-TGTGGGAAGATTATTT
* **
73888 TGAGGCAATGTTTGAAGATTAT
1 TGAGGAAATGTGGGAAGATTAT
73910 AAGAGAATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (24 bp):
TGAGGAAATGTGGGAAGATTATTT
Found at i:77810 original size:32 final size:32
Alignment explanation
Indices: 77769--77829 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
77759 GTGTAATGTA
77769 GAGCTGTTGGTATAGGTGTATACCAACGGCCC
1 GAGCTGTTGGTATAGGTGTATACCAACGGCCC
77801 GAGCTGTTGGTATAGGTGTATACCAACGG
1 GAGCTGTTGGTATAGGTGTATACCAACGG
77830 ACAGGCATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (32 bp):
GAGCTGTTGGTATAGGTGTATACCAACGGCCC
Found at i:77843 original size:30 final size:32
Alignment explanation
Indices: 77768--77844 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
77758 TGTGTAATGT
* *
77768 AGAGCTGTTGGTATAGGTGTATACCAACGGCC
1 AGAGCTATTGGTATAGGTGTATACCAACGGAC
* *
77800 CGAGCTGTTGGTATAGGTGTATACCAACGGAC
1 AGAGCTATTGGTATAGGTGTATACCAACGGAC
77832 AG-GC-ATTGGTATA
1 AGAGCTATTGGTATA
77845 CCGTATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 8 0.20
31 2 0.05
32 31 0.76
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (32 bp):
AGAGCTATTGGTATAGGTGTATACCAACGGAC
Done.