Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014487.1 Corchorus olitorius cultivar O-4 contig14520, 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: 72182
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:30 original size:8 final size:9
Alignment explanation
Indices: 4--28 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1 AAT
4 TTCTTTTTC
1 TTCTTTTTC
13 TTCTTTTTC
1 TTCTTTTTC
22 TTCTTTT
1 TTCTTTT
29 CTATCCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:3053 original size:18 final size:19
Alignment explanation
Indices: 3030--3457 Score: 123
Period size: 19 Copynumber: 21.0 Consensus size: 19
3020 AAAAAAAGAG
3030 AAAGAA-TTGGTAACTAAA
1 AAAGAATTTGGTAACTAAA
* *
3048 AAAGAATTTGGCAA-TTAA
1 AAAGAATTTGGTAACTAAA
3066 AAAGAA-TTGGTAACTAAA
1 AAAGAATTTGGTAACTAAA
*
3084 AAAGAATTTGGTAAAGT-AA
1 AAAGAATTTGGT-AACTAAA
**
3103 AAAGAATTTGGTATTTAAAGAGTA
1 AAAGAATTTGGTAACT--A-A--A
* *
3127 AAAGTAAGATTGGTAATTAAA
1 AAAG-AA-TTTGGTAACTAAA
*
3148 AAA-AA--TGGTAATTAAAGAGTA
1 AAAGAATTTGGTAACT--A-A--A
*
3169 AAAGTAAGATTGGTAACTAAA
1 AAAG-AA-TTTGGTAACTAAA
3190 AAAGAATTTGGTAA-TCAAA
1 AAAGAATTTGGTAACT-AAA
3209 AAGAGTAAAAGTAAAATTGGTAACTAAA
1 AA-AG---AA-T----TTGGTAACTAAA
*
3237 AAAGAATTTGGTAATTAAAGAGTA
1 AAAGAATTTGGTAACT--A-A--A
*
3261 AAAGTAAAATTGGTAACTAAAA
1 AAAG--AATTTGGTAACT-AAA
*
3283 AAAGAATTTGGTAATTAGAGAGTA
1 AAAGAATTTGGTAACT--A-A--A
*
3307 AAAGTAAATTTGGTAA-TTAA
1 AAAG--AATTTGGTAACTAAA
*
3327 AAATAA-TTGGTAACTAAAA
1 AAAGAATTTGGTAACT-AAA
* *
3346 AAAGAA-TTAGTAAAGT-AA
1 AAAGAATTTGGT-AACTAAA
* *
3364 AAAGAATTTGATAAAGT-AA
1 AAAGAATTTGGT-AACTAAA
* *
3383 AAGGAATTTGGTAAAGT-AA
1 AAAGAATTTGGT-AACTAAA
*
3402 AAAGAATTTGGTAA-TTAA
1 AAAGAATTTGGTAACTAAA
* *
3420 AAGGAATTTGGTAAAGT-AA
1 AAAGAATTTGGT-AACTAAA
*
3439 AAAGAATTTGGTAATTAAA
1 AAAGAATTTGGTAACTAAA
3458 GAATGAAAAT
Statistics
Matches: 325, Mismatches: 31, Indels: 107
0.70 0.07 0.23
Matches are distributed among these distances:
16 8 0.02
17 14 0.04
18 57 0.18
19 114 0.35
20 25 0.08
21 15 0.05
22 9 0.03
23 7 0.02
24 21 0.06
25 5 0.02
26 35 0.11
27 2 0.01
28 12 0.04
29 1 0.00
ACGTcount: A:0.53, C:0.02, G:0.18, T:0.27
Consensus pattern (19 bp):
AAAGAATTTGGTAACTAAA
Found at i:3077 original size:36 final size:37
Alignment explanation
Indices: 3030--3115 Score: 138
Period size: 36 Copynumber: 2.3 Consensus size: 37
3020 AAAAAAAGAG
* *
3030 AAAGAATTGGTAACTAAAAAAGAATTTGG-CAATTAA
1 AAAGAATTGGTAACTAAAAAAGAATTTGGTAAAGTAA
3066 AAAGAATTGGTAACTAAAAAAGAATTTGGTAAAGTAA
1 AAAGAATTGGTAACTAAAAAAGAATTTGGTAAAGTAA
3103 AAAGAATTTGGTA
1 AAAGAA-TTGGTA
3116 TTTAAAGAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
36 29 0.63
37 11 0.24
38 6 0.13
ACGTcount: A:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (37 bp):
AAAGAATTGGTAACTAAAAAAGAATTTGGTAAAGTAA
Found at i:3305 original size:46 final size:45
Alignment explanation
Indices: 3101--3329 Score: 338
Period size: 45 Copynumber: 5.1 Consensus size: 45
3091 TTGGTAAAGT
* * *
3101 AAAAAGAATTTGGTATTTAAAGAGTAAAAGTAAGATTGGTAATTA
1 AAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAAATTGGTAACTA
*
3146 AAAAA-AA--TGGTAATTAAAGAGTAAAAGTAAGATTGGTAACTA
1 AAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAAATTGGTAACTA
*
3188 AAAAAGAATTTGGTAATCAAAAAGAGTAAAAGTAAAATTGGTAACTA
1 AAAAAGAATTTGGTAAT--TAAAGAGTAAAAGTAAAATTGGTAACTA
3235 AAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAAATTGGTAACTAA
1 AAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAAATTGGTAACT-A
* * *
3281 AAAAAGAATTTGGTAATTAGAGAGTAAAAGTAAATTTGGTAATTA
1 AAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAAATTGGTAACTA
3326 AAAA
1 AAAA
3330 TAATTGGTAA
Statistics
Matches: 170, Mismatches: 8, Indels: 12
0.89 0.04 0.06
Matches are distributed among these distances:
42 38 0.22
43 2 0.01
44 2 0.01
45 43 0.25
46 42 0.25
47 43 0.25
ACGTcount: A:0.53, C:0.02, G:0.18, T:0.27
Consensus pattern (45 bp):
AAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAAATTGGTAACTA
Found at i:3384 original size:56 final size:56
Alignment explanation
Indices: 3324--3453 Score: 149
Period size: 56 Copynumber: 2.3 Consensus size: 56
3314 ATTTGGTAAT
*
3324 TAAAAATAA-TTGGTAACTAAAAAAAGAA-TTAGTAAAGTAAAAAGAATTTGATAAAG
1 TAAAAAGAATTTGGTAA-TAAAAAAAGAATTTAGT-AAGTAAAAAGAATTTGATAAAG
* * * * * *
3380 TAAAAGGAATTTGGTAA-AGTAAAAAGAATTTGGTAATTAAAAGGAATTTGGTAAAG
1 TAAAAAGAATTTGGTAATA-AAAAAAGAATTTAGTAAGTAAAAAGAATTTGATAAAG
3436 TAAAAAGAATTTGGTAAT
1 TAAAAAGAATTTGGTAAT
3454 TAAAGAATGA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
55 1 0.02
56 50 0.81
57 11 0.18
ACGTcount: A:0.53, C:0.01, G:0.18, T:0.28
Consensus pattern (56 bp):
TAAAAAGAATTTGGTAATAAAAAAAGAATTTAGTAAGTAAAAAGAATTTGATAAAG
Found at i:3390 original size:37 final size:37
Alignment explanation
Indices: 3355--3457 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
3345 AAAAGAATTA
3355 GTAAAGTAAAAAGAATTTGATAAAGTAAAAGGAATTTG
1 GTAAAGTAAAAAGAATTTGAT-AAGTAAAAGGAATTTG
* *
3393 GTAAAGTAAAAAGAATTTGGTAATTAAAAGGAATTTG
1 GTAAAGTAAAAAGAATTTGATAAGTAAAAGGAATTTG
* *
3430 GTAAAGTAAAAAGAATTTGGTAATTAAA
1 GTAAAGTAAAAAGAATTTGATAAGTAAA
3458 GAATGAAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
37 43 0.68
38 20 0.32
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.28
Consensus pattern (37 bp):
GTAAAGTAAAAAGAATTTGATAAGTAAAAGGAATTTG
Found at i:3447 original size:19 final size:19
Alignment explanation
Indices: 3344--3452 Score: 159
Period size: 19 Copynumber: 5.8 Consensus size: 19
3334 TGGTAACTAA
*
3344 AAAAAGAA-TTAGTAAAGT
1 AAAAAGAATTTGGTAAAGT
*
3362 AAAAAGAATTTGATAAAGT
1 AAAAAGAATTTGGTAAAGT
*
3381 AAAAGGAATTTGGTAAAGT
1 AAAAAGAATTTGGTAAAGT
*
3400 AAAAAGAATTTGGT-AATT
1 AAAAAGAATTTGGTAAAGT
*
3418 AAAAGGAATTTGGTAAAGT
1 AAAAAGAATTTGGTAAAGT
3437 AAAAAGAATTTGGTAA
1 AAAAAGAATTTGGTAA
3453 TTAAAGAATG
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
18 24 0.30
19 56 0.70
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (19 bp):
AAAAAGAATTTGGTAAAGT
Found at i:3472 original size:37 final size:38
Alignment explanation
Indices: 3355--3498 Score: 120
Period size: 37 Copynumber: 3.8 Consensus size: 38
3345 AAAAGAATTA
* * **
3355 GTAAAGTAAAAAGAATTTGATAAAGT-AA-AAGGAATTT
1 GTAAAGTAAAAAGAATTTGGT-AATTAAAGAAGGAAAAT
**
3392 GGTAAAGTAAAAAGAATTTGGTAATT-AA-AAGGAATTT
1 -GTAAAGTAAAAAGAATTTGGTAATTAAAGAAGGAAAAT
*
3429 GGTAAAGTAAAAAGAATTTGGTAATTAAAGAATGAAAAT
1 -GTAAAGTAAAAAGAATTTGGTAATTAAAGAAGGAAAAT
*
3468 -TAAAGAGTAAAATGAA-TTGGATAATTAAAGA
1 GT-AA-AGTAAAAAGAATTTGG-TAATTAAAGA
3499 GTAATTGGTA
Statistics
Matches: 95, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
37 41 0.43
38 28 0.29
39 26 0.27
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (38 bp):
GTAAAGTAAAAAGAATTTGGTAATTAAAGAAGGAAAAT
Found at i:3477 original size:25 final size:27
Alignment explanation
Indices: 3449--3610 Score: 87
Period size: 25 Copynumber: 6.2 Consensus size: 27
3439 AAAGAATTTG
3449 GTAATTAAAGAA-T-GAAAATTAAAGA
1 GTAATTAAAGAATTGGAAAATTAAAGA
* *
3474 GTAA--AATGAATTGGATAATTAAAGA
1 GTAATTAAAGAATTGGAAAATTAAAGA
* *
3499 GTAATTGGTAAA-ATTTGG-TAATTAAAGA
1 GTAA-T--TAAAGAATTGGAAAATTAAAGA
* *
3527 GTAA--AATGAATTGGATAATTAAAGA
1 GTAATTAAAGAATTGGAAAATTAAAGA
* *
3552 GTAATTGGTAAA-ATTTGG-TAATTAAAGA
1 GTAA-T--TAAAGAATTGGAAAATTAAAGA
* * *
3580 GTAA--AATGAAATGGATAATTAAAGA
1 GTAATTAAAGAATTGGAAAATTAAAGA
3605 GTAATT
1 GTAATT
3611 GGTAAAATTT
Statistics
Matches: 108, Mismatches: 11, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
23 9 0.08
24 10 0.09
25 47 0.44
28 28 0.26
29 10 0.09
30 4 0.04
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (27 bp):
GTAATTAAAGAATTGGAAAATTAAAGA
Found at i:3522 original size:28 final size:29
Alignment explanation
Indices: 3484--3629 Score: 156
Period size: 28 Copynumber: 5.4 Consensus size: 29
3474 GTAAAATGAA
3484 TTGGATAATTAAAGAGTAATTGGTAAAAT
1 TTGGATAATTAAAGAGTAATTGGTAAAAT
*
3513 TTGG-TAATTAAAGAGTAAAAT-G---AA-
1 TTGGATAATTAAAGAGT-AATTGGTAAAAT
3537 TTGGATAATTAAAGAGTAATTGGTAAAAT
1 TTGGATAATTAAAGAGTAATTGGTAAAAT
*
3566 TTGG-TAATTAAAGAGTAAAAT-G--AAA-
1 TTGGATAATTAAAGAGT-AATTGGTAAAAT
3591 -TGGATAATTAAAGAGTAATTGGTAAAAT
1 TTGGATAATTAAAGAGTAATTGGTAAAAT
*
3619 TT-GAAAATTAA
1 TTGGATAATTAA
3630 GAAGTAAAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 29
0.74 0.04 0.22
Matches are distributed among these distances:
24 13 0.13
25 28 0.29
26 3 0.03
27 3 0.03
28 36 0.37
29 15 0.15
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (29 bp):
TTGGATAATTAAAGAGTAATTGGTAAAAT
Found at i:3527 original size:53 final size:53
Alignment explanation
Indices: 3465--3644 Score: 317
Period size: 53 Copynumber: 3.4 Consensus size: 53
3455 AAAGAATGAA
3465 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
1 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
3518 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
1 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
* **
3571 AATTAAAGAGTAAAATGAAATGGATAATTAAAGAGTAATTGGTAAAATTTGAA
1 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
3624 AATT-AAGAAGTAAAATGAATT
1 AATTAAAG-AGTAAAATGAATT
3645 AATTAAAAGT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
52 3 0.02
53 119 0.98
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (53 bp):
AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
Found at i:3636 original size:21 final size:20
Alignment explanation
Indices: 3612--3663 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
3602 AGAGTAATTG
3612 GTAAAATTTGAA-AATTAAGAA
1 GTAAAA-TTGAATAATTAA-AA
3633 GTAAAA-TGAATTAATTAAAA
1 GTAAAATTGAA-TAATTAAAA
3653 GTAAAA-TGAAT
1 GTAAAATTGAAT
3664 TTGGAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.17
20 12 0.41
21 12 0.41
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (20 bp):
GTAAAATTGAATAATTAAAA
Found at i:3656 original size:20 final size:21
Alignment explanation
Indices: 3624--3664 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
3614 AAAATTTGAA
3624 AATTAAGAAGTAAAATGAATT
1 AATTAAGAAGTAAAATGAATT
3645 AATTAA-AAGTAAAATGAATT
1 AATTAAGAAGTAAAATGAATT
3665 TGGAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (21 bp):
AATTAAGAAGTAAAATGAATT
Found at i:3672 original size:106 final size:105
Alignment explanation
Indices: 3465--3685 Score: 281
Period size: 106 Copynumber: 2.1 Consensus size: 105
3455 AAAGAATGAA
* **
3465 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGTAATTAAAGAGTA
1 AATTAAAGAGTAAAATGAAATGGATAATTAAAGAGTAATTGGTAAAATTTGAAAATTAAAGAGTA
* * *
3530 AAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
66 AAATGAATTGAATAAGTAAAGAGTAATTGG-AAAATTTGGC
3571 AATTAAAGAGTAAAATGAAATGGATAATTAAAGAGTAATTGGTAAAATTTGAAAATT-AAGAAGT
1 AATTAAAGAGTAAAATGAAATGGATAATTAAAGAGTAATTGGTAAAATTTGAAAATTAAAG-AGT
3635 AAAATGAATT-AATTAAAAGTAAA-A-TGAATTTGG-AAATTTGGC
65 AAAATGAATTGAA-T--AAGTAAAGAGT-AA-TTGGAAAATTTGGC
*
3677 ACTTAAAGA
1 AATTAAAGA
3686 AAAAAGGGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
105 4 0.04
106 85 0.83
107 3 0.03
108 10 0.10
ACGTcount: A:0.50, C:0.01, G:0.19, T:0.30
Consensus pattern (105 bp):
AATTAAAGAGTAAAATGAAATGGATAATTAAAGAGTAATTGGTAAAATTTGAAAATTAAAGAGTA
AAATGAATTGAATAAGTAAAGAGTAATTGGAAAATTTGGC
Found at i:3705 original size:106 final size:105
Alignment explanation
Indices: 3465--3714 Score: 271
Period size: 106 Copynumber: 2.4 Consensus size: 105
3455 AAAGAATGAA
* * **
3465 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGTAATTAAAGAGTA
1 AATTAAAGAGAAAAAGGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGAAAATTAAAGAGTA
* * *
3530 AAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
66 AAATGAATTGAATAAGTAAAGAGTAATTGG-AAAATTTGGC
* * *
3571 AATTAAAGAGTAAAATGAAATGGATAATTAAAGAGTAATTGGTAAAATTTGAAAATT-AAGAAGT
1 AATTAAAGAGAAAAAGGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGAAAATTAAAG-AGT
3635 AAAATGAATT-AATTAAAAGTAAA-A-TGAATTTGG-AAATTTGGC
65 AAAATGAATTGAA-T--AAGTAAAGAGT-AA-TTGGAAAATTTGGC
*
3677 ACTTAAAGA-AAAAAGGGTAATTGG-TAATTAAAGAGTAA
1 AATTAAAGAGAAAAA-GG-AATTGGATAATTAAAGAGTAA
3715 AATGGATTTA
Statistics
Matches: 126, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
105 8 0.06
106 100 0.79
107 8 0.06
108 10 0.08
ACGTcount: A:0.50, C:0.01, G:0.20, T:0.30
Consensus pattern (105 bp):
AATTAAAGAGAAAAAGGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGAAAATTAAAGAGTA
AAATGAATTGAATAAGTAAAGAGTAATTGGAAAATTTGGC
Found at i:3792 original size:28 final size:29
Alignment explanation
Indices: 3740--3812 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
3730 AAAAGAGTAA
**
3740 GAGAGAGTAAAAGGAAAATTTGGTTAATT
1 GAGAGAGTAAAAGGAAAATCCGGTTAATT
*
3769 GAGAGAGTAAGA-GAAAATCCGGTTAATT
1 GAGAGAGTAAAAGGAAAATCCGGTTAATT
*
3797 -AAAGAGTAAAAGGAAA
1 GAGAGAGTAAAAGGAAA
3813 TTGGCTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 9 0.24
28 18 0.47
29 11 0.29
ACGTcount: A:0.49, C:0.03, G:0.27, T:0.21
Consensus pattern (29 bp):
GAGAGAGTAAAAGGAAAATCCGGTTAATT
Found at i:3813 original size:27 final size:28
Alignment explanation
Indices: 3743--3813 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
3733 AGAGTAAGAG
** *
3743 AGAGTAAAAGGAAAATTTGGTTAATTGAG
1 AGAGTAAAAGG-AAATCCGGTTAATTGAA
* *
3772 AGAGTAAGAGAAAATCCGGTTAATT-AA
1 AGAGTAAAAGGAAATCCGGTTAATTGAA
3799 AGAGTAAAAGGAAAT
1 AGAGTAAAAGGAAAT
3814 TGGCTAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
27 14 0.40
28 12 0.34
29 9 0.26
ACGTcount: A:0.49, C:0.03, G:0.25, T:0.23
Consensus pattern (28 bp):
AGAGTAAAAGGAAATCCGGTTAATTGAA
Found at i:12254 original size:278 final size:279
Alignment explanation
Indices: 11757--12313 Score: 1010
Period size: 278 Copynumber: 2.0 Consensus size: 279
11747 AAAAATCTCT
* *
11757 TTGGAGATATTGGTGAAAGGGTATCGAACGTATCAATTAATTTTATCCAGAAATTGATAAAAGGA
1 TTGGAGATATTGGTGAAAGGGTACCGAACGTATCAATCAATTTTATCCAGAAATTGATAAAAGGA
*
11822 TGCGAGGAAAATAAATATTCATTTTGTTGCAAAAAGTAAATAAAGAGTGCAGTGAAAATGAGAGA
66 TGCGAGGAAAATAAATATTCATTTTGTTGCAAAAAGTAAATAAAGAGTGCAGTGAAAATAAGAGA
*
11887 TTTGCTTTGAGTGCAGCAACATAAAAATAATCAAACGATTTGTAGATCCTAACTCAAAGTCACAT
131 TTTGCTTTAAGTGCAGCAACATAAAAATAATCAAACGATTTGTAGATCCTAACTCAAAGTCACAT
*
11952 AAACGTGTTTAAATCATTGATTCCAGACTCAGAAAACAAAAGATTGTTGTAAAAAGGGTATTTTC
196 AAACGTATTTAAATCATTGATTCCAGACTCAGAAAACAAAAGATTGTTGTAAAAAGGGTATTTTC
*
12017 TTGA-TTCAAATGAGAGAA
261 TTGATTTCAAACGAGAGAA
* * *
12035 TTGGAGATCTTGGTGAAAGGGTACCGAACGTGTCAATCAATTTTGTCCAGAAATTGATAAAAGGA
1 TTGGAGATATTGGTGAAAGGGTACCGAACGTATCAATCAATTTTATCCAGAAATTGATAAAAGGA
12100 TGCGAGGAAAATAAATATTCATTTTGTTGCAAAAAGTAAATAAAGAGTGCAGTGAAAATAAGAGA
66 TGCGAGGAAAATAAATATTCATTTTGTTGCAAAAAGTAAATAAAGAGTGCAGTGAAAATAAGAGA
12165 TTTGCTTTAAGTGCAGCAACATAAAAATAATCAAACGATTTGTAGATCCTGAA-TCAAAGTCACA
131 TTTGCTTTAAGTGCAGCAACATAAAAATAATCAAACGATTTGTAGATCCT-AACTCAAAGTCACA
12229 TAAACGTATTTAAATCATTGATTCCAGACTCAGAAAACAAAAGATTGTTGTAAAAAGGGTATTTT
195 TAAACGTATTTAAATCATTGATTCCAGACTCAGAAAACAAAAGATTGTTGTAAAAAGGGTATTTT
12294 CTTGATTTCAAACGAGAGAA
260 CTTGATTTCAAACGAGAGAA
12314 ATAACAAGGA
Statistics
Matches: 268, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
278 253 0.94
279 15 0.06
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.28
Consensus pattern (279 bp):
TTGGAGATATTGGTGAAAGGGTACCGAACGTATCAATCAATTTTATCCAGAAATTGATAAAAGGA
TGCGAGGAAAATAAATATTCATTTTGTTGCAAAAAGTAAATAAAGAGTGCAGTGAAAATAAGAGA
TTTGCTTTAAGTGCAGCAACATAAAAATAATCAAACGATTTGTAGATCCTAACTCAAAGTCACAT
AAACGTATTTAAATCATTGATTCCAGACTCAGAAAACAAAAGATTGTTGTAAAAAGGGTATTTTC
TTGATTTCAAACGAGAGAA
Found at i:21346 original size:17 final size:17
Alignment explanation
Indices: 21324--21358 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
21314 AAAATAAAAA
21324 TTTAAGGTTAAAGGAAT
1 TTTAAGGTTAAAGGAAT
*
21341 TTTAAGGTTAAATGAAT
1 TTTAAGGTTAAAGGAAT
21358 T
1 T
21359 CTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (17 bp):
TTTAAGGTTAAAGGAAT
Found at i:21595 original size:58 final size:59
Alignment explanation
Indices: 21492--21602 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 59
21482 TAAATAATGA
* *
21492 CTTATTTGGCCAAAATTAAGTGTTCATGGGCTTATTTGGTCAAAATCAAAGTCCAATCG
1 CTTATTTGGCCAAAATTAAGAGTTCATGGGCTTATTTGGCCAAAATCAAAGTCCAATCG
* * *
21551 CTTATTTGGTCAAAATTAA-AG-TCCTGGGGCTTATTTGGCCAAAATTAAAGTC
1 CTTATTTGGCCAAAATTAAGAGTTCAT-GGGCTTATTTGGCCAAAATCAAAGTC
21603 TAGGGACTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
57 3 0.07
58 25 0.54
59 18 0.39
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (59 bp):
CTTATTTGGCCAAAATTAAGAGTTCATGGGCTTATTTGGCCAAAATCAAAGTCCAATCG
Found at i:21612 original size:29 final size:29
Alignment explanation
Indices: 21492--21616 Score: 128
Period size: 29 Copynumber: 4.3 Consensus size: 29
21482 TAAATAATGA
**
21492 CTTATTTGGCCAAAATT-AAGTGTTCATGGG
1 CTTATTTGGCCAAAATTAAAGTCCT-A-GGG
* * * **
21522 CTTATTTGGTCAAAATCAAAGTCCAATCG
1 CTTATTTGGCCAAAATTAAAGTCCTAGGG
* *
21551 CTTATTTGGTCAAAATTAAAGTCCTGGGG
1 CTTATTTGGCCAAAATTAAAGTCCTAGGG
21580 CTTATTTGGCCAAAATTAAAGT-CTAGGG
1 CTTATTTGGCCAAAATTAAAGTCCTAGGG
21608 ACTTATTTG
1 -CTTATTTG
21617 ACCATTACCC
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
28 5 0.06
29 54 0.68
30 16 0.20
31 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (29 bp):
CTTATTTGGCCAAAATTAAAGTCCTAGGG
Found at i:21613 original size:58 final size:60
Alignment explanation
Indices: 21490--21616 Score: 145
Period size: 58 Copynumber: 2.2 Consensus size: 60
21480 TCTAAATAAT
* * *
21490 GACTTATTTGGCCAAAATTAAGTGTTCATGGGCTTATTTGGTCAAAATCAAAGTCCAATC
1 GACTTATTTGGCCAAAATTAAGAGTTCATGGGCTTATTTGGCCAAAATCAAAGTCCAAGC
* * * * *
21550 G-CTTATTTGGTCAAAATTAA-AG-TCCTGGGGCTTATTTGGCCAAAATTAAAGT-CTAGG
1 GACTTATTTGGCCAAAATTAAGAGTTCAT-GGGCTTATTTGGCCAAAATCAAAGTCCAAGC
21607 GACTTATTTG
1 GACTTATTTG
21617 ACCATTACCC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
57 6 0.11
58 32 0.56
59 18 0.32
60 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (60 bp):
GACTTATTTGGCCAAAATTAAGAGTTCATGGGCTTATTTGGCCAAAATCAAAGTCCAAGC
Found at i:24378 original size:13 final size:13
Alignment explanation
Indices: 24360--24388 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
24350 ATATATATTA
24360 TTATAAATAATAT
1 TTATAAATAATAT
24373 TTATAAATAATAT
1 TTATAAATAATAT
24386 TTA
1 TTA
24389 GAACATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATAAATAATAT
Found at i:26539 original size:22 final size:20
Alignment explanation
Indices: 26495--26539 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
26485 AAATGGAAAT
*
26495 AAAAGAAAATAAAGAAGGGC
1 AAAAGAAAATAAAGAAGGCC
26515 AAAAGATAAATAAAGAAAGGCC
1 AAAAGA-AAATAAAG-AAGGCC
26537 AAA
1 AAA
26540 CCCAAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 8 0.36
22 8 0.36
ACGTcount: A:0.67, C:0.07, G:0.20, T:0.07
Consensus pattern (20 bp):
AAAAGAAAATAAAGAAGGCC
Found at i:26882 original size:21 final size:22
Alignment explanation
Indices: 26845--26899 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 22
26835 TTCTCATCAA
26845 ATCAGTCTTCATTTGCTT-CTTC
1 ATCA-TCTTCATTTGCTTGCTTC
26867 ATCATCTT-ATTATGCTTGCTTC
1 ATCATCTTCATT-TGCTTGCTTC
26889 ACTTCATCTTC
1 A--TCATCTTC
26900 CAATTCCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.11
21 9 0.32
22 9 0.32
24 7 0.25
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.49
Consensus pattern (22 bp):
ATCATCTTCATTTGCTTGCTTC
Found at i:30784 original size:75 final size:75
Alignment explanation
Indices: 30661--30812 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
30651 CAAAACCGAC
30661 AAACCTGTAACCCAAATGACCCAAGAATAATATAAATTAAAATTATATTTTATTTAATAAAATCC
1 AAACCTGTAACCCAAATGACCCAAGAATAATATAAATTAAAATTATATTTTATTTAATAAAATCC
30726 ATATTGTTAT
66 ATATTGTTAT
30736 AAACCTGTAACCCAAATGACCCAAGAATAATATAAATTAAAATTATATTTTATTTAATAAAATCC
1 AAACCTGTAACCCAAATGACCCAAGAATAATATAAATTAAAATTATATTTTATTTAATAAAATCC
30801 ATATTGTTAT
66 ATATTGTTAT
30811 AA
1 AA
30813 TTTTAACCAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (75 bp):
AAACCTGTAACCCAAATGACCCAAGAATAATATAAATTAAAATTATATTTTATTTAATAAAATCC
ATATTGTTAT
Found at i:33242 original size:92 final size:92
Alignment explanation
Indices: 33134--33318 Score: 300
Period size: 92 Copynumber: 2.0 Consensus size: 92
33124 GCTTTTTAAT
* *
33134 TAAATTAGTAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAAT-AAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
33198 AGTTTTTAGTGGAGTAAAACTATAAAAG
66 AG-TTTTAGTGGACTAAAACTATAAAAG
* *
33226 TAAAATAGTAAAATGGTAAGAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
33291 AGTTTTAGTTGACTAAAACTATAAAAG
66 AGTTTTAGTGGACTAAAACTATAAAAG
33318 T
1 T
33319 TTAATTAATG
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
92 77 0.90
93 9 0.10
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (92 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTAGTGGACTAAAACTATAAAAG
Found at i:37243 original size:20 final size:20
Alignment explanation
Indices: 37218--37258 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
37208 TTATGTCATA
*
37218 TCTACTTTGAAACTTTTCGG
1 TCTACTTCGAAACTTTTCGG
37238 TCTACTTCGAAACTTTTCGG
1 TCTACTTCGAAACTTTTCGG
37258 T
1 T
37259 TATATCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.44
Consensus pattern (20 bp):
TCTACTTCGAAACTTTTCGG
Found at i:39280 original size:12 final size:12
Alignment explanation
Indices: 39263--39288 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39253 TAAATAATTT
39263 AGATTTTATAGA
1 AGATTTTATAGA
39275 AGATTTTATAGA
1 AGATTTTATAGA
39287 AG
1 AG
39289 CTTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (12 bp):
AGATTTTATAGA
Found at i:39551 original size:21 final size:21
Alignment explanation
Indices: 39494--39740 Score: 276
Period size: 21 Copynumber: 12.1 Consensus size: 21
39484 GAAATATATA
*
39494 AAACTTTGGGGTTTGACTTTC
1 AAACTTTGGGGTTTGACTATC
** *
39515 AAAAATTGAGGTTTGACTATC
1 AAACTTTGGGGTTTGACTATC
* * * *
39536 AAAATTTAGGGATTGACCATC
1 AAACTTTGGGGTTTGACTATC
39557 AAACTTTGGGGTTTGACTATC
1 AAACTTTGGGGTTTGACTATC
*
39578 AAACTTTGGGGTTTGACAATC
1 AAACTTTGGGGTTTGACTATC
*
39599 AAACTTTGGAGTTTGACTATC
1 AAACTTTGGGGTTTGACTATC
* *
39620 AAAATTTGGGGATTGACTATC
1 AAACTTTGGGGTTTGACTATC
*
39641 AAACTTTGGGGTTTGACCATC
1 AAACTTTGGGGTTTGACTATC
* *
39662 AAACTTTGGGGTTTGGCTACC
1 AAACTTTGGGGTTTGACTATC
* *
39683 AAAATTTGGGGTTTGACCATC
1 AAACTTTGGGGTTTGACTATC
*
39704 -AA---TGGGGTTTGACCATC
1 AAACTTTGGGGTTTGACTATC
39721 -AA---TGGGGTTTGACTATC
1 AAACTTTGGGGTTTGACTATC
39738 AAA
1 AAA
39741 ATTTTGGTGA
Statistics
Matches: 195, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
17 31 0.16
18 2 0.01
20 2 0.01
21 160 0.82
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (21 bp):
AAACTTTGGGGTTTGACTATC
Found at i:39711 original size:17 final size:17
Alignment explanation
Indices: 39689--39739 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
39679 TACCAAAATT
39689 TGGGGTTTGACCATCAA
1 TGGGGTTTGACCATCAA
39706 TGGGGTTTGACCATCAA
1 TGGGGTTTGACCATCAA
*
39723 TGGGGTTTGACTATCAA
1 TGGGGTTTGACCATCAA
39740 AATTTTGGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (17 bp):
TGGGGTTTGACCATCAA
Found at i:39845 original size:17 final size:17
Alignment explanation
Indices: 39819--39852 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39809 TAATTAAATT
39819 TTGATAGTCAAACCCCA
1 TTGATAGTCAAACCCCA
*
39836 TTGATGGTCAAACCCCA
1 TTGATAGTCAAACCCCA
39853 AATTTTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (17 bp):
TTGATAGTCAAACCCCA
Found at i:39884 original size:21 final size:21
Alignment explanation
Indices: 39845--39885 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39835 ATTGATGGTC
* * *
39845 AAACCCCAAATTTTGATAGTT
1 AAACCACAAAGTTTAATAGTT
39866 AAACCACAAAGTTTAATAGT
1 AAACCACAAAGTTTAATAGT
39886 CAACACGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (21 bp):
AAACCACAAAGTTTAATAGTT
Found at i:39977 original size:18 final size:19
Alignment explanation
Indices: 39942--39978 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
39932 CCACAAAACC
39942 GTATTTAAGACAAAATTTT
1 GTATTTAAGACAAAATTTT
39961 GTATTTAAGAC-AAATTTT
1 GTATTTAAGACAAAATTTT
39979 ATAAGGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (19 bp):
GTATTTAAGACAAAATTTT
Found at i:42921 original size:74 final size:74
Alignment explanation
Indices: 42795--42942 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
42785 CCACATCTAC
* *
42795 TTTACAACGTGTACCGTACACGTGTCTAAAACCGTTTTTTAACCTAAATAATTCTAACCTTTCCT
1 TTTACAACGTGTACCGTACACGTGTCCAAAACCATTTTTTAACCTAAATAATTCTAACCTTTCCT
42860 AAGCGTCCA
66 AAGCGTCCA
*
42869 TTTACAACGTGTACCGTACACGTGTCCAAAACCATTTTTTAACCTAAGTAATTCTAACCTTTCCT
1 TTTACAACGTGTACCGTACACGTGTCCAAAACCATTTTTTAACCTAAATAATTCTAACCTTTCCT
42934 AAGCGTCCA
66 AAGCGTCCA
42943 CCTTATTTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (74 bp):
TTTACAACGTGTACCGTACACGTGTCCAAAACCATTTTTTAACCTAAATAATTCTAACCTTTCCT
AAGCGTCCA
Found at i:47174 original size:38 final size:38
Alignment explanation
Indices: 47092--47174 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
47082 GCACTCTTCC
* * **
47092 AATCAAATTTACCCCTGCACTACAATGGTTACTCTTTT
1 AATCAAATTTACCCCTGCACTACAATGGTCACACTCAT
*
47130 AATCAAATTTACCCCTGCACTACAATGGTCAGAC-CAT
1 AATCAAATTTACCCCTGCACTACAATGGTCACACTCAT
47167 AATTCAAA
1 AA-TCAAA
47175 AGTTCAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30
Consensus pattern (38 bp):
AATCAAATTTACCCCTGCACTACAATGGTCACACTCAT
Found at i:55707 original size:75 final size:75
Alignment explanation
Indices: 55583--55735 Score: 238
Period size: 75 Copynumber: 2.0 Consensus size: 75
55573 TGCCAGTTTC
* *
55583 TTTATTGCATTTTTAGTCATCTTGTTTTAAATCTTTGAAGCATTTATCTGGATTTTTCACCA-AT
1 TTTATTGCATTTTAAGTCATCTTGTTTTAAATCTTTGAAGCATTAATCTGGA-TTTTCACCAGAT
55647 AATGATATAAT
65 AATGATATAAT
* *
55658 TTTATTGCATTTTAAGTCAT-TTCGTTTTGAATCTTTGAAGCATTAATCTGGATTTTGACCAGAT
1 TTTATTGCATTTTAAGTCATCTT-GTTTTAAATCTTTGAAGCATTAATCTGGATTTTCACCAGAT
55722 AATGATATAAT
65 AATGATATAAT
55733 TTT
1 TTT
55736 GATGTGAATG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
74 10 0.14
75 62 0.86
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.48
Consensus pattern (75 bp):
TTTATTGCATTTTAAGTCATCTTGTTTTAAATCTTTGAAGCATTAATCTGGATTTTCACCAGATA
ATGATATAAT
Found at i:60778 original size:7 final size:7
Alignment explanation
Indices: 60766--60804 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
60756 CATCTACATC
60766 TCCAATG
1 TCCAATG
60773 TCCAATG
1 TCCAATG
60780 TCCAATG
1 TCCAATG
60787 TCCAATG
1 TCCAATG
60794 TCCAATG
1 TCCAATG
60801 TCCA
1 TCCA
60805 TCATCAGGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (7 bp):
TCCAATG
Found at i:61175 original size:14 final size:14
Alignment explanation
Indices: 61156--61187 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
61146 GGTTCCATGA
61156 TTAGAATTCGAGTT
1 TTAGAATTCGAGTT
*
61170 TTAGAATTCGATTT
1 TTAGAATTCGAGTT
61184 TTAG
1 TTAG
61188 TAGTGGCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (14 bp):
TTAGAATTCGAGTT
Found at i:64357 original size:167 final size:162
Alignment explanation
Indices: 64271--65164 Score: 672
Period size: 167 Copynumber: 5.6 Consensus size: 162
64261 GGATTTCAGT
* * *
64271 TTCGAGGAGAGATTTTTTTGGCGTGGGGGATGTCCAACAAGCTCACCTCACTCCGACACACGACC
1 TTCGAGGAGAGCTTTTTTTGGCGTGGGGGATGTCCAACAAGCTCATCTCACTCCGACACACGACA
* * *
64336 TTTCAGCACTCGTTGCGCAAAAAACGCATCTGAAATGAGCGTTTTCCTAAAAACGATGTTTTGCG
66 TTTGAGCACTCGTTGCGCAAAAAACGCATCCGAAATGAGCGTTTTCCTAAGAACGATGTTTTGCG
64401 CAC-AA-GCGC-A--AAGTTGAGGCTTTGGGC
131 CACAAACGCGCAACTAAGTTGAGGCTTTGGGC
* * * * * * *
64428 TTCGAGGAGAGCTTTGTTTGGCGTGTGGGCTGTCTAAAAAGCTCATCTCACTCCAACACACAACA
1 TTCGAGGAGAGCTTTTTTTGGCGTGGGGGATGTCCAACAAGCTCATCTCACTCCGACACACGACA
* * * * * * * *
64493 TTTTAGCACGCGTTGCGCAGAAGACGCATCTGGAATGAGCGTTTTCCTATGAATGATGTTTTGCG
66 TTTGAGCACTCGTTGCGCAAAAAACGCATCCGAAATGAGCGTTTTCCTAAGAACGATGTTTTGCG
* * *
64558 AACAAA----CATACAAAGTTAAGGCTTTGGGC
131 CACAAACGCGCA-ACTAAGTTGAGGCTTTGGGC
* * ** * *
64587 TTTGAGGAGAGCTTTATTT-G-GTATGGGACGTTCCAACAAGCTCATCTCACTCTGATC-CACGA
1 TTCGAGGAGAGCTTTTTTTGGCGTGGGGGATG-TCCAACAAGCTCATCTCACTCCGA-CACACGA
* ** * ** *
64649 AATTTGAGCACTTATTGCGCAAGAAACTTATCC-AGAATGAGCGTATTCCTAAGAACGATGTTTT
64 CATTTGAGCACTCGTTGCGCAAAAAACGCATCCGA-AATGAGCGTTTTCCTAAGAACGATGTTTT
* * *
64713 GTGCACAAACGCACAAAACCGTGAAGCTGAGGCTTTGGGC
128 GCGCACAAACGCGC--AA-C-T-AAGTTGAGGCTTTGGGC
** * * *
64753 TTCGAGGAGAGCTTTTTTTATCGTGGGGGCTGTCCAACAAGCTCAGCTCACTCCGACATACGACA
1 TTCGAGGAGAGCTTTTTTTGGCGTGGGGGATGTCCAACAAGCTCATCTCACTCCGACACACGACA
* * * * ** * * * *
64818 TTTGAGCACTCCTTGCTCAGAAAACGCATCTGGTATAAGCGTTTTCATAAAAACGATATTTT--G
66 TTTGAGCACTCGTTGCGCAAAAAACGCATCCGAAATGAGCGTTTTCCTAAGAACGATGTTTTGCG
*
64881 ------CGTGC-A--AAGTTGAGGCTTTGGGC
131 CACAAACGCGCAACTAAGTTGAGGCTTTGGGC
* * * * * * *
64904 TTCAAGGAGAGCTTTGTTTGGCATGGGGGAT-TCCCGACAAGCTCATCTCACTTCGACCCACGAT
1 TTCGAGGAGAGCTTTTTTTGGCGTGGGGGATGT-CCAACAAGCTCATCTCACTCCGACACACGAC
* ** * * * * *
64968 ATTTGAGCACTCTTTGCATAGAAAACGCATCTGGAATGAGTGTTTTCCTAAGAACGATGTTTTGT
65 ATTTGAGCACTCGTTGCGCAAAAAACGCATCCGAAATGAGCGTTTTCCTAAGAACGATGTTTTGC
**
65033 GCACAAAAC-CGCAAAATCGTGTTGTTGAGGCTTTGGGC
130 GCAC-AAACGCGC--AA-C-T-AAGTTGAGGCTTTGGGC
* * * * * * ** * *
65071 TTCGAGGAGAGCTTTGTTTGGTGT-GGGAATTGCCCAACAAGCCCAGCTCACTTTGACACATGAA
1 TTCGAGGAGAGCTTTTTTTGGCGTGGGGGA-TGTCCAACAAGCTCATCTCACTCCGACACACGAC
* * *
65135 ATTCGAGCGCTCGTTGCGTAAAAAACGCAT
65 ATTTGAGCACTCGTTGCGCAAAAAACGCAT
65165 TCAGAATGAG
Statistics
Matches: 576, Mismatches: 120, Indels: 72
0.75 0.16 0.09
Matches are distributed among these distances:
150 1 0.00
151 120 0.21
153 1 0.00
155 1 0.00
156 1 0.00
157 122 0.21
158 82 0.14
159 39 0.07
160 1 0.00
162 2 0.00
163 1 0.00
164 2 0.00
165 1 0.00
166 37 0.06
167 159 0.28
168 6 0.01
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (162 bp):
TTCGAGGAGAGCTTTTTTTGGCGTGGGGGATGTCCAACAAGCTCATCTCACTCCGACACACGACA
TTTGAGCACTCGTTGCGCAAAAAACGCATCCGAAATGAGCGTTTTCCTAAGAACGATGTTTTGCG
CACAAACGCGCAACTAAGTTGAGGCTTTGGGC
Found at i:64771 original size:482 final size:481
Alignment explanation
Indices: 63787--65031 Score: 1477
Period size: 482 Copynumber: 2.6 Consensus size: 481
63777 CCAAAGAAGT
* * * * * * * * * * *
63787 CTTCGAGGATAACTTTGTTTGGCATGGGGGCTGTACAAGAAGCTCATCTCACTCTGATACATGAT
1 CTTCGAGGAGAGCTTTTTTTGGCGTGGGGGCTGTCCAACAAGCTCACCTCACTCCGACACACGAC
** **
63852 ATTTGAGCACTATTTGCGCAAAAAAC-CATCTGGAATGAGCGTTTTCCTACGAACGATGTTTTGC
66 ATTTGAGCACTCCTTGCGCAAAAAACGCATCTGGAATGAGCGTTTTCCTAAAAACGATGTTTTGC
* * *
63916 GCACAAACGCGAAAAGTTGAGGCTTTGGACTTCAAGGTG-GCTTTGTTTGGCATGGGGAATGTCA
131 GCAC-AA-GCGCAAAGTTGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTGGCATGGGG-ATGTCA
* * *
63980 AACAAGCTTATCTCACTACGACACACGACATTTGAGCACTCGTTGCGCAAAAAACGCATCCGGAA
193 AA-AAGCTCATCTCACTACGACACACGACATTTGAGCACTCGTTGCGCAGAAAACGCATCTGGAA
* * * * * * *
64045 TGAGCGTTTTCCTATGAACAATGTTTGGCGAATAAACGCGCTAAGTTGAGGCTTTGGGCTTCGAG
257 TGAGCGTTTTCCTATGAACGATGTTTTGCGAACAAACACACAAAGTTAAGGCTTTGGGCTTCGAG
* * * * *
64110 CAGAACTTTTTTTGGCATGGGGGCTTTCTAACAAGCTCATCTCACTCCGATCCACGACATTTGAG
322 CAGAACTTTATTTGGCATGGGGACGTTCCAACAAGCTCATCTCACTCCGATCCACGAAATTTGAG
* *
64175 CACTCGTTACGCAAAAAACTCATCCGAAATGAGTGTATTCCTAAGAACAATGTTTTGCGCACAAA
387 CACTCATTACGCAAAAAACTCATCCGAAATGAGCGTATTCCTAAGAACAATGTTTTGCGCACAAA
* * * *
64240 CGCGCAAAACTGCGTAGTTAAGGATTTCAG
452 CGCACAAAACCGCGAAGCTAAGGATTTCAG
* * *
64270 TTTCGAGGAGAGATTTTTTTGGCGTGGGGGATGTCCAACAAGCTCACCTCACTCCGACACACGAC
1 CTTCGAGGAGAGCTTTTTTTGGCGTGGGGGCTGTCCAACAAGCTCACCTCACTCCGACACACGAC
* * * *
64335 CTTTCAGCACTCGTTGCGCAAAAAACGCATCTGAAATGAGCGTTTTCCTAAAAACGATGTTTTGC
66 ATTTGAGCACTCCTTGCGCAAAAAACGCATCTGGAATGAGCGTTTTCCTAAAAACGATGTTTTGC
* * *
64400 GCACAAGCGCAAAGTTGAGGCTTTGGGCTTCGAGGAGAGCTTTGTTTGGCGTGTGGGCTGTCTAA
131 GCACAAGCGCAAAGTTGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTGGCATG-GGGATGTC-AA
* * * * * *
64465 AAAGCTCATCTCACTCCAACACACAACATTTTAGCACGCGTTGCGCAGAAGACGCATCTGGAATG
194 AAAGCTCATCTCACTACGACACACGACATTTGAGCACTCGTTGCGCAGAAAACGCATCTGGAATG
* * * *
64530 AGCGTTTTCCTATGAATGATGTTTTGCGAACAAACATACAAAGTTAAGGCTTTGGGCTTTGAGGA
259 AGCGTTTTCCTATGAACGATGTTTTGCGAACAAACACACAAAGTTAAGGCTTTGGGCTTCGAGCA
* * *
64595 GAGCTTTATTTGGTAT-GGGACGTTCCAACAAGCTCATCTCACTCTGATCCACGAAATTTGAGCA
324 GAACTTTATTTGGCATGGGGACGTTCCAACAAGCTCATCTCACTCCGATCCACGAAATTTGAGCA
* * * * * *
64659 CTTATTGCGCAAGAAACTTATCC-AGAATGAGCGTATTCCTAAGAACGATGTTTTGTGCACAAAC
389 CTCATTACGCAAAAAACTCATCCGA-AATGAGCGTATTCCTAAGAACAATGTTTTGCGCACAAAC
* * * **
64723 GCACAAAACCGTGAAGCTGAGGCTTTGGG
453 GCACAAAACCGCGAAGCTAAGGATTTCAG
** * *
64752 CTTCGAGGAGAGCTTTTTTTATCGTGGGGGCTGTCCAACAAGCTCAGCTCACTCCGACATACGAC
1 CTTCGAGGAGAGCTTTTTTTGGCGTGGGGGCTGTCCAACAAGCTCACCTCACTCCGACACACGAC
* * * * * *
64817 ATTTGAGCACTCCTTGCTCAGAAAACGCATCTGGTATAAGCGTTTTCATAAAAACGATATTTT--
66 ATTTGAGCACTCCTTGCGCAAAAAACGCATCTGGAATGAGCGTTTTCCTAAAAACGATGTTTTGC
* *
64880 G--C--GTGCAAAGTTGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTGGCATGGGGGAT-TCCCG
131 GCACAAGCGCAAAGTTGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTGGCAT-GGGGATGT--CA
* * * * * **
64940 ACAAGCTCATCTCACTTCGACCCACGATATTTGAGCACTCTTTGCATAGAAAACGCATCTGGAAT
193 AAAAGCTCATCTCACTACGACACACGACATTTGAGCACTCGTTGCGCAGAAAACGCATCTGGAAT
* *
65005 GAGTGTTTTCCTAAGAACGATGTTTTG
258 GAGCGTTTTCCTATGAACGATGTTTTG
65032 TGCACAAAAC
Statistics
Matches: 645, Mismatches: 109, Indels: 23
0.83 0.14 0.03
Matches are distributed among these distances:
475 1 0.00
476 124 0.19
477 2 0.00
478 1 0.00
480 1 0.00
481 1 0.00
482 255 0.40
483 215 0.33
484 45 0.07
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (481 bp):
CTTCGAGGAGAGCTTTTTTTGGCGTGGGGGCTGTCCAACAAGCTCACCTCACTCCGACACACGAC
ATTTGAGCACTCCTTGCGCAAAAAACGCATCTGGAATGAGCGTTTTCCTAAAAACGATGTTTTGC
GCACAAGCGCAAAGTTGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTGGCATGGGGATGTCAAAA
AGCTCATCTCACTACGACACACGACATTTGAGCACTCGTTGCGCAGAAAACGCATCTGGAATGAG
CGTTTTCCTATGAACGATGTTTTGCGAACAAACACACAAAGTTAAGGCTTTGGGCTTCGAGCAGA
ACTTTATTTGGCATGGGGACGTTCCAACAAGCTCATCTCACTCCGATCCACGAAATTTGAGCACT
CATTACGCAAAAAACTCATCCGAAATGAGCGTATTCCTAAGAACAATGTTTTGCGCACAAACGCA
CAAAACCGCGAAGCTAAGGATTTCAG
Found at i:65014 original size:151 final size:151
Alignment explanation
Indices: 64740--65031 Score: 381
Period size: 151 Copynumber: 1.9 Consensus size: 151
64730 ACCGTGAAGC
* * * * *
64740 TGAGGCTTTGGGCTTCGAGGAGAGCTTTTTTTATCGTGGGGGCTGTCCAACAAGCTCAGCTCACT
1 TGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTAGCATGGGGGATGTCCAACAAGCTCAGCTCACT
* *
64805 CCGACATACGACATTTGAGCACTCCTTGCTCAGAAAACGCATCTGGTATAAGCGTTTTCATAAAA
66 CCGACACACGACATTTGAGCACTCCTTGCTCAGAAAACGCATCTGGAATAAGCGTTTTCATAAAA
64870 ACGATATTTTGCGTGCAAAGT
131 ACGATATTTTGCGTGCAAAGT
* * *
64891 TGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTGGCATGGGGGAT-TCCCGACAAGCTCATCTCAC
1 TGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTAGCATGGGGGATGT-CCAACAAGCTCAGCTCAC
* * * * * * *
64955 TTCGACCCACGATATTTGAGCACTCTTTGCAT-AGAAAACGCATCTGGAATGAGTGTTTTCCTAA
65 TCCGACACACGACATTTGAGCACTCCTTGC-TCAGAAAACGCATCTGGAATAAGCGTTTTCATAA
* *
65019 GAACGATGTTTTG
129 AAACGATATTTTG
65032 TGCACAAAAC
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
150 1 0.01
151 118 0.98
152 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (151 bp):
TGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTAGCATGGGGGATGTCCAACAAGCTCAGCTCACT
CCGACACACGACATTTGAGCACTCCTTGCTCAGAAAACGCATCTGGAATAAGCGTTTTCATAAAA
ACGATATTTTGCGTGCAAAGT
Found at i:65072 original size:318 final size:313
Alignment explanation
Indices: 64275--65089 Score: 835
Period size: 318 Copynumber: 2.6 Consensus size: 313
64265 TTCAGTTTCG
* * * * * * ** *
64275 AGGAGAGATTTTTTTGGCGTGGGGGATGTCCAACAAGCTCACCTCACTCCGACACACGACCTTTC
1 AGGAGAGCTTTATTTGGCATGGGGGAT-TCCAACAAGCTCATCTCACTTCGACCCACGAAATTTG
* * * *
64340 AGCACTCGTTGCGCAA-AAAACGCATCTGAAATGAGCGTTTTCCTAAAAACGATGTTTTGCGCAC
65 AGCACTC-TT-TGCAAGAAAACGCATCTGGAATGAGCGTTTTCCTAAGAACGATGTTTTGTGCAC
* * * *
64404 -AAGCGC-AAA----GTTGAGGCTTTGGGCTTCGAGGAGAGCTTTGTTTGGCGTGTGGGCTGTCT
128 AAACCGCAAAACGTGGTTGAGGCTTTGGGCTTCGAGGAGAGCTTTGTTTAGCGTGGGGGCTGTCC
* * * *
64463 AAAAAGCTCATCTCACTCCAACACACAACATTTTAGCACGCGTTGCGCAGAAGACGCATCTGGAA
193 AAAAAGCTCAGCTCACTCCAACACACAACATTTGAGCACGCCTTGCGCAGAAAACGCATCTGGAA
* * ** * * **
64528 TGAGCGTTTTCCTATGAATGATGTTTTGCGAACAAACATACAAAGTTAAGGCTTTGGGCTTTG
258 TAAGCGTTTTCATAAAAACGATATTTTGCG-------ATACAAAGTTAAGGCTTTGGGCTTCA
* * *
64591 AGGAGAGCTTTATTTGGTATGGGACG-TTCCAACAAGCTCATCTCAC-TCTGATCCACGAAATTT
1 AGGAGAGCTTTATTTGGCATGGG-GGATTCCAACAAGCTCATCTCACTTC-GACCCACGAAATTT
** ** *
64654 GAGCACT-TATTGCGCAAG-AAACTTATCCAGAATGAGCGTATTCCTAAGAACGATGTTTTGTGC
64 GAGCACTCT-TT--GCAAGAAAACGCATCTGGAATGAGCGTTTTCCTAAGAACGATGTTTTGTGC
* * * *
64717 ACAAACGCACAAAACCGTGAAGCTGAGGCTTTGGGCTTCGAGGAGAGCTTTTTTTATCGTGGGGG
126 ACAAAC-CGCAAAA-CGTG--GTTGAGGCTTTGGGCTTCGAGGAGAGCTTTGTTTAGCGTGGGGG
* * * * * *
64782 CTGTCCAACAAGCTCAGCTCACTCCGACATACGACATTTGAGCACTCCTTGCTCAGAAAACGCAT
187 CTGTCCAAAAAGCTCAGCTCACTCCAACACACAACATTTGAGCACGCCTTGCGCAGAAAACGCAT
* * *
64847 CTGGTATAAGCGTTTTCATAAAAACGATATTTTGCG-TGCAAAGTTGAGGCTTTGGGCTTCA
252 CTGGAATAAGCGTTTTCATAAAAACGATATTTTGCGATACAAAGTTAAGGCTTTGGGCTTCA
* * *
64908 AGGAGAGCTTTGTTTGGCATGGGGGATTCCCGACAAGCTCATCTCACTTCGACCCACGATATTTG
1 AGGAGAGCTTTATTTGGCATGGGGGATT-CCAACAAGCTCATCTCACTTCGACCCACGAAATTTG
*
64973 AGCACTCTTTGCATAGAAAACGCATCTGGAATGAGTGTTTTCCTAAGAACGATGTTTTGTGCACA
65 AGCACTCTTTGCA-AGAAAACGCATCTGGAATGAGCGTTTTCCTAAGAACGATGTTTTGTGCAC-
65038 AAACCGCAAAATCGTGTTGTTGAGGCTTTGGGCTTCGAGGAGAGCTTTGTTT
128 AAACCGCAAAA-CGTG--GTTGAGGCTTTGGGCTTCGAGGAGAGCTTTGTTT
65090 GGTGTGGGAA
Statistics
Matches: 408, Mismatches: 68, Indels: 44
0.78 0.13 0.08
Matches are distributed among these distances:
313 1 0.00
314 2 0.00
315 77 0.19
316 26 0.06
317 49 0.12
318 124 0.30
319 7 0.02
325 122 0.30
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (313 bp):
AGGAGAGCTTTATTTGGCATGGGGGATTCCAACAAGCTCATCTCACTTCGACCCACGAAATTTGA
GCACTCTTTGCAAGAAAACGCATCTGGAATGAGCGTTTTCCTAAGAACGATGTTTTGTGCACAAA
CCGCAAAACGTGGTTGAGGCTTTGGGCTTCGAGGAGAGCTTTGTTTAGCGTGGGGGCTGTCCAAA
AAGCTCAGCTCACTCCAACACACAACATTTGAGCACGCCTTGCGCAGAAAACGCATCTGGAATAA
GCGTTTTCATAAAAACGATATTTTGCGATACAAAGTTAAGGCTTTGGGCTTCA
Found at i:69876 original size:41 final size:41
Alignment explanation
Indices: 69825--69907 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
69815 TAACATATGG
* *
69825 CCACAGAGATCATCTGCTGCAGAAGCCGTCAACAAAGAATA
1 CCACAAAGATCATCTGCCGCAGAAGCCGTCAACAAAGAATA
* * * *
69866 CCACAAAGATCATCTGCCGTAGAGGCCGTCGATAAAGAATA
1 CCACAAAGATCATCTGCCGCAGAAGCCGTCAACAAAGAATA
69907 C
1 C
69908 TGCCGCAGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (41 bp):
CCACAAAGATCATCTGCCGCAGAAGCCGTCAACAAAGAATA
Done.