Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007600.1 Corchorus capsularis cultivar CVL-1 contig07621, 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: 39766
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:49 original size:33 final size:33
Alignment explanation
Indices: 2--73 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
1 G
*
2 CCATGGCTAAGCCGCCCTC-CTGGGGCGACACTA
1 CCATGGCCAAGCCG-CCTCGCTGGGGCGACACTA
* * *
35 CCATGGCCAGGCCGCCTCGCTGGGGCGGCCCTA
1 CCATGGCCAAGCCGCCTCGCTGGGGCGACACTA
68 CCATGG
1 CCATGG
74 ATAGACCGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 4 0.12
33 30 0.88
ACGTcount: A:0.14, C:0.40, G:0.32, T:0.14
Consensus pattern (33 bp):
CCATGGCCAAGCCGCCTCGCTGGGGCGACACTA
Found at i:83 original size:33 final size:32
Alignment explanation
Indices: 17--97 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
7 GCTAAGCCGC
* * *
17 CCTCCTGGGGCGACACTACCATGGCCAGGCCG
1 CCTCCTGGGGCGGCACTACCATGGACAGACCG
* *
49 CCTCGCTGGGGCGGCCCTACCATGGATAGACCG
1 CCTC-CTGGGGCGGCACTACCATGGACAGACCG
*
82 CCCCCTTGGGGCGGCA
1 CCTCC-TGGGGCGGCA
98 TCGGTACTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 5 0.12
33 35 0.88
ACGTcount: A:0.14, C:0.40, G:0.33, T:0.14
Consensus pattern (32 bp):
CCTCCTGGGGCGGCACTACCATGGACAGACCG
Found at i:256 original size:33 final size:32
Alignment explanation
Indices: 138--254 Score: 162
Period size: 32 Copynumber: 3.6 Consensus size: 32
128 AGAAAGCCTT
* * *
138 GCCGCCCTAGTGGGGCGGCTAGCCGTGTCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGACAGA
*
170 GCCGTCCTAGTGGGGCGGCTAGCCGTGACAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGACAGA
* * *
202 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCCGA
1 GCCGTCCTAGTGGGGAGGCT-AGCCGTGACAGA
235 GCCGTCCTAGTGGGGAGGCT
1 GCCGTCCTAGTGGGGAGGCT
255 CCACGTGGCT
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 49 0.63
33 29 0.37
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (32 bp):
GCCGTCCTAGTGGGGAGGCTAGCCGTGACAGA
Found at i:372 original size:57 final size:58
Alignment explanation
Indices: 284--401 Score: 202
Period size: 57 Copynumber: 2.1 Consensus size: 58
274 AGTGAAAAAC
284 TGGCAAAGGTCAAAGGACAAAAGTGTAAAAAATGGGGCGGTGAATAAC-AAAATAGGG
1 TGGCAAAGGTCAAAGGACAAAAGTGTAAAAAATGGGGCGGTGAATAACAAAAATAGGG
* * *
341 TGGCAAAGGTCAAAGGGCAAAAGTGTAAAAAATGGGGCGGTGAATAGCAAAAATATGG
1 TGGCAAAGGTCAAAGGACAAAAGTGTAAAAAATGGGGCGGTGAATAACAAAAATAGGG
399 TGG
1 TGG
402 TATTTAGCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 46 0.81
58 11 0.19
ACGTcount: A:0.43, C:0.08, G:0.33, T:0.15
Consensus pattern (58 bp):
TGGCAAAGGTCAAAGGACAAAAGTGTAAAAAATGGGGCGGTGAATAACAAAAATAGGG
Found at i:1304 original size:22 final size:22
Alignment explanation
Indices: 1278--1326 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1268 GAATTTCGAG
* *
1278 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
1300 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
1322 AACCT
1 AACCT
1327 CTCTAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:1412 original size:23 final size:22
Alignment explanation
Indices: 1383--1437 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1373 CAATTAAATT
*
1383 TTGATAACCAACAATATGAGATG
1 TTGATAACCAAC-ATATGAGATA
** *
1406 TTGATAACCTTCATATGATATA
1 TTGATAACCAACATATGAGATA
1428 TTGATAACCA
1 TTGATAACCA
1438 TGTTATGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (22 bp):
TTGATAACCAACATATGAGATA
Found at i:1554 original size:23 final size:23
Alignment explanation
Indices: 1487--1612 Score: 102
Period size: 23 Copynumber: 5.6 Consensus size: 23
1477 AATCGCACTC
*
1487 TGAAATTTTGAT-AATC-ACACTA
1 TGAAATTTTGATAAATCTTC-CTA
*
1509 TG-AATTTGTGAT-AA-CCTCGCTA
1 TGAAATTT-TGATAAATCTTC-CTA
1531 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
1554 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
1577 TAAAATTTTGATAACT-TTCTTA
1 TGAAATTTTGATAAATCTTCCTA
*
1599 TGAAATCTTGATAA
1 TGAAATTTTGATAA
1613 CTACAAATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
21 6 0.07
22 34 0.39
23 44 0.51
24 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (23 bp):
TGAAATTTTGATAAATCTTCCTA
Found at i:1583 original size:46 final size:45
Alignment explanation
Indices: 1511--1612 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 45
1501 TCACACTATG
* *
1511 AATTTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTCCTATAA
1 AATTT-TGATAAACCTCCCTATAAAATTTTGATAAAT-TTCCTATAA
* * *
1557 AATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGA
1 AATTTTGATAAACCTCCCTATAAAATTTTGATAAATTTCCTATAA
*
1602 AATCTTGATAA
1 AATTTTGATAA
1613 CTACAAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
45 21 0.43
46 28 0.57
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (45 bp):
AATTTTGATAAACCTCCCTATAAAATTTTGATAAATTTCCTATAA
Found at i:3405 original size:22 final size:22
Alignment explanation
Indices: 3380--3691 Score: 143
Period size: 22 Copynumber: 14.5 Consensus size: 22
3370 TCACACTTTA
*
3380 AAATTTTGATAATCACACTATG
1 AAATTTTGATAATCTCACTATG
** * *
3402 AAATTGAGATAACCTCGCTATG
1 AAATTTTGATAATCTCACTATG
*
3424 AAATTTTGATAAATCTTC-CTATA
1 AAATTTTGAT-AATC-TCACTATG
* * * *
3447 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGAT-AATCTCACTATG
* *
3470 AAATTTTGATAACTTTC-TTATG
1 AAATTTTGATAA-TCTCACTATG
*
3492 AAATCTTGATAA-CT-AC----
1 AAATTTTGATAATCTCACTATG
* *
3508 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAATCTCACTATG
** * *
3530 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAATCTCACTATG
* *
3552 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAATCTCACTATG
* * *
3574 AAATCTTGATCTATAT-ACTATG
1 AAATTTTGAT-AATCTCACTATG
* *
3596 AAATTTTGATAACCCTC-TTATG
1 AAATTTTGATAA-TCTCACTATG
* *
3618 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAATCT-CACTATG
* * *
3640 AAAATTTGATAACCTTC-GTATG
1 AAATTTTGATAATC-TCACTATG
*
3662 AAAGTTTGAT-ATCCTCAC--TG
1 AAATTTTGATAAT-CTCACTATG
3682 -AATTTTGATA
1 AAATTTTGATA
3692 TCCTCCCTGA
Statistics
Matches: 216, Mismatches: 53, Indels: 44
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
19 8 0.04
20 5 0.02
21 6 0.03
22 138 0.64
23 42 0.19
24 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAATCTCACTATG
Found at i:3450 original size:23 final size:23
Alignment explanation
Indices: 3419--3503 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
3409 GATAACCTCG
*
3419 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* * *
3442 CTATAAAATTTTAATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
3465 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
3487 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
3504 CTACAAATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 16 0.31
23 35 0.69
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:3735 original size:19 final size:19
Alignment explanation
Indices: 3666--3729 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
3656 CGTATGAAAG
*
3666 TTTGATATCCTCACTGAAT
1 TTTGATATCCTCCCTGAAT
3685 TTTGATATCCTCCCTGAAT
1 TTTGATATCCTCCCTGAAT
*
3704 TTTGGTATCCTCCCTGAAAT
1 TTTGATATCCTCCCTG-AAT
3724 TTTGAT
1 TTTGAT
3730 TACTCCATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 33 0.80
20 8 0.20
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (19 bp):
TTTGATATCCTCCCTGAAT
Found at i:3886 original size:21 final size:22
Alignment explanation
Indices: 3835--3886 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
3825 AATCACATTT
* *
3835 TGAAAAATTGATAACCTCTTTA
1 TGAAAATTTGATAACATCTTTA
3857 TGAAAATTTGATAACATCTTTA
1 TGAAAATTTGATAACATCTTTA
3879 T-AAAATTT
1 TGAAAATTT
3887 TGTTGACCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (22 bp):
TGAAAATTTGATAACATCTTTA
Found at i:3888 original size:22 final size:22
Alignment explanation
Indices: 3842--4127 Score: 125
Period size: 22 Copynumber: 13.0 Consensus size: 22
3832 TTTTGAAAAA
* *
3842 TTGATAACCTCTTTATGAAAAT
1 TTGATAACATCTTTATGAAATT
*
3864 TTGATAACATCTTTATAAAATT
1 TTGATAACATCTTTATGAAATT
* * ** *
3886 TTGTTGACCCCTCTATGAAATT
1 TTGATAACATCTTTATGAAATT
* **
3908 TTGATAATCA-CATTATTTAATT
1 TTGATAA-CATCTTTATGAAATT
* *
3930 TTGATAA-ACCCGCTT-TGAAATT
1 TTGATAACA-TC-TTTATGAAATT
* * **
3952 TTGGTAACAACACTATGAAATT
1 TTGATAACATCTTTATGAAATT
3974 TTGAT-A-ATCTTCATAT-AAATT
1 TTGATAACATCTT--TATGAAATT
3995 TTGATAATCCTATCTTTATGAAATT
1 TTGATAA--C-ATCTTTATGAAATT
4020 TTGAT-A-ATCTTCATAT-AAATT
1 TTGATAACATCTT--TATGAAATT
4041 TTGATAATCCTATCTTTATGAAATT
1 TTGATAA--C-ATCTTTATGAAATT
* * *
4066 TCGATAATCA-CTCTATGAGA-T
1 TTGATAA-CATCTTTATGAAATT
*
4087 TTGATAAC--CTTCTATCAAATT
1 TTGATAACATCTT-TATGAAATT
* *
4108 TTGGT-AC-TCCTTATGAAATT
1 TTGATAACATCTTTATGAAATT
4128 GAGACTTTTA
Statistics
Matches: 201, Mismatches: 38, Indels: 52
0.69 0.13 0.18
Matches are distributed among these distances:
19 2 0.01
20 24 0.12
21 36 0.18
22 95 0.47
23 5 0.02
24 8 0.04
25 21 0.10
26 10 0.05
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (22 bp):
TTGATAACATCTTTATGAAATT
Found at i:4019 original size:25 final size:23
Alignment explanation
Indices: 3965--4186 Score: 139
Period size: 21 Copynumber: 9.7 Consensus size: 23
3955 GTAACAACAC
3965 TATGAAATTTTGATAAT-CTTCA
1 TATGAAATTTTGATAATCCTTCA
*
3987 TAT-AAATTTTGATAATCCTATCTT
1 TATGAAATTTTGATAATCCT-TC-A
4011 TATGAAATTTTGATAAT-CTTCA
1 TATGAAATTTTGATAATCCTTCA
*
4033 TAT-AAATTTTGATAATCCTATCTT
1 TATGAAATTTTGATAATCCT-TC-A
*
4057 TATGAAATTTCGATAATCAC-TC-
1 TATGAAATTTTGATAATC-CTTCA
*
4079 TATGAGA-TTTGATAA-CCTTC-
1 TATGAAATTTTGATAATCCTTCA
* * *
4099 TATCAAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATAATCCTTCA
*
4121 TGAAATTGAGACTTTT-ATAA-CCTTCGTA
1 T---A-TGA-AATTTTGATAATCCTTC--A
*
4149 TATGAAATTTTGATAA-CC-ACA
1 TATGAAATTTTGATAATCCTTCA
*
4170 CTATAAAATTTTGATAA
1 -TATGAAATTTTGATAA
4187 CCTCCCGATG
Statistics
Matches: 160, Mismatches: 17, Indels: 46
0.72 0.08 0.21
Matches are distributed among these distances:
19 1 0.01
20 8 0.05
21 40 0.25
22 36 0.22
23 12 0.08
24 19 0.12
25 32 0.20
26 5 0.03
27 5 0.03
28 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (23 bp):
TATGAAATTTTGATAATCCTTCA
Found at i:4021 original size:46 final size:46
Alignment explanation
Indices: 3965--4074 Score: 211
Period size: 46 Copynumber: 2.4 Consensus size: 46
3955 GTAACAACAC
3965 TATGAAATTTTGATAATCTTCATATAAATTTTGATAATCCTATCTT
1 TATGAAATTTTGATAATCTTCATATAAATTTTGATAATCCTATCTT
4011 TATGAAATTTTGATAATCTTCATATAAATTTTGATAATCCTATCTT
1 TATGAAATTTTGATAATCTTCATATAAATTTTGATAATCCTATCTT
*
4057 TATGAAATTTCGATAATC
1 TATGAAATTTTGATAATC
4075 ACTCTATGAG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (46 bp):
TATGAAATTTTGATAATCTTCATATAAATTTTGATAATCCTATCTT
Found at i:4090 original size:67 final size:67
Alignment explanation
Indices: 3964--4110 Score: 160
Period size: 67 Copynumber: 2.2 Consensus size: 67
3954 GGTAACAACA
* * * *
3964 CTATGAAATTTTGATAATCTTCATATAAATTTTGATAATCCTATCTTTATGAAATTTTGATAATC
1 CTATCAAATTTTGATAATCTTCATATAAATTTCGATAATCCTATCTCTATGAAATTTTGATAACC
4029 TT
66 TT
* *
4031 CATAT-AAATTTTGATAATCCTATCTTTATGAAATTTCGATAAT-C-A-CTCTATGAGA-TTTGA
1 C-TATCAAATTTTGATAAT-CT-TC-ATAT-AAATTTCGATAATCCTATCTCTATGAAATTTTGA
4091 TAACCTT
61 TAACCTT
4098 CTATCAAATTTTG
1 CTATCAAATTTTG
4111 GTACTCCTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
66 3 0.04
67 34 0.49
68 13 0.19
69 3 0.04
70 4 0.06
71 12 0.17
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (67 bp):
CTATCAAATTTTGATAATCTTCATATAAATTTCGATAATCCTATCTCTATGAAATTTTGATAACC
TT
Found at i:4241 original size:22 final size:22
Alignment explanation
Indices: 4149--4271 Score: 81
Period size: 22 Copynumber: 5.6 Consensus size: 22
4139 AACCTTCGTA
4149 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* * *
4171 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * * **
4193 GATGAAGTATT-AGTAACC-TTC
1 TATGAAATTTTGA-TAACCACAC
*
4214 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCACAC
* * *
4237 TATGAAA-TTCGTATAACCTCGC
1 TATGAAATTTTG-ATAACCACAC
*
4259 TATGACATTTTGA
1 TATGAAATTTTGA
4272 AATCTTTTTG
Statistics
Matches: 74, Mismatches: 21, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
21 5 0.07
22 64 0.86
23 5 0.07
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:4370 original size:24 final size:22
Alignment explanation
Indices: 4309--4492 Score: 99
Period size: 22 Copynumber: 8.3 Consensus size: 22
4299 TTGTGATAAT
* *
4309 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
4331 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
**
4353 TAA-CATGATCCTATGAAATTTTGG
1 TAACCA--A-CCTATGAAATTTTAA
**
4377 TAACC-ACTCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* * **
4399 TAA-CTACACTATGGAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
4421 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
4443 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
4465 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
4487 TAACCA
1 TAACCA
4493 CATAGAGACA
Statistics
Matches: 137, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.04
22 110 0.80
23 5 0.04
24 15 0.11
25 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:4381 original size:46 final size:44
Alignment explanation
Indices: 4316--4426 Score: 109
Period size: 46 Copynumber: 2.5 Consensus size: 44
4306 AATTAACCAC
***
4316 CCTATGAAATTTCAATAACCAAC-CTAAGAAATTTTAATAACATGA
1 CCTATGAAATTTTGGTAACCAACTCTAAGAAATTTTAATAAC-T-A
* **
4361 TCCTATGAAATTTTGGTAACC-ACTCTATGAAATTTTGGTAACTA
1 -CCTATGAAATTTTGGTAACCAACTCTAAGAAATTTTAATAACTA
*
4405 CACTATGGAATTTTGGTAACCA
1 C-CTATGAAATTTTGGTAACCA
4427 CACTATGGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.02
44 19 0.35
45 3 0.05
46 32 0.58
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCAACTCTAAGAAATTTTAATAACTA
Found at i:4421 original size:44 final size:42
Alignment explanation
Indices: 4361--4490 Score: 145
Period size: 44 Copynumber: 3.0 Consensus size: 42
4351 AATAACATGA
* *
4361 TCCTATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAAC
1 TCCTATGGAATTTTGGTAACCACTCTATGAAATTTTGATAAC
* *
4403 TACACTATGGAATTTTGGTAACCACACTATGGAATTTTGATAACC
1 T-C-CTATGGAATTTTGGTAACCACTCTATGAAATTTTGATAA-C
* **
4448 TCCTCATGGAATTATAATAACCA-TCTTATGAAATTTTGATAAC
1 TCCT-ATGGAATTTTGGTAACCACTC-TATGAAATTTTGATAAC
4491 CACATAGAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
42 1 0.01
43 5 0.07
44 66 0.89
45 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (42 bp):
TCCTATGGAATTTTGGTAACCACTCTATGAAATTTTGATAAC
Found at i:4779 original size:30 final size:31
Alignment explanation
Indices: 4745--4809 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
4735 TGTCAATTTA
* *
4745 GAAATATGTTTTTAAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
4775 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
4806 GAAA
1 GAAA
4810 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:13150 original size:63 final size:63
Alignment explanation
Indices: 13049--13424 Score: 644
Period size: 63 Copynumber: 6.0 Consensus size: 63
13039 GAGAGATTTT
* *
13049 CTGGTAAAACTTATGTACCTGGTATTAGCGGTGACACTGTTTATGAACCAAAGCAAAATATTG
1 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
* *
13112 CTGGTAAAACTCATGTACCTGGTATTGGTGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
1 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
*
13175 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAGTATTG
1 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
* * *
13238 CTGGTAAAACTCATGTAACTGGTATTAGTGGTTGGCACTGTTTATGAACCAAAGCAACATATTG
1 CTGGTAAAACTCATGTACCTGGTATTAGCGG-TGGCACTGTTTATGAACCAAAGCAAAATATTG
13302 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
1 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
* * *
13365 CTGGTAATACTAATGTACCTGGTATTAGCGGTGGCACTGTTCATGAACCAAAGCAAAATA
1 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATA
13425 AAGGTTCTTT
Statistics
Matches: 295, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
63 236 0.80
64 59 0.20
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (63 bp):
CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
Found at i:13333 original size:127 final size:126
Alignment explanation
Indices: 13049--13424 Score: 653
Period size: 127 Copynumber: 3.0 Consensus size: 126
13039 GAGAGATTTT
* *
13049 CTGGTAAAACTTATGTACCTGGTATTAGCGGTGACACTGTTTATGAACCAAAGCAAAATATTGCT
1 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCT
*
13114 GGTAAAACTCATGTACCTGGTATTGGTGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
66 GGTAAAACTCATGTACCTGGTATTAGTGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
*
13175 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAGTATTGCT
1 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCT
* *
13240 GGTAAAACTCATGTAACTGGTATTAGTGGTTGGCACTGTTTATGAACCAAAGCAACATATTG
66 GGTAAAACTCATGTACCTGGTATTAGTGG-TGGCACTGTTTATGAACCAAAGCAAAATATTG
13302 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCT
1 CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCT
* * * *
13367 GGTAATACTAATGTACCTGGTATTAGCGGTGGCACTGTTCATGAACCAAAGCAAAATA
66 GGTAAAACTCATGTACCTGGTATTAGTGGTGGCACTGTTTATGAACCAAAGCAAAATA
13425 AAGGTTCTTT
Statistics
Matches: 236, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
126 116 0.49
127 120 0.51
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (126 bp):
CTGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCT
GGTAAAACTCATGTACCTGGTATTAGTGGTGGCACTGTTTATGAACCAAAGCAAAATATTG
Found at i:13371 original size:190 final size:189
Alignment explanation
Indices: 13049--13421 Score: 647
Period size: 190 Copynumber: 2.0 Consensus size: 189
13039 GAGAGATTTT
* *
13049 CTGGTAAAACTTATGTACCTGGTATTAGCGGTGACACTGTTTATGAACCAAAGCAAAATATTGCT
1 CTGGTAAAACTCATGTAACTGGTATTAGCGGTGACACTGTTTATGAACCAAAGCAAAATATTGCT
* *
13114 GGTAAAACTCATGTACCTGGTATTGGTGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCTGG
66 GGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCTGG
* *
13179 TAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAGTATTG
131 TAAAACTAATGTACCTGGTATTAGCGGTGGCACTGTTCATGAACCAAAGCAAAGTATTG
* * *
13238 CTGGTAAAACTCATGTAACTGGTATTAGTGGTTGGCACTGTTTATGAACCAAAGCAACATATTGC
1 CTGGTAAAACTCATGTAACTGGTATTAGCGG-TGACACTGTTTATGAACCAAAGCAAAATATTGC
13303 TGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCTG
65 TGGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCTG
*
13368 GTAATACTAATGTACCTGGTATTAGCGGTGGCACTGTTCATGAACCAAAGCAAA
130 GTAAAACTAATGTACCTGGTATTAGCGGTGGCACTGTTCATGAACCAAAGCAAA
13422 ATAAAGGTTC
Statistics
Matches: 173, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
189 28 0.16
190 145 0.84
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (189 bp):
CTGGTAAAACTCATGTAACTGGTATTAGCGGTGACACTGTTTATGAACCAAAGCAAAATATTGCT
GGTAAAACTCATGTACCTGGTATTAGCGGTGGCACTGTTTATGAACCAAAGCAAAATATTGCTGG
TAAAACTAATGTACCTGGTATTAGCGGTGGCACTGTTCATGAACCAAAGCAAAGTATTG
Found at i:16925 original size:16 final size:16
Alignment explanation
Indices: 16906--16956 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
16896 ATAAAATAAT
16906 AATTCTTCAAAAAAAG
1 AATTCTTCAAAAAAAG
** * *
16922 AATTAAT-AAAATAAT
1 AATTCTTCAAAAAAAG
16937 AATTCTTCAAAAAAAG
1 AATTCTTCAAAAAAAG
16953 AATT
1 AATT
16957 AATAAAATAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (16 bp):
AATTCTTCAAAAAAAG
Found at i:16926 original size:31 final size:31
Alignment explanation
Indices: 16888--16969 Score: 164
Period size: 31 Copynumber: 2.6 Consensus size: 31
16878 GTAAGAAGAT
16888 AAGAATTAATAAAATAATAATTCTTCAAAAA
1 AAGAATTAATAAAATAATAATTCTTCAAAAA
16919 AAGAATTAATAAAATAATAATTCTTCAAAAA
1 AAGAATTAATAAAATAATAATTCTTCAAAAA
16950 AAGAATTAATAAAATAATAA
1 AAGAATTAATAAAATAATAA
16970 CAATGTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (31 bp):
AAGAATTAATAAAATAATAATTCTTCAAAAA
Found at i:19287 original size:10 final size:10
Alignment explanation
Indices: 19274--19307 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
19264 GGATGATAAA
*
19274 AAATGAGATG
1 AAATAAGATG
19284 AAATAAGATG
1 AAATAAGATG
19294 AAATAAGATG
1 AAATAAGATG
19304 AAAT
1 AAAT
19308 GTGGACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
AAATAAGATG
Found at i:23593 original size:15 final size:15
Alignment explanation
Indices: 23573--23602 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23563 GAGTATTTTC
23573 ATTAATAATAATTGA
1 ATTAATAATAATTGA
23588 ATTAATAATAATTGA
1 ATTAATAATAATTGA
23603 GTAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTAATAATAATTGA
Found at i:23882 original size:42 final size:43
Alignment explanation
Indices: 23831--23924 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
23821 AGTGTATTAC
*
23831 CTAA-ATTCTA-CTACATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAG
*
23872 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTACATCTCTAGATAATTCATCAAAATAAAG
*
23917 TTAATATT
1 CTAATATT
23925 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAG
Found at i:25845 original size:40 final size:40
Alignment explanation
Indices: 25801--25882 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
25791 GACACAATGG
*
25801 TAATGTTACAGTGAAGTTTAACATTATATATATATATATA
1 TAATGTTACAGTGAAGTTTAACACTATATATATATATATA
25841 TAATGTTACAGTGAAGTTTAACACTATATATATATATATA
1 TAATGTTACAGTGAAGTTTAACACTATATATATATATATA
25881 TA
1 TA
25883 TATATTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (40 bp):
TAATGTTACAGTGAAGTTTAACACTATATATATATATATA
Found at i:25872 original size:2 final size:2
Alignment explanation
Indices: 25865--25895 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
25855 AGTTTAACAC
25865 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25896 AACAAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26728 original size:54 final size:54
Alignment explanation
Indices: 26669--26775 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
26659 GATTGAGTTG
* *
26669 TATATTATATGGTCTTAGGAACTTAGTTTCTTCTTATTAATTTTAAATTATTTA
1 TATATTATATGGTCTTAGGAACTTAATTTCTTCTTATTAACTTTAAATTATTTA
26723 TATATTATATGGTCTTAGGAACTTAATTTCTTCTTATTAACTTTAAATTATTT
1 TATATTATATGGTCTTAGGAACTTAATTTCTTCTTATTAACTTTAAATTATTT
26776 TGTGTCCTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (54 bp):
TATATTATATGGTCTTAGGAACTTAATTTCTTCTTATTAACTTTAAATTATTTA
Found at i:36072 original size:24 final size:24
Alignment explanation
Indices: 36027--36072 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
36017 CCAAACAACA
* * **
36027 TTAATTAGTTTTAATATTAGATAT
1 TTAATTAGTTTAAACAGGAGATAT
36051 TTAATTAGTTTAAACAGGAGAT
1 TTAATTAGTTTAAACAGGAGAT
36073 TACTATAATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (24 bp):
TTAATTAGTTTAAACAGGAGATAT
Found at i:36891 original size:16 final size:15
Alignment explanation
Indices: 36866--36895 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36856 AAAATGATTA
36866 AAATACTTTTTCCTT
1 AAATACTTTTTCCTT
36881 AAATACTTTTTCCTT
1 AAATACTTTTTCCTT
36896 GGATCAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATACTTTTTCCTT
Found at i:37904 original size:17 final size:17
Alignment explanation
Indices: 37877--37919 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
37867 TAATTAAAAT
37877 TTAAATATTG-AAATTA
1 TTAAATATTGAAAATTA
37893 TTAAAGTATTGAAAATTA
1 TTAAA-TATTGAAAATTA
*
37911 TTTAATATT
1 TTAAATATT
37920 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 9 0.38
18 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
TTAAATATTGAAAATTA
Found at i:38674 original size:151 final size:151
Alignment explanation
Indices: 38396--38676 Score: 445
Period size: 151 Copynumber: 1.9 Consensus size: 151
38386 AAGGAAGAAT
* ** *
38396 ATAGTTTTTATGTTTTTATTTAATAAGGGTAATTTTGGTTTTGTAATAAAATGGTAAGATAAATT
1 ATAGTTTTTATATTTTTATTTAATAAGGGTAATTTTGGTTTAATAATAAAATGGTAAGACAAATT
* *
38461 TGACAATGAAAATTTGGTCCAAAACACACCCCTCCCAAATACCCCGATTTGAAGGGGCGGAAAAT
66 CGAAAATGAAAATTTGGTCCAAAACACACCCCTCCCAAATACCCCGATTTGAAGGGGCGGAAAAT
38526 GGGGGGATTTGGAGGGGTGGA
131 GGGGGGATTTGGAGGGGTGGA
* * *
38547 ATAGTTTTTATATTTTTATTTAATAAGGGTATTTTTGGTTTAATAATAACATGGTAGGACAAATT
1 ATAGTTTTTATATTTTTATTTAATAAGGGTAATTTTGGTTTAATAATAAAATGGTAAGACAAATT
* * * *
38612 CGAAAATGAAAATTTGGTTCAAAACCCACCCCTCCCAAATACCCCGATTTGGAGGGGTGGAAAAT
66 CGAAAATGAAAATTTGGTCCAAAACACACCCCTCCCAAATACCCCGATTTGAAGGGGCGGAAAAT
38677 AGGATTGGCC
Statistics
Matches: 117, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
151 117 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (151 bp):
ATAGTTTTTATATTTTTATTTAATAAGGGTAATTTTGGTTTAATAATAAAATGGTAAGACAAATT
CGAAAATGAAAATTTGGTCCAAAACACACCCCTCCCAAATACCCCGATTTGAAGGGGCGGAAAAT
GGGGGGATTTGGAGGGGTGGA
Done.