Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006790.1 Corchorus capsularis cultivar CVL-1 contig06811, 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: 70435
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:3260 original size:30 final size:31
Alignment explanation
Indices: 3224--3295 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 31
3214 AGTAAAAGGG
3224 GCAATCAGTAATTAAGTTCAATAAGAAA-AA
1 GCAATCAGTAATTAAGTTCAATAAGAAAGAA
* * * *
3254 GTAATCAGTGATTAGGTTCAATAAGAAAGAT
1 GCAATCAGTAATTAAGTTCAATAAGAAAGAA
3285 GCAATCAGTAA
1 GCAATCAGTAA
3296 AAAGGTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (31 bp):
GCAATCAGTAATTAAGTTCAATAAGAAAGAA
Found at i:3337 original size:22 final size:23
Alignment explanation
Indices: 3287--3361 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 23
3277 AGAAAGATGC
* *
3287 AATCAGTAAAAAGGTAAAATGGT
1 AATCAGTAAAGAGGTAAAATGAT
*
3310 AATCAGTAAAGAGG-AAAGTGAT
1 AATCAGTAAAGAGGTAAAATGAT
*
3332 AATCAGTAAAGA-GTAATA-GA-
1 AATCAGTAAAGAGGTAAAATGAT
3352 AATCAGTAAA
1 AATCAGTAAA
3362 TCAGTAATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.22
21 3 0.07
22 20 0.43
23 13 0.28
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.20
Consensus pattern (23 bp):
AATCAGTAAAGAGGTAAAATGAT
Found at i:3392 original size:34 final size:33
Alignment explanation
Indices: 3346--3467 Score: 111
Period size: 34 Copynumber: 3.5 Consensus size: 33
3336 AGTAAAGAGT
*
3346 AATAGAAATCAGTAAATCAGTAATCAGGTGAAAA
1 AATAGTAATCAGTAAATCAGTAATCAGGT-AAAA
* * * *
3380 GATAGTAATCAGTAAATC-GATAATTAAGAGTCCATAT
1 AATAGTAATCAGTAAATCAG-TAA-TCAG-GT--AAAA
* *
3417 AATAGTAATCAGTGAATCAGTAATCATGTAAAAA
1 AATAGTAATCAGTAAATCAGTAATCAGGT-AAAA
3451 AATAGTAATCAGTAAAT
1 AATAGTAATCAGTAAAT
3468 TGATAACTAA
Statistics
Matches: 69, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
33 1 0.01
34 37 0.54
35 5 0.07
36 4 0.06
37 21 0.30
38 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (33 bp):
AATAGTAATCAGTAAATCAGTAATCAGGTAAAA
Found at i:3428 original size:71 final size:71
Alignment explanation
Indices: 3345--3482 Score: 213
Period size: 71 Copynumber: 1.9 Consensus size: 71
3335 CAGTAAAGAG
* * *
3345 TAATAGAAATCAGTAAATCAGTAATCAGGTGAAAAGATAGTAATCAGTAAATCGATAATTAAGAG
1 TAATAGAAATCAGTAAATCAGTAATCAGGTAAAAAAATAGTAATCAGTAAATCGATAACTAAGAG
3410 TCCATA
66 TCCATA
* * * *
3416 TAATAGTAATCAGTGAATCAGTAATCATGTAAAAAAATAGTAATCAGTAAATTGATAACTAAGAG
1 TAATAGAAATCAGTAAATCAGTAATCAGGTAAAAAAATAGTAATCAGTAAATCGATAACTAAGAG
3481 TC
66 TC
3483 AAGGTAAGAG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (71 bp):
TAATAGAAATCAGTAAATCAGTAATCAGGTAAAAAAATAGTAATCAGTAAATCGATAACTAAGAG
TCCATA
Found at i:3520 original size:32 final size:32
Alignment explanation
Indices: 3476--3541 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
3466 ATTGATAACT
*
3476 AAGAGTCAAGGTAAGAGAT-TAATCAGTAATTA
1 AAGAGTCAAGGTAA-AAATATAATCAGTAATTA
*
3508 AAGAGTCTAGGTAAAAATAGTAATCAGTAATTA
1 AAGAGTCAAGGTAAAAATA-TAATCAGTAATTA
3541 A
1 A
3542 GTGAAAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 3 0.10
32 13 0.43
33 14 0.47
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (32 bp):
AAGAGTCAAGGTAAAAATATAATCAGTAATTA
Found at i:3557 original size:26 final size:26
Alignment explanation
Indices: 3528--3616 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 26
3518 GTAAAAATAG
3528 TAATCAGTAATTAAGTGAAAAGAGAT
1 TAATCAGTAATTAAGTGAAAAGAGAT
*
3554 TAATCAGAGTCAA--AAGT-AATAGTA-AT
1 TAATC--AGT-AATTAAGTGAAAAG-AGAT
3580 CAGTAAATCAGTAATTAAGTGAAAAGAGAT
1 ---T-AATCAGTAATTAAGTGAAAAGAGAT
3610 TAATCAG
1 TAATCAG
3617 AGTCAAAGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 24
0.65 0.03 0.32
Matches are distributed among these distances:
26 17 0.35
27 8 0.16
28 6 0.12
29 8 0.16
30 10 0.20
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (26 bp):
TAATCAGTAATTAAGTGAAAAGAGAT
Found at i:3625 original size:26 final size:26
Alignment explanation
Indices: 3540--3625 Score: 61
Period size: 26 Copynumber: 3.2 Consensus size: 26
3530 ATCAGTAATT
3540 AAGTGAAAAGAGATTAATCAGAGTCAA
1 AAGTGAAAAGAGATTAATCAGAGTC-A
* * *
3567 AAGT-AATAGTA-ATCAGTAAATCAGTAAT-T
1 AAGTGAAAAG-AGAT---T-AATCAG-AGTCA
3596 AAGTGAAAAGAGATTAATCAGAGTCA
1 AAGTGAAAAGAGATTAATCAGAGTCA
3622 AAGT
1 AAGT
3626 AGTAGTAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 19
0.64 0.09 0.28
Matches are distributed among these distances:
25 2 0.05
26 16 0.36
27 6 0.14
29 6 0.14
30 12 0.27
31 2 0.05
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (26 bp):
AAGTGAAAAGAGATTAATCAGAGTCA
Found at i:3633 original size:55 final size:55
Alignment explanation
Indices: 3529--3763 Score: 400
Period size: 55 Copynumber: 4.3 Consensus size: 55
3519 TAAAAATAGT
*
3529 AATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC-AAAGTAATAGTAATCAGTA
* *
3585 AATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
3640 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
3695 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
3750 AATC-GATAATTAAG
1 AATCAG-TAATTAAG
3764 AGTTAAAATG
Statistics
Matches: 174, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
54 1 0.01
55 137 0.79
56 36 0.21
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
Found at i:3644 original size:29 final size:29
Alignment explanation
Indices: 3611--3700 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
3601 AAAAGAGATT
3611 AATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGAGTCAAAGTAGTAGTAATCAGTA
* * ** *
3640 AATC--AGT--AATTAAGTA-AAAAGAGATT
1 AATCAGAGTCAAAGT-AGTAGTAATCAG-TA
3666 AATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGAGTCAAAGTAGTAGTAATCAGTA
3695 AATCAG
1 AATCAG
3701 TAATTAAGTA
Statistics
Matches: 44, Mismatches: 10, Indels: 14
0.65 0.15 0.21
Matches are distributed among these distances:
25 7 0.16
26 9 0.20
27 3 0.07
28 3 0.07
29 15 0.34
30 7 0.16
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (29 bp):
AATCAGAGTCAAAGTAGTAGTAATCAGTA
Found at i:4003 original size:22 final size:22
Alignment explanation
Indices: 3978--4514 Score: 196
Period size: 21 Copynumber: 24.5 Consensus size: 22
3968 GGTATCTGAA
* * *
3978 AAAGGGTAAAATGGTAATTAGT
1 AAAGAGTAAAATAGTAATCAGT
4000 AAAGAGTAAAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
4022 AAAAAGTAAGAA-GGTAATCA--
1 AAAGAGTAA-AATAGTAATCAGT
*
4042 ACAAGAGTAAAATAGTACTCAGT
1 A-AAGAGTAAAATAGTAATCAGT
*
4065 AAAAAGT-AAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
4086 -AAGAGTAAAAAAGTAATAAGT
1 AAAGAGTAAAATAGTAATCAGT
* * *
4107 -AAGAAGTAAAA-GGAAATTAGT
1 AAAG-AGTAAAATAGTAATCAGT
* *
4128 -TAGAGTAAAA-AGGTGATCAGT
1 AAAGAGTAAAATA-GTAATCAGT
4149 AAAGAGTAAAA-AGCTAATCAG-
1 AAAGAGTAAAATAG-TAATCAGT
*
4170 CAAGAAGTAAAA-AGGTAATCAGT
1 AAAG-AGTAAAATA-GTAATCAGT
* * * *
4193 AAAAAGCAAAA-GGCAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* * *
4214 AAAAAGT-AAAGAGTAATCAAT
1 AAAGAGTAAAATAGTAATCAGT
* **
4235 AAA-AG-AAGAATGGTAAAAAGT
1 AAAGAGTAA-AATAGTAATCAGT
* * **
4256 AAAGAGTAATCAGTAAAGGAAGAATGGT
1 AAAGAGTAA--A--ATAGTAATCA--GT
**
4284 AAAGAGT-AAAGGGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
*
4305 AAAAAGTAAAA-AGATAATCAGT
1 AAAGAGTAAAATAG-TAATCAGT
* *
4327 AAAGAATAAAATAGTAA-AAGGT
1 AAAGAGTAAAATAGTAATCA-GT
** *
4349 AATCAATAAAAAGTAATGATAATCAGT
1 AAAGAGT-AAAA-T-A-G-TAATCAGT
*
4376 AAA-AGGT-AAA-A-TAGTAATCAGT
1 AAAGA-GTAAAATAGTA--AT-CAGT
*
4398 -AAGAGCAAAATAGTAATCA--
1 AAAGAGTAAAATAGTAATCAGT
* * *
4417 ACGATAGTAAAAAAGTAATCAGT
1 A-AAGAGTAAAATAGTAATCAGT
4440 AAA-AGGTAAAATAGTAATCAGT
1 AAAGA-GTAAAATAGTAATCAGT
* * * *
4462 -AAGAGCAAAATGGTTATTAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
4483 -TAGAGTAAAATAGTAATCTGT
1 AAAGAGTAAAATAGTAATCAGT
4504 AAAGAGTAAAA
1 AAAGAGTAAAA
4515 GGTGATCAGT
Statistics
Matches: 389, Mismatches: 78, Indels: 96
0.69 0.14 0.17
Matches are distributed among these distances:
19 2 0.01
20 21 0.05
21 157 0.40
22 152 0.39
23 21 0.05
24 4 0.01
25 5 0.01
26 8 0.02
27 9 0.02
28 10 0.03
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (22 bp):
AAAGAGTAAAATAGTAATCAGT
Found at i:4077 original size:21 final size:22
Alignment explanation
Indices: 3948--4514 Score: 225
Period size: 22 Copynumber: 25.8 Consensus size: 22
3938 AATAGCATGC
3948 AATCAGTAAAAAAGTAAAA-AGGT
1 AATCAGT-AAAAAGTAAAATA-GT
* *
3971 -ATCTG-AAAAAGGGTAAAATGGT
1 AATCAGTAAAAA--GTAAAATAGT
* *
3993 AATTAGTAAAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAATAGT
*
4015 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAAAGTAA-AATAGT
*
4037 AATCA--ACAAGAGTAAAATAGT
1 AATCAGTA-AAAAGTAAAATAGT
*
4058 ACTCAGTAAAAAGT-AAATAGT
1 AATCAGTAAAAAGTAAAATAGT
* *
4079 AATCAGT-AAGAGTAAAAAAGT
1 AATCAGTAAAAAGTAAAATAGT
* * * *
4100 AATAAGTAAGAAGTAAAA-GGA
1 AATCAGTAAAAAGTAAAATAGT
* * *
4121 AATTAGT-TAGAGTAAAA-AGGT
1 AATCAGTAAAAAGTAAAATA-GT
* *
4142 GATCAGTAAAGAGTAAAA-AGCT
1 AATCAGTAAAAAGTAAAATAG-T
* *
4164 AATCAGCAAGAAGTAAAA-AGGT
1 AATCAGTAAAAAGTAAAATA-GT
* * *
4186 AATCAGTAAAAAGCAAAA-GGC
1 AATCAGTAAAAAGTAAAATAGT
*
4207 AATCAGTAAAAAGT-AAAGAGT
1 AATCAGTAAAAAGTAAAATAGT
* *
4228 AATCAAT-AAAAG-AAGAATGGT
1 AATCAGTAAAAAGTAA-AATAGT
** * * *
4249 AAAAAGTAAAGAGTAATCAGTAAAGG
1 AATCAGTAAAAAGTAA--A--ATAGT
** * **
4275 AAGAATGGTAAAGAGT-AAAGGGT
1 AATCA--GTAAAAAGTAAAATAGT
4298 AATCAGTAAAAAGTAAAA-AGAT
1 AATCAGTAAAAAGTAAAATAG-T
4320 AATCAGTAAAGAA-TAAAATAGT
1 AATCAGTAAA-AAGTAAAATAGT
* *
4342 AA-AAGGTAATCAA-TAAAAAGTAATGAT
1 AATCA-GTAA-AAAGT-AAAA-T-A-G-T
*
4369 AATCAGTAAAAGGTAAAATAGT
1 AATCAGTAAAAAGTAAAATAGT
* *
4391 AATCAGT-AAGAGCAAAATAGT
1 AATCAGTAAAAAGTAAAATAGT
* * *
4412 AATCA--ACGATAGTAAAAAAGT
1 AATCAGTA-AAAAGTAAAATAGT
*
4433 AATCAGTAAAAGGTAAAATAGT
1 AATCAGTAAAAAGTAAAATAGT
* * *
4455 AATCAGT-AAGAGCAAAATGGT
1 AATCAGTAAAAAGTAAAATAGT
* * * *
4476 TATTAGT-TAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAATAGT
* *
4497 AATCTGTAAAGAGTAAAA
1 AATCAGTAAAAAGTAAAA
4515 GGTGATCAGT
Statistics
Matches: 410, Mismatches: 90, Indels: 89
0.70 0.15 0.15
Matches are distributed among these distances:
20 29 0.07
21 152 0.37
22 164 0.40
23 24 0.06
24 7 0.02
25 3 0.01
26 12 0.03
27 9 0.02
28 10 0.02
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (22 bp):
AATCAGTAAAAAGTAAAATAGT
Found at i:4239 original size:35 final size:34
Alignment explanation
Indices: 4211--4308 Score: 115
Period size: 35 Copynumber: 2.8 Consensus size: 34
4201 AAAGGCAATC
4211 AGTAAAAAGTAAAGAGTAATCAATAAAAGAAGAAT
1 AGTAAAAAGTAAAGAGTAATCAATAAAAG-AGAAT
* * *
4246 GGTAAAAAGTAAAGAGTAATCAGTAAAGGAAGAAT
1 AGTAAAAAGTAAAGAGTAATCAATAAAAG-AGAAT
* * * *
4281 GGTAAAGAGTAAAGGGTAATCAGTAAAA
1 AGTAAAAAGTAAAGAGTAATCAATAAAA
4309 AGTAAAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.56, C:0.03, G:0.23, T:0.17
Consensus pattern (34 bp):
AGTAAAAAGTAAAGAGTAATCAATAAAAGAGAAT
Found at i:4264 original size:149 final size:149
Alignment explanation
Indices: 3983--4257 Score: 333
Period size: 149 Copynumber: 1.8 Consensus size: 149
3973 CTGAAAAAGG
* * * * *
3983 GTAAAATGGTAATTAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGA
1 GTAAAAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAAGTAAAAAGGTAATCAACAAAA
* * * * * * *
4048 GTAAAATAGTACTCAGTAAAAAGTAAATAGTAATCAGTAAGAGTAAAAAAGTAATAAGTAAGAAG
66 GCAAAATAGCAATCAGTAAAAAGTAAAGAGTAATCAATAAAAGTAAAAAAGTAAAAAGTAAGAAG
4113 TAAAAGGAAATTAGTTAGA
131 TAAAAGGAAATTAGTTAGA
* *
4132 GTAAAAAGGTGATCAGTAAAGAGTAAAA-AGCTAATCAGCAAGAAGTAAAAAGGTAATCAGTA-A
1 GTAAAAAGGTAATCAGTAAAGAGTAAAATAG-TAATCAGCAAAAAGTAAAAAGGTAATCA--ACA
* **
4195 AAAGCAAAA-GGCAATCAGTAAAAAGTAAAGAGTAATCAATAAAAG-AAGAATGGTAAAAAGTAA
63 AAAGCAAAATAGCAATCAGTAAAAAGTAAAGAGTAATCAATAAAAGTAA-AAAAGTAAAAAGTAA
4258 AGAGTAATCA
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
148 4 0.04
149 92 0.88
150 8 0.08
151 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.19
Consensus pattern (149 bp):
GTAAAAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAAGTAAAAAGGTAATCAACAAAA
GCAAAATAGCAATCAGTAAAAAGTAAAGAGTAATCAATAAAAGTAAAAAAGTAAAAAGTAAGAAG
TAAAAGGAAATTAGTTAGA
Found at i:4389 original size:49 final size:50
Alignment explanation
Indices: 4288--4392 Score: 142
Period size: 49 Copynumber: 2.1 Consensus size: 50
4278 AATGGTAAAG
* *
4288 AGTAAAGGGTAATCAGTAAAAAGTAAAAAGATAATCAGTAAAGAATAAAAT
1 AGTAAAAGGTAATCAATAAAAAGT-AAAAGATAATCAGTAAAGAATAAAAT
* *
4339 AGTAAAAGGTAATCAATAAAAAGT-AATGATAATCAGTAAA-AGGTAAAAT
1 AGTAAAAGGTAATCAATAAAAAGTAAAAGATAATCAGTAAAGA-ATAAAAT
4388 AGTAA
1 AGTAA
4393 TCAGTAAGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
48 1 0.02
49 26 0.53
51 22 0.45
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (50 bp):
AGTAAAAGGTAATCAATAAAAAGTAAAAGATAATCAGTAAAGAATAAAAT
Found at i:4604 original size:28 final size:27
Alignment explanation
Indices: 4573--4625 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4563 GTAAAAAGTG
4573 GTAATCAATAAAAGAGAGTAAGGAAAGA
1 GTAATCAATAAAA-AGAGTAAGGAAAGA
***
4601 GTAATTGGTAAAAAGAGTAAGGAAA
1 GTAATCAATAAAAAGAGTAAGGAAA
4626 AAAATGACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (27 bp):
GTAATCAATAAAAAGAGTAAGGAAAGA
Found at i:10788 original size:202 final size:201
Alignment explanation
Indices: 10329--10901 Score: 896
Period size: 202 Copynumber: 2.8 Consensus size: 201
10319 AAAGCCATTC
* * *
10329 AAAAGATCTT-ACAACCAAAACAACGTCGTTGCGTAAGGGTTTTCGCAACGACATATAATTGCTT
1 AAAAGAT-TTCACAACCAAAACAACGTCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTT
* * * *
10393 TTAAATCACTTTGGCAACTACCTAAAGGTCGTTCTGTAAGTGTTTTGGAAACGACATTTAATCAT
65 TTAAATTATTTTGGCAACTACCTAGAGGTCGTTATGTAAGTGTTTTGGAAACGACATTTAATCAT
* * *
10458 TTCTAAAAGTTATTCATAACCAATTAAAGTGGTTGCAAAAATTATTACGCAACCAATCAAATGTT
130 TTTTAAAAGTTATTCGTAACCAATTAAAGTGGTTGCAAAAATTATTACACAACCAATCAAATGTT
10523 GCTACGT
195 GCTACGT
** * *
10530 AAAAGATTTCACAACCAAAACAACGTCGTTATGTAAAGGTTTTCGCAACGACATTTACTCGTTTT
1 AAAAGATTTCACAACCAAAACAACGTCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
* * *
10595 TAAATTGTTTTGGCAACTACCTAGAGGTCGTTGTGTAAGTGTTTTGGAAACGACTTTTAATCATT
66 TAAATTATTTTGGCAACTACCTAGAGGTCGTTATGTAAGTGTTTTGGAAACGACATTTAATCATT
* *
10660 TTTAAAAGTTATTCGTAACCAACTAAAAGTGGTTGCGAAAATTATTACACAACCAATCAAATGTT
131 TTTAAAAGTTATTCGTAACCAA-TTAAAGTGGTTGCAAAAATTATTACACAACCAATCAAATGTT
10725 GCTACGT
195 GCTACGT
*
10732 AAAAGATTTCACAACCAAAACAACGTCGTTGCGTAAGGGTTTTCGCAACAACATTTAATCGTTTT
1 AAAAGATTTCACAACCAAAACAACGTCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
* * *
10797 TAAATTATTTTGGTAACTACCTAGAGGTCGTTACGTAAGTGTTTTGGAAACGACATTTAATCGTT
66 TAAATTATTTTGGCAACTACCTAGAGGTCGTTATGTAAGTGTTTTGGAAACGACATTTAATCATT
* *
10862 TTTAGAAGTTATCCGTAACCAATTAAAGTGGTTGCAAAAA
131 TTTAAAAGTTATTCGTAACCAATTAAAGTGGTTGCAAAAA
10902 AATTTTTCGC
Statistics
Matches: 337, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
200 2 0.01
201 150 0.45
202 185 0.55
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (201 bp):
AAAAGATTTCACAACCAAAACAACGTCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
TAAATTATTTTGGCAACTACCTAGAGGTCGTTATGTAAGTGTTTTGGAAACGACATTTAATCATT
TTTAAAAGTTATTCGTAACCAATTAAAGTGGTTGCAAAAATTATTACACAACCAATCAAATGTTG
CTACGT
Found at i:11689 original size:48 final size:48
Alignment explanation
Indices: 11634--11725 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
11624 AGATTACACC
*
11634 TTGTAAAAACAAGGGTGATGAAAAGTGAAAGACAAGATTGATCACAAT
1 TTGTAAAAACAAGGGTGATGAAAAGTAAAAGACAAGATTGATCACAAT
* *
11682 TTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAAGGTTGATCA
1 TTGTAAAAACAAGGGTGATGAAAAGTAAAAGACAAGATTGATCA
11726 AACAACAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.48, C:0.07, G:0.24, T:0.22
Consensus pattern (48 bp):
TTGTAAAAACAAGGGTGATGAAAAGTAAAAGACAAGATTGATCACAAT
Found at i:11700 original size:25 final size:24
Alignment explanation
Indices: 11634--11727 Score: 68
Period size: 23 Copynumber: 4.0 Consensus size: 24
11624 AGATTACACC
*
11634 TTGTAAAAACAAGGGTGATGAAAA
1 TTGTAAAAACAAGGGTGATCAAAA
* * ** *
11658 GTG-AAAGACAAGATTGATCACAAT
1 TTGTAAAAACAAGGGTGATCA-AAA
*
11682 TTGTAAAAACAAGGGTGATGAAAA
1 TTGTAAAAACAAGGGTGATCAAAA
* *
11706 --GTAAAAGATAAGGTTGATCAAA
1 TTGTAAAA-ACAAGGGTGATCAAA
11728 CAACAATTTG
Statistics
Matches: 52, Mismatches: 15, Indels: 7
0.70 0.20 0.09
Matches are distributed among these distances:
22 6 0.12
23 25 0.48
24 8 0.15
25 13 0.25
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.21
Consensus pattern (24 bp):
TTGTAAAAACAAGGGTGATCAAAA
Found at i:18950 original size:10 final size:10
Alignment explanation
Indices: 18935--18959 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18925 TAACTCCAAT
18935 TATGGACTTA
1 TATGGACTTA
18945 TATGGACTTA
1 TATGGACTTA
18955 TATGG
1 TATGG
18960 GCTGAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (10 bp):
TATGGACTTA
Found at i:19111 original size:19 final size:18
Alignment explanation
Indices: 19079--19115 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
19069 TTGAAATAAT
19079 TCTTCAATTATCTTCAAG
1 TCTTCAATTATCTTCAAG
*
19097 TCTTCAAATTGTCTTCAAG
1 TCTTC-AATTATCTTCAAG
19116 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAG
Found at i:20389 original size:29 final size:29
Alignment explanation
Indices: 20347--20404 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
20337 TCAAAAATTG
20347 GGGGAATAAAGATCAATCCATAAACAATC
1 GGGGAATAAAGATCAATCCATAAACAATC
20376 GGGGAATAAAGATCAATCCATAAACAATC
1 GGGGAATAAAGATCAATCCATAAACAATC
20405 CAAATCCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (29 bp):
GGGGAATAAAGATCAATCCATAAACAATC
Found at i:27472 original size:10 final size:10
Alignment explanation
Indices: 27457--27481 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27447 TAACTCCAAT
27457 TATGGACTTA
1 TATGGACTTA
27467 TATGGACTTA
1 TATGGACTTA
27477 TATGG
1 TATGG
27482 GCTAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (10 bp):
TATGGACTTA
Found at i:32583 original size:14 final size:13
Alignment explanation
Indices: 32560--32602 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
32550 TAATGCACCC
32560 AAAACATTTAATA
1 AAAACATTTAATA
32573 AAAATCATTT-ATA
1 AAAA-CATTTAATA
*
32586 AAAACAATTTATTA
1 AAAAC-ATTTAATA
32600 AAA
1 AAA
32603 GTAGTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 15 0.58
14 10 0.38
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAACATTTAATA
Found at i:42249 original size:18 final size:19
Alignment explanation
Indices: 42188--42249 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 19
42178 ACTGACTTGC
*
42188 TTAATTACCCTGAATTAAG
1 TTAACTACCCTGAATTAAG
* *
42207 TTGACTA--CTGAATT-AC
1 TTAACTACCCTGAATTAAG
*
42223 TTAATTACCCTGAATTAAG
1 TTAACTACCCTGAATTAAG
42242 TT-ACTACC
1 TTAACTACC
42250 TTACTTAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 12 0.36
19 8 0.24
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (19 bp):
TTAACTACCCTGAATTAAG
Found at i:42257 original size:31 final size:31
Alignment explanation
Indices: 42151--42444 Score: 293
Period size: 35 Copynumber: 8.8 Consensus size: 31
42141 TTCTTACTAA
42151 ACTTAATTACCCTGAATTAAGTCGATTACTGACTT
1 ACTTAATTACCCTGAATTAA---G-TTACTGACTT
* *
42186 GCTTAATTACCCTGAATTAAGTTGACTACTGAATT
1 ACTTAATTACCCTGAATTAAG-T---TACTGACTT
42221 ACTTAATTACCCTGAATTAAGTTACT-ACCTT
1 ACTTAATTACCCTGAATTAAGTTACTGA-CTT
* *
42252 ACTTAATTTCCCTGAACTAAGTTACTAACTGACTTT
1 ACTTAATTACCCTGAATTAAG-T--T-ACTGAC-TT
* * *
42288 ACTTAATTACCCTGAATTAAGCTACTTACTG
1 ACTTAATTACCCTGAATTAAGTTACTGACTT
* *
42319 ACTTAATTACCCTGAATTAAGTTGCCTATTACTT
1 ACTTAATTACCCTGAATTAAGTT-AC--TGACTT
*
42353 ACTTAATTACCCTGAATTAAGTTGCTGACTT
1 ACTTAATTACCCTGAATTAAGTTACTGACTT
42384 ACTTAATTACCCTGAATTAAGCTATTCACTGACTT
1 ACTTAATTACCCTGAATTAAG---TT-ACTGACTT
*
42419 ACTTAATTGCCCTGAATTAAGTTACT
1 ACTTAATTACCCTGAATTAAGTTACT
42445 TATTACTGAT
Statistics
Matches: 223, Mismatches: 19, Indels: 38
0.80 0.07 0.14
Matches are distributed among these distances:
30 1 0.00
31 77 0.35
32 11 0.05
33 2 0.01
34 32 0.14
35 78 0.35
36 22 0.10
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (31 bp):
ACTTAATTACCCTGAATTAAGTTACTGACTT
Found at i:43195 original size:30 final size:29
Alignment explanation
Indices: 43161--43218 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
43151 CTAAAAAAAC
43161 CAATCCTCATACACAACTTACTTAAAAATT
1 CAATCCTCATACA-AACTTACTTAAAAATT
* * *
43191 CAATCTTTATATAAACTTACTTAAAAAT
1 CAATCCTCATACAAACTTACTTAAAAAT
43219 CCAACCTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (29 bp):
CAATCCTCATACAAACTTACTTAAAAATT
Found at i:43326 original size:30 final size:30
Alignment explanation
Indices: 43250--43327 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
43240 CAGTCTTTCT
* *
43250 CTTAAACATTTAATCTATATTTATAAATTA
1 CTTAAAAATTTAATCTTTATTTATAAATTA
* **
43280 CTCAAAAATACAATCTTTATTTATAAATTA
1 CTTAAAAATTTAATCTTTATTTATAAATTA
* * *
43310 TTTAAAGATTTTATCTTT
1 CTTAAAAATTTAATCTTT
43328 CAACACAGTG
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (30 bp):
CTTAAAAATTTAATCTTTATTTATAAATTA
Found at i:44876 original size:20 final size:20
Alignment explanation
Indices: 44851--44890 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
44841 GAACAAATGA
44851 GATGGCGGCATGTAAAACTG
1 GATGGCGGCATGTAAAACTG
44871 GATGGCGGCATGTAAAACTG
1 GATGGCGGCATGTAAAACTG
44891 TTTTAGGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.20
Consensus pattern (20 bp):
GATGGCGGCATGTAAAACTG
Found at i:49379 original size:17 final size:17
Alignment explanation
Indices: 49357--49390 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49347 TATAAATCGA
49357 CCAATCAAGTTGATTGG
1 CCAATCAAGTTGATTGG
49374 CCAATCAAGTTGATTGG
1 CCAATCAAGTTGATTGG
49391 TCTGAAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
CCAATCAAGTTGATTGG
Found at i:49465 original size:15 final size:15
Alignment explanation
Indices: 49429--49477 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
49419 TTTTTCACTT
49429 TTTAGTTTAATGAAGTA
1 TTTAGTTTAA-GAAG-A
49446 TTTAGTTTAAGAAGA
1 TTTAGTTTAAGAAGA
*
49461 TTTAGTTTAAGAGGA
1 TTTAGTTTAAGAAGA
49476 TT
1 TT
49478 CATGGAGCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 17 0.55
16 4 0.13
17 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (15 bp):
TTTAGTTTAAGAAGA
Found at i:53019 original size:14 final size:13
Alignment explanation
Indices: 52989--53016 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52979 AATTTAGGTC
52989 AAGATTTGAAAAA
1 AAGATTTGAAAAA
53002 AAGATTTGAAAAA
1 AAGATTTGAAAAA
53015 AA
1 AA
53017 AGAAGGAAAA
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:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAGATTTGAAAAA
Found at i:66154 original size:87 final size:87
Alignment explanation
Indices: 65935--66202 Score: 412
Period size: 87 Copynumber: 3.0 Consensus size: 87
65925 TAGCATCCTT
* *
65935 AAAGACAGATTCGGTGAGCTCGGTGCAGCATATTTTCAAACAGATCATGGTCATTCGGTGAATCA
1 AAAGTCAGATTCGGTGAGCTCGGTGCAGCATATTTTCAAATAGATCATGGTCATTCGGTGAATCA
*
66000 AGTTAATGCGGTGCCTTACTTCTTC
66 AGTTAATGCGGTG-C--ATTTCTTC
* *
66025 AAAGTCAGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGATCATGGTCCTTCGGTGAATCA
1 AAAGTCAGATTCGGTGAGCTCGGTGCAGCATATTTTCAAATAGATCATGGTCATTCGGTGAATCA
66090 AGTTAATGCGGTGCATTTCTTC
66 AGTTAATGCGGTGCATTTCTTC
* * *
66112 AAAGT-TGAATTTGGTGAGCTCGGTGCAGCATATTTTCAAATAGATCATGGTGATTCGGTGAATC
1 AAAGTCAG-ATTCGGTGAGCTCGGTGCAGCATATTTTCAAATAGATCATGGTCATTCGGTGAATC
*
66176 AAGTTAAGGCGGTGCATTTCTTC
65 AAGTTAATGCGGTGCATTTCTTC
66199 AAAG
1 AAAG
66203 AAAGGAAGTC
Statistics
Matches: 166, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
86 1 0.01
87 90 0.54
89 1 0.01
90 74 0.45
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (87 bp):
AAAGTCAGATTCGGTGAGCTCGGTGCAGCATATTTTCAAATAGATCATGGTCATTCGGTGAATCA
AGTTAATGCGGTGCATTTCTTC
Found at i:67712 original size:16 final size:18
Alignment explanation
Indices: 67691--67724 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
67681 CCAACAATAA
67691 GGCAATT-A-TGAGCAAG
1 GGCAATTCAGTGAGCAAG
67707 GGCAATTCAGTGAGCAAG
1 GGCAATTCAGTGAGCAAG
67725 AGAAGGGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.18
Consensus pattern (18 bp):
GGCAATTCAGTGAGCAAG
Found at i:70239 original size:16 final size:14
Alignment explanation
Indices: 70206--70235 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
70196 AATTTAGGTC
70206 AAGATTTGAAAAAA
1 AAGATTTGAAAAAA
70220 AAGATTTGAAAAAA
1 AAGATTTGAAAAAA
70234 AA
1 AA
70236 AAGAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (14 bp):
AAGATTTGAAAAAA
Done.