Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008266.1 Corchorus capsularis cultivar CVL-1 contig08287, 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: 19922
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Found at i:3748 original size:80 final size:80
Alignment explanation
Indices: 3631--3812 Score: 265
Period size: 80 Copynumber: 2.3 Consensus size: 80
3621 AAAAGGAGTA
* *
3631 AGGAAGTAAAAGTAGTAAATCAGTAAATCAGTAATTAAGAGTCAAGGTAAAGGGATTAATCAGTA
1 AGGAAGTAAAAGTAGT-AATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGGGATAAATCAGTA
3696 AATTCATAATTAAAAG
65 AATTCATAATTAAAAG
* * * *
3712 AGGAAGCAAAAGTAGTAATCAGTAGATTAGTAATTAAGAGTCAAAGTAAAGGGATAAATCAGTGA
1 AGGAAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGGGATAAATCAGTAA
* *
3777 ATTGATAATTAAGAG
66 ATTCATAATTAAAAG
* *
3792 AGAAAGTAAAATTAGTAATCA
1 AGGAAGTAAAAGTAGTAATCA
3813 ATAATTAAGA
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 75 0.83
81 15 0.17
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.24
Consensus pattern (80 bp):
AGGAAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGGGATAAATCAGTAA
ATTCATAATTAAAAG
Found at i:3812 original size:40 final size:38
Alignment explanation
Indices: 3634--3819 Score: 131
Period size: 40 Copynumber: 4.7 Consensus size: 38
3624 AGGAGTAAGG
* **
3634 AAGTAAAAGTAGTAAATCAGTAAATCAGTAATTAAGAGTCA
1 AAGTAAAAGTAGT-AATCAGT-AATTA-TAATTAAGAGAGA
* * * * * *
3675 AGGTAAAGGGATTAATCAGTAAATTCATAATTAAAAGAGG
1 AAGTAAAAGTAGTAATCAGT-AATT-ATAATTAAGAGAGA
* **
3715 AAGCAAAAGTAGTAATCAGTAGATTAGTAATTAAGAGTCA
1 AAGTAAAAGTAGTAATCAGTA-ATTA-TAATTAAGAGAGA
* *
3755 AAGTAAAGGGA-TAAATCAGTGAATTGATAATTAAGAGAGA
1 AAGTAAAAGTAGT-AATCAGT-AATT-ATAATTAAGAGAGA
* *
3795 AAGTAAAATTAGTAATCAATAATTA
1 AAGTAAAAGTAGTAATCAGTAATTA
3820 AGAAAGGAAG
Statistics
Matches: 111, Mismatches: 27, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
38 1 0.01
39 7 0.06
40 90 0.81
41 13 0.12
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.25
Consensus pattern (38 bp):
AAGTAAAAGTAGTAATCAGTAATTATAATTAAGAGAGA
Found at i:3974 original size:7 final size:7
Alignment explanation
Indices: 3964--4332 Score: 89
Period size: 7 Copynumber: 51.6 Consensus size: 7
3954 AATTAGTAAT
3964 TAAAGAG
1 TAAAGAG
3971 TAAA-ATGG
1 TAAAGA--G
*
3979 TAAGGAG
1 TAAAGAG
3986 TAAAAGAG
1 T-AAAGAG
**
3994 TAATCAG
1 TAAAGAG
4001 TAAAGAG
1 TAAAGAG
*
4008 GAAA-ATGG
1 TAAAGA--G
4016 TAAAGAG
1 TAAAGAG
*
4023 TATAGAG
1 TAAAGAG
**
4030 TAATCAG
1 TAAAGAG
4037 TAAAGAG
1 TAAAGAG
*
4044 AAAAGAG
1 TAAAGAG
* *
4051 AAAAAAAG
1 -TAAAGAG
4059 TAAAGAG
1 TAAAGAG
**
4066 TAATCAG
1 TAAAGAG
4073 TAAAGAG
1 TAAAGAG
*
4080 -AAAAATGG
1 TAAAGA--G
*
4088 TAAAATAG
1 T-AAAGAG
* *
4096 TAATTAAAT
1 TAA--AGAG
4105 TCAAGAGAG
1 T-AA-AGAG
*
4114 TAAAATAG
1 T-AAAGAG
**
4122 TAATTAG
1 TAAAGAG
4129 TAAAGAG
1 TAAAGAG
*
4136 AAAAGAG
1 TAAAGAG
4143 TAAAGAG
1 TAAAGAG
4150 TAAAGAG
1 TAAAGAG
**
4157 TAATCAG
1 TAAAGAG
4164 T-AAGA-
1 TAAAGAG
*
4169 AAAATG-G
1 TAAA-GAG
*
4176 TAAAAAG
1 TAAAGAG
4183 T-AAGAG
1 TAAAGAG
4189 TAATCA-AG
1 TAA--AGAG
4197 TAAAG-G
1 TAAAGAG
* *
4203 AAAAATAG
1 -TAAAGAG
4211 TAAAGAG
1 TAAAGAG
*
4218 TAAAGGG
1 TAAAGAG
4225 TAAAGAG
1 TAAAGAG
** *
4232 TAATTAT
1 TAAAGAG
4239 TAAAGA-
1 TAAAGAG
*
4245 AAAATG-G
1 TAAA-GAG
4252 TAAAGAG
1 TAAAGAG
4259 TAAAGAG
1 TAAAGAG
**
4266 TAATCAG
1 TAAAGAG
4273 TAAAG-G
1 TAAAGAG
*
4279 -AAAAATGG
1 TAAAGA--G
4287 TAAAGAG
1 TAAAGAG
*
4294 TAAAGAA
1 TAAAGAG
**
4301 TAATCAG
1 TAAAGAG
*
4308 TAAGGAG
1 TAAAGAG
***
4315 TAATTCG
1 TAAAGAG
4322 TAAAGAG
1 TAAAGAG
4329 TAAA
1 TAAA
4333 ATGATAAAAA
Statistics
Matches: 255, Mismatches: 75, Indels: 64
0.65 0.19 0.16
Matches are distributed among these distances:
5 3 0.01
6 22 0.09
7 175 0.69
8 34 0.13
9 15 0.06
10 6 0.02
ACGTcount: A:0.55, C:0.02, G:0.23, T:0.19
Consensus pattern (7 bp):
TAAAGAG
Found at i:4037 original size:36 final size:36
Alignment explanation
Indices: 3964--4091 Score: 161
Period size: 36 Copynumber: 3.5 Consensus size: 36
3954 AATTAGTAAT
* *
3964 TAAAGAGTAAAATGGTAAGGAGTAAAAGAGTAATCAG
1 TAAAGAGGAAAATGGTAAAGAGT-AAAGAGTAATCAG
*
4001 TAAAGAGGAAAATGGTAAAGAGTATAGAGTAATCAG
1 TAAAGAGGAAAATGGTAAAGAGTAAAGAGTAATCAG
* *
4037 TAAAGA-GAAAA-GAGAAAAAAAGTAAAGAGTAATCAG
1 TAAAGAGGAAAATG-G-TAAAGAGTAAAGAGTAATCAG
*
4073 TAAAGAGAAAAATGGTAAA
1 TAAAGAGGAAAATGGTAAA
4092 ATAGTAATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
34 1 0.01
35 6 0.08
36 45 0.57
37 26 0.33
38 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.25, T:0.16
Consensus pattern (36 bp):
TAAAGAGGAAAATGGTAAAGAGTAAAGAGTAATCAG
Found at i:4060 original size:29 final size:29
Alignment explanation
Indices: 4028--4084 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
4018 AAGAGTATAG
* *
4028 AGTAATCAGTAAAGAGAAAAGAGAAAAAA
1 AGTAAACAGTAAACAGAAAAGAGAAAAAA
* * *
4057 AGTAAAGAGTAATCAGTAAAGAGAAAAA
1 AGTAAACAGTAAACAGAAAAGAGAAAAA
4085 TGGTAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.63, C:0.04, G:0.21, T:0.12
Consensus pattern (29 bp):
AGTAAACAGTAAACAGAAAAGAGAAAAAA
Found at i:4166 original size:35 final size:35
Alignment explanation
Indices: 4110--4614 Score: 201
Period size: 35 Copynumber: 14.2 Consensus size: 35
4100 TAAATTCAAG
* *
4110 AGAGTAAAATAGTAATTAGTAAAGAGAAAAGAGTAA
1 AGAGT-AAAGAGTAATCAGTAAAGAGAAAAGAGTAA
4146 AGAGTAAAGAGTAATCAGT-AAGA-AAAATG-GTAA
1 AGAGTAAAGAGTAATCAGTAAAGAGAAAA-GAGTAA
* *
4179 AAAGT-AAGAGTAATCAAGTAAAGGAAAAATAGTAAAGAGTAA
1 AGAGTAAAGAGTAATC-AGTAAA-G------AGAAAAGAGTAA
* * *
4221 AGGGTAAAGAGTAATTATTAAAGA-AAAATG-GTAA
1 AGAGTAAAGAGTAATCAGTAAAGAGAAAA-GAGTAA
4255 AGAGTAAAGAGTAATCAGTAAAG-GAAAA-ATGGTAA
1 AGAGTAAAGAGTAATCAGTAAAGAGAAAAGA--GTAA
* * * ***
4290 AGAGTAAAGAATAATCAGTAAGGAGTAATTCGTAA
1 AGAGTAAAGAGTAATCAGTAAAGAGAAAAGAGTAA
* * * *
4325 AGAGTAAA-A-TGAT-A-AAAAGAAATAAAGTGTAA
1 AGAGTAAAGAGTAATCAGTAAAGAGA-AAAGAGTAA
** * * *
4357 TCAGTAAAAGAAG-AAT-GGTAAAAAGTAAAGAGTAA
1 AGAGT-AAAG-AGTAATCAGTAAAGAGAAAAGAGTAA
** * *
4392 TCAGTAAAGGAAG-AAT-GGTAAAGAGTAAAGAGTAA
1 AGAGTAAA-G-AGTAATCAGTAAAGAGAAAAGAGTAA
** ** * * *
4427 TCAGTAAAGGAAAAAT-GGTAAAGAGTAAAGAATAA
1 AGAGTAAA-GAGTAATCAGTAAAGAGAAAAGAGTAA
** *
4462 TCAGTAAGGAGTAATTC-GTAAAGAGTAAAATGA-TAAAA
1 AGAGTAAAGAGTAA-TCAGTAAAGAG-AAAA-GAGT--AA
*
4500 AGAAATAAAGAGTAATCAGTAAA-AGAAGAATG-GTAA
1 AG-AGTAAAGAGTAATCAGTAAAGAGAA-AA-GAGTAA
*
4536 AAAGTAAAGAGTAATCAGTAAAG-GAAGAATG-GTAA
1 AGAGTAAAGAGTAATCAGTAAAGAGAA-AA-GAGTAA
* * **
4571 AGAGTAAAGGGTAATCAGTAAAAAGATAATCAGTAA
1 AGAGTAAAGAGTAATCAGTAAAGAGA-AAAGAGTAA
4607 AGAGTAAA
1 AGAGTAAA
4615 ATAGTAAAAG
Statistics
Matches: 375, Mismatches: 52, Indels: 84
0.73 0.10 0.16
Matches are distributed among these distances:
31 4 0.01
32 20 0.05
33 21 0.06
34 47 0.13
35 191 0.51
36 34 0.09
37 5 0.01
38 11 0.03
39 15 0.04
41 3 0.01
42 15 0.04
43 9 0.02
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.19
Consensus pattern (35 bp):
AGAGTAAAGAGTAATCAGTAAAGAGAAAAGAGTAA
Found at i:4374 original size:88 final size:88
Alignment explanation
Indices: 4259--4420 Score: 238
Period size: 88 Copynumber: 1.8 Consensus size: 88
4249 TGGTAAAGAG
* *
4259 TAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGT-AAGG-AGTAATTCG
1 TAAAGAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAG-AA-TCG
4322 TAAAGAGTAAAATGATAAAAAGAAA
64 TAAAGAGTAAAATGATAAAAAGAAA
* * * *
4347 TAAAGTGTAATCAGTAAAAGAAGAATGGTAAAAAGTAAAGAGTAATCAGTAAAGGAAGAATGGTA
1 TAAAGAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAGAATCGTA
4412 AAGAGTAAA
66 AAGAGTAAA
4421 GAGTAATCAG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 58 0.88
89 6 0.09
90 2 0.03
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.19
Consensus pattern (88 bp):
TAAAGAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAGAATCGTA
AAGAGTAAAATGATAAAAAGAAA
Found at i:4411 original size:158 final size:158
Alignment explanation
Indices: 4224--4592 Score: 686
Period size: 158 Copynumber: 2.3 Consensus size: 158
4214 AGAGTAAAGG
* * *
4224 GTAAAGAGTAATTATTAAA-GAAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGGAAAAATGGT
1 GTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAGAGTAAAGAGTAATCAGTAAAGGAAAAATGGT
*
4288 AAAGAGTAAAGAATAATCAGTAAGGAGTAATTCGTAAAGAGTAAAATGATAAAAAGAAATAAAGT
66 AAAGAGTAAAGAATAATCAGTAAGGAGTAATTCGTAAAGAGTAAAATGATAAAAAGAAATAAAGA
4353 GTAATCAGTAAAAGAAGAATGGTAAAAA
131 GTAATCAGTAAAAGAAGAATGGTAAAAA
4381 GTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAGAGTAAAGAGTAATCAGTAAAGGAAAAATGGT
1 GTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAGAGTAAAGAGTAATCAGTAAAGGAAAAATGGT
4446 AAAGAGTAAAGAATAATCAGTAAGGAGTAATTCGTAAAGAGTAAAATGATAAAAAGAAATAAAGA
66 AAAGAGTAAAGAATAATCAGTAAGGAGTAATTCGTAAAGAGTAAAATGATAAAAAGAAATAAAGA
4511 GTAATCAGTAAAAGAAGAATGGTAAAAA
131 GTAATCAGTAAAAGAAGAATGGTAAAAA
*
4539 GTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAGAGTAAAGGGTAATCAGTAAA
1 GTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAGAGTAAAGAGTAATCAGTAAA
4593 AAGATAATCA
Statistics
Matches: 206, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
157 17 0.08
158 189 0.92
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.19
Consensus pattern (158 bp):
GTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAGAGTAAAGAGTAATCAGTAAAGGAAAAATGGT
AAAGAGTAAAGAATAATCAGTAAGGAGTAATTCGTAAAGAGTAAAATGATAAAAAGAAATAAAGA
GTAATCAGTAAAAGAAGAATGGTAAAAA
Found at i:4433 original size:21 final size:20
Alignment explanation
Indices: 4374--4475 Score: 57
Period size: 21 Copynumber: 5.5 Consensus size: 20
4364 AAGAAGAATG
*
4374 GTAAAAAGTAAAGAGTAATCA
1 GTAAAGAGTAAAGA-TAATCA
*
4395 GTAAAG-G--AAG--AAT-G
1 GTAAAGAGTAAAGATAATCA
4409 GTAAAGAGTAAAGAGTAATCA
1 GTAAAGAGTAAAGA-TAATCA
*
4430 GTAAAG-G--AA-A-AAT-G
1 GTAAAGAGTAAAGATAATCA
4444 GTAAAGAGTAAAGAATAATCA
1 GTAAAGAGTAAAG-ATAATCA
*
4465 GTAAGGAGTAA
1 GTAAAGAGTAA
4476 TTCGTAAAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 28
0.64 0.06 0.29
Matches are distributed among these distances:
14 12 0.20
15 8 0.13
17 6 0.10
18 5 0.08
19 1 0.02
20 8 0.13
21 21 0.34
ACGTcount: A:0.54, C:0.03, G:0.25, T:0.18
Consensus pattern (20 bp):
GTAAAGAGTAAAGATAATCA
Found at i:4532 original size:88 final size:88
Alignment explanation
Indices: 4417--4578 Score: 247
Period size: 88 Copynumber: 1.8 Consensus size: 88
4407 TGGTAAAGAG
* *
4417 TAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGT-AAGG-AGTAATTCG
1 TAAAGAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAG-AA-TCG
4480 TAAAGAGTAAAATGATAAAAAGAAA
64 TAAAGAGTAAAATGATAAAAAGAAA
* * *
4505 TAAAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTAAAGAGTAATCAGTAAAGGAAGAATGGTA
1 TAAAGAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAGAATCGTA
4570 AAGAGTAAA
66 AAGAGTAAA
4579 GGGTAATCAG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
88 59 0.88
89 6 0.09
90 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.23, T:0.19
Consensus pattern (88 bp):
TAAAGAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAGAATCGTA
AAGAGTAAAATGATAAAAAGAAA
Found at i:4586 original size:123 final size:120
Alignment explanation
Indices: 3988--4623 Score: 576
Period size: 123 Copynumber: 5.3 Consensus size: 120
3978 GTAAGGAGTA
* *
3988 AAAGAGTAATCAGTAAAGAGGAAAATGGTAAAGAG-TATAGAGTAATCAGTAAAGAGAAAAGA-G
1 AAAGAGTAATCAGTAAAGA-GAAAATGGTAAAAAGATAAAGAGTAATCAGTAAA-AGAAAA-ATG
** * * **
4051 AAAAAAAGTAAAGAGTAATCAGTAAAGAGAAAAATGGTAAAATAGTAATTA-AATTCAAGAGAGT
63 GTAAAAAGTAAAGAGTAATCAGTAAAG-GAAAAATGGT-AAAGAGTAA--AGGA-T-AA-TCAGT
* * *
4115 AAAATAGTAATTAGTAAAGAGAAAA-GAGTAAAGAG-TAAAGAGTAATCAGT--AAGAAAAATGG
1 -AAAGAGTAATCAGTAAAGAGAAAATG-GTAAAAAGATAAAGAGTAATCAGTAAAAGAAAAATGG
*
4176 TAAAAAGT-AAGAGTAATCAAGTAAAGGAAAAATAGTAAAGAGTAAAGG-------GT
64 TAAAAAGTAAAGAGTAATC-AGTAAAGGAAAAATGGTAAAGAGTAAAGGATAATCAGT
* * * *
4226 AAAGAGTAATTATTAAAGA-AAAATGGTAAAGAG-TAAAGAGTAATCAGTAAAGGAAAAATGGTA
1 AAAGAGTAATCAGTAAAGAGAAAATGGTAAAAAGATAAAGAGTAATCAGTAAAAGAAAAATGGTA
* * * * * * **
4289 AAGAGTAAAGAATAATCAGT-AAGGAGTAATTCGTAAAGAGTAAAATGATAAAAAGAAAT
66 AAAAGTAAAGAGTAATCAGTAAAGGA-AAAATGGTAAAGAGT-AAAGGATAATCAG---T
* * *
4348 AAAGTGTAATCAGTAAA-AGAAGAATGGTAAAAAG-TAAAGAGTAATCAGTAAAGGAAGAATGGT
1 AAAGAGTAATCAGTAAAGAGAA-AATGGTAAAAAGATAAAGAGTAATCAGTAAAAGAAAAATGGT
* *
4411 AAAGAGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGT
65 AAAAAGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGGATAATCAGT
* * *
4467 AAGGAGTAATTC-GTAAAGAGTAAAATGATAAAAAGAAATAAAGAGTAATCAGTAAAAGAAGAAT
1 AAAGAGTAA-TCAGTAAAGAG-AAAATGGTAAAAAG--ATAAAGAGTAATCAGTAAAAGAAAAAT
* *
4531 GGTAAAAAGTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAGAGTAAAGGGTAATCAGT
62 GGTAAAAAGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGGATAATCAGT
* *
4590 AAAAAGATAATCAGTAAAGAGTAAAATAGTAAAA
1 AAAGAG-TAATCAGTAAAGAG-AAAATGGTAAAA
4624 GGTAATCAGT
Statistics
Matches: 435, Mismatches: 42, Indels: 66
0.80 0.08 0.12
Matches are distributed among these distances:
109 27 0.06
110 23 0.05
111 34 0.08
112 13 0.03
119 14 0.03
120 16 0.04
121 3 0.01
122 34 0.08
123 177 0.41
124 48 0.11
125 1 0.00
126 1 0.00
127 27 0.06
128 17 0.04
ACGTcount: A:0.56, C:0.03, G:0.23, T:0.19
Consensus pattern (120 bp):
AAAGAGTAATCAGTAAAGAGAAAATGGTAAAAAGATAAAGAGTAATCAGTAAAAGAAAAATGGTA
AAAAGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGGATAATCAGT
Found at i:4602 original size:15 final size:15
Alignment explanation
Indices: 4582--4638 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
4572 GAGTAAAGGG
4582 TAATCAGTAAAAAGA
1 TAATCAGTAAAAAGA
*
4597 TAATCAGTAAAGAGTA
1 TAATCAGTAAAAAG-A
* *
4613 AAAT-AGT-AAAAGG
1 TAATCAGTAAAAAGA
4626 TAATCAGTAAAAA
1 TAATCAGTAAAAA
4639 AAATAATGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 3 0.09
14 7 0.21
15 20 0.59
16 4 0.12
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (15 bp):
TAATCAGTAAAAAGA
Found at i:4606 original size:29 final size:28
Alignment explanation
Indices: 4573--4636 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
4563 AATGGTAAAG
*
4573 AGTAAAGGGT-AATCAGTAAAAAGATAATC
1 AGTAAAGAGTAAAT-AGT-AAAAGATAATC
*
4602 AGTAAAGAGTAAAATAGTAAAAGGTAATC
1 AGTAAAGAGT-AAATAGTAAAAGATAATC
4631 AGTAAA
1 AGTAAA
4637 AAAAATAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 25 0.81
30 3 0.10
31 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (28 bp):
AGTAAAGAGTAAATAGTAAAAGATAATC
Found at i:4624 original size:123 final size:123
Alignment explanation
Indices: 3984--4222 Score: 130
Period size: 127 Copynumber: 1.9 Consensus size: 123
3974 AATGGTAAGG
* * * *
3984 AGTAAAAGAGTAA-TCAGTAAAGAGGAAAATGGT--AAAG-AGTATAGAGTAATCAGTAAAGAGA
1 AGTAAAA-AGTAATTC-GTAAAGAGTAAAATGATAAAAAGAAATAAAGAGTAATCAGTAAA-AGA
* *
4045 A-AA-GAGAAAAAAAGTAAAGAGTAATCAGTAAAGAGAAAAATGGTAAAATAGTAATTA-AATTC
63 AGAATG-G-TAAAAAGTAAAGAGTAATCAGTAAAG-GAAAAATGGT-AAAGAGTAA--AGAA-T-
**
4107 AAGAG
120 AA-TC
* *
4112 AGTAAAATAGTAATTAGTAAAGAG-AAAA-GAGT--AAAG-AGTAAAGAGTAATCAGT--AAGAA
1 AGTAAAA-AGTAATTCGTAAAGAGTAAAATGA-TAAAAAGAAATAAAGAGTAATCAGTAAAAGAA
* *
4170 AAATGGTAAAAAGT-AAGAGTAATCAAGTAAAGGAAAAATAGTAAAGAGTAAAG
64 GAATGGTAAAAAGTAAAGAGTAATC-AGTAAAGGAAAAATGGTAAAGAGTAAAG
4223 GGTAAAGAGT
Statistics
Matches: 98, Mismatches: 7, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
120 1 0.01
122 8 0.08
123 19 0.19
124 18 0.18
125 4 0.04
126 2 0.02
127 25 0.26
128 20 0.20
129 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.18
Consensus pattern (123 bp):
AGTAAAAAGTAATTCGTAAAGAGTAAAATGATAAAAAGAAATAAAGAGTAATCAGTAAAAGAAGA
ATGGTAAAAAGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATC
Found at i:4673 original size:22 final size:21
Alignment explanation
Indices: 4648--4794 Score: 136
Period size: 22 Copynumber: 6.8 Consensus size: 21
4638 AAAATAATGA
4648 TAATCAGTAAATGGTAAAATAG
1 TAATCAGTAAA-GGTAAAATAG
* *
4670 TAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAG-GTAAAATAG
* * * *
4691 TAATCAGTGAGGGCAAAATGG
1 TAATCAGTAAAGGTAAAATAG
*
4712 TAATCAGTAAAGATTAAAATAG
1 TAATCAGTAAAG-GTAAAATAG
* *
4734 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGT-AAAGGTAA-AATAG
4756 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAG-GTAAAATAG
4778 TAATCAGTAAAAGGTAA
1 TAATCAGT-AAAGGTAA
4795 TTAGTAAGAG
Statistics
Matches: 104, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.01
21 41 0.39
22 53 0.51
23 9 0.09
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.22
Consensus pattern (21 bp):
TAATCAGTAAAGGTAAAATAG
Found at i:4715 original size:86 final size:85
Alignment explanation
Indices: 4620--4785 Score: 205
Period size: 86 Copynumber: 1.9 Consensus size: 85
4610 GTAAAATAGT
**
4620 AAAAGGTAATCAGTAAA-A-AAAATAATGATAATCAGTAAATGGTAA-AATAGTAATCAGT-AAG
1 AAAAGGTAATCAGTAAAGATAAAAT-A-G-TAATCAGTAAAAAGTAAGAA-AGTAATCAGTAAAG
*
4681 AGCAAAATGGTAATCAGTGAGGGC
62 AGCAAAATAGTAATCAGTGAGGGC
*
4705 AAAATGGTAATCAGTAAAGATTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAG
1 AAAA-GGTAATCAGTAAAGA-TAAAATAGTAATCAGTAAAAAGTAAGAAAGTAATCAGTAAAGAG
*
4770 TAAAATAGTAATCAGT
64 CAAAATAGTAATCAGT
4786 AAAAGGTAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
85 4 0.06
86 37 0.53
87 23 0.33
88 1 0.01
89 5 0.07
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (85 bp):
AAAAGGTAATCAGTAAAGATAAAATAGTAATCAGTAAAAAGTAAGAAAGTAATCAGTAAAGAGCA
AAATAGTAATCAGTGAGGGC
Found at i:4744 original size:15 final size:15
Alignment explanation
Indices: 4726--4789 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
4716 CAGTAAAGAT
4726 TAAAATAGTAATCAG
1 TAAAATAGTAATCAG
**
4741 TAAAA-AGTAAGAAGG
1 TAAAATAGTAATCA-G
**
4756 T--AATCAGTAAAGAG
1 TAAAAT-AGTAATCAG
4770 TAAAATAGTAATCAG
1 TAAAATAGTAATCAG
4785 TAAAA
1 TAAAA
4790 GGTAATTAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
13 2 0.05
14 8 0.21
15 25 0.66
16 3 0.08
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (15 bp):
TAAAATAGTAATCAG
Found at i:4767 original size:44 final size:44
Alignment explanation
Indices: 4580--4794 Score: 194
Period size: 44 Copynumber: 4.9 Consensus size: 44
4570 AAGAGTAAAG
* * ** *
4580 GGTAATCAGTAAAAAG-ATAATCAGTAAAGAGTAAAATAGTAAAA-
1 GGTAATCAGTAAAGAGTAAAAT-AGTAATCAGTAAAA-GGTAAAAT
*
4624 GGTAATCAGTAAA-A--AAAATAATGATAATCAGTAAATGGTAAAAT
1 GGTAATCAGTAAAGAGTAAAAT-A-G-TAATCAGTAAAAGGTAAAAT
* * * * * *
4668 AGTAATCAGT-AAGAGCAAAATGGTAATCAGT-GAGGGCAAAAT
1 GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGGTAAAAT
* *
4710 GGTAATCAGTAAAGATTAAAATAGTAATCAGTAAAAAGTAAGAA-
1 GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGGTAA-AAT
4754 GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGGTAA
1 GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGGTAA
4795 TTAGTAAGAG
Statistics
Matches: 141, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
42 22 0.16
43 36 0.26
44 76 0.54
45 2 0.01
46 5 0.04
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.22
Consensus pattern (44 bp):
GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGGTAAAAT
Found at i:4801 original size:21 final size:21
Alignment explanation
Indices: 4731--4830 Score: 80
Period size: 21 Copynumber: 4.7 Consensus size: 21
4721 AAGATTAAAA
* *
4731 TAGTAATCAGTAAAAAGTAAG
1 TAGTAATCAGTAAAAGGTAAT
* *
4752 AAGGTAATCAGT-AAAGAGTAAAA
1 TA-GTAATCAGTAAAAG-GT-AAT
4775 TAGTAATCAGTAAAAGGTAAT
1 TAGTAATCAGTAAAAGGTAAT
* *
4796 TAGTAA-GAGCAAAATGGTAAT
1 TAGTAATCAGTAAAA-GGTAAT
*
4817 TAGTAA-GAGTAAAA
1 TAGTAATCAGTAAAA
4831 TAGTAATCAG
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
20 6 0.09
21 31 0.47
22 22 0.33
23 7 0.11
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (21 bp):
TAGTAATCAGTAAAAGGTAAT
Found at i:4831 original size:21 final size:21
Alignment explanation
Indices: 4783--4852 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
4773 AATAGTAATC
4783 AGTAAAA-GGTAATTAGTAAG
1 AGTAAAATGGTAATTAGTAAG
*
4803 AGCAAAATGGTAATTAGTAAG
1 AGTAAAATGGTAATTAGTAAG
* *
4824 AGTAAAATAGTAATCAGTAAAG
1 AGTAAAATGGTAATTAGT-AAG
*
4846 ACTAAAA
1 AGTAAAA
4853 GGTGATCAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 6 0.14
21 28 0.65
22 9 0.21
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTAAAATGGTAATTAGTAAG
Found at i:4835 original size:35 final size:35
Alignment explanation
Indices: 4746--4836 Score: 87
Period size: 35 Copynumber: 2.5 Consensus size: 35
4736 ATCAGTAAAA
*
4746 AGTAAGAAGGT-AATCAGTAAAGAGTAAAATAGTAATC
1 AGTAA-AAGGTAAAT-AGT-AAGAGCAAAATAGTAATC
* * *
4783 AGTAAAAGGTAATTAGTAAGAGCAAAATGGTAATT
1 AGTAAAAGGTAAATAGTAAGAGCAAAATAGTAATC
*
4818 AGTAAGA-GTAAAATAGTAA
1 AGTAAAAGGT-AAATAGTAA
4837 TCAGTAAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
34 2 0.04
35 29 0.63
36 8 0.17
37 7 0.15
ACGTcount: A:0.52, C:0.03, G:0.22, T:0.23
Consensus pattern (35 bp):
AGTAAAAGGTAAATAGTAAGAGCAAAATAGTAATC
Found at i:4943 original size:13 final size:13
Alignment explanation
Indices: 4925--4971 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
4915 GGTAATCAAT
4925 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
4938 AAAAGAGTAATTAG
1 AAAAGAG-AGTAAG
4952 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
4965 AAAAGAG
1 AAAAGAG
4972 TATAAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:4947 original size:28 final size:27
Alignment explanation
Indices: 4916--4973 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
4906 GTAAAAAGTG
4916 GTAATCAATAAAAGAGAGTAAGAAAAGA
1 GTAATCAATAAAA-AGAGTAAGAAAAGA
* *
4944 GTAATTAGTAAAAAGAGTAAGAAAAGA
1 GTAATCAATAAAAAGAGTAAGAAAAGA
4971 GTA
1 GTA
4974 TAAATGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.59, C:0.02, G:0.22, T:0.17
Consensus pattern (27 bp):
GTAATCAATAAAAAGAGTAAGAAAAGA
Found at i:6466 original size:42 final size:42
Alignment explanation
Indices: 6418--6503 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 42
6408 ATGCATGGGA
*
6418 CATTGCACGGGCCATCGCAC-GAGCCATCCGGCCACAACCAGC
1 CATTGCACAGGCCATCGCACAG-GCCATCCGGCCACAACCAGC
*
6460 CATTGCACAGGCCATCGCACAGGCCATCCGGCCACAACCGGC
1 CATTGCACAGGCCATCGCACAGGCCATCCGGCCACAACCAGC
6502 CA
1 CA
6504 CTTGACCCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.24, C:0.43, G:0.23, T:0.09
Consensus pattern (42 bp):
CATTGCACAGGCCATCGCACAGGCCATCCGGCCACAACCAGC
Found at i:6479 original size:12 final size:12
Alignment explanation
Indices: 6458--6487 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6448 GCCACAACCA
*
6458 GCCATTGCACAG
1 GCCATCGCACAG
6470 GCCATCGCACAG
1 GCCATCGCACAG
6482 GCCATC
1 GCCATC
6488 CGGCCACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.23, T:0.13
Consensus pattern (12 bp):
GCCATCGCACAG
Found at i:8528 original size:13 final size:12
Alignment explanation
Indices: 8510--8540 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
8500 AGTTATATCG
8510 AAAAATAAAAATA
1 AAAAATAAAAA-A
8523 AAAAATAAAAAA
1 AAAAATAAAAAA
8535 AAAAAT
1 AAAAAT
8541 TTTCGACTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAATAAAAAA
Found at i:10161 original size:33 final size:31
Alignment explanation
Indices: 10122--10235 Score: 131
Period size: 33 Copynumber: 3.6 Consensus size: 31
10112 CTAATTGTGA
10122 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAACAATTCTGTTTTGGTTG-A-ATAGCAT
*
10155 TAAAAACAATTCTGTTTTGGTTGATTATAGCAT
1 TGAAAACAATTCTGTTTTGGTTGA--ATAGCAT
* * *
10188 TGCAAATAATCCTGTTTTGGTTG-ATAGCAT
1 TGAAAACAATTCTGTTTTGGTTGAATAGCAT
* *
10218 TGAAAATAAATCTGTTTT
1 TGAAAACAATTCTGTTTT
10236 TGGTGACGAG
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
30 22 0.31
32 1 0.01
33 48 0.68
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (31 bp):
TGAAAACAATTCTGTTTTGGTTGAATAGCAT
Found at i:15144 original size:69 final size:69
Alignment explanation
Indices: 15029--15192 Score: 282
Period size: 69 Copynumber: 2.4 Consensus size: 69
15019 TAGACAAAAG
*
15029 GTCGCGTGGCCGGTTG-TGGCCGGGCA---TGGCCGAGTCGTTTGGCCGGTTGTAGCCGGACATG
1 GTCGCGTGGCCGG-TGATGGCCGGACATGTTGGCCGAGTCGTTTGGCCGGTTGTAGCCGGACATG
15090 TCCAT
65 TCCAT
15095 GTCGCGTGGCCGGTGATGGCCGGACATGTTGGCCGAGTCGTTTGGCCGGTTGTAGCCGGACATGT
1 GTCGCGTGGCCGGTGATGGCCGGACATGTTGGCCGAGTCGTTTGGCCGGTTGTAGCCGGACATGT
15160 CCAT
66 CCAT
15164 GTCGCGTGGCCGGTGATGGCCGGACATGT
1 GTCGCGTGGCCGGTGATGGCCGGACATGT
15193 CCATGTCGCG
Statistics
Matches: 93, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
65 2 0.02
66 22 0.24
69 69 0.74
ACGTcount: A:0.10, C:0.25, G:0.41, T:0.24
Consensus pattern (69 bp):
GTCGCGTGGCCGGTGATGGCCGGACATGTTGGCCGAGTCGTTTGGCCGGTTGTAGCCGGACATGT
CCAT
Found at i:15186 original size:33 final size:33
Alignment explanation
Indices: 15029--15221 Score: 205
Period size: 33 Copynumber: 5.7 Consensus size: 33
15019 TAGACAAAAG
* *
15029 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT
** *
15062 GTCGTTTGGCCGGTTGTAGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
15095 GTCGCGTGGCCGG-TGATGGCCGGACATGTTGGCCGA-
1 GTCGCGTGGCCGGTTG-TGGCCGGACATG-T--CC-AT
** *
15131 GTCGTTTGGCCGGTTGTAGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
15164 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
15197 GTCGCGTGGCCGGTCTTGTGGCCGG
1 GTCGCGTGGCCGG--TTGTGGCCGG
15222 TGTTGCGCGG
Statistics
Matches: 134, Mismatches: 14, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
32 6 0.04
33 90 0.67
34 1 0.01
35 8 0.06
36 26 0.19
37 3 0.02
ACGTcount: A:0.09, C:0.26, G:0.41, T:0.24
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Done.