Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold802
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: 14269
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Found at i:1600 original size:50 final size:50
Alignment explanation
Indices: 1538--1648 Score: 161
Period size: 50 Copynumber: 2.2 Consensus size: 50
1528 AATTAACTAG
* * * **
1538 ATGTATCAATACATTGAAAAATGTATCGATACATTTGGGTTAAAAAA-AGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTAAG-TAAAAAATAGA
1588 ATGTATCGATACATTGAAAAATATATCGATACATCTAAGTAAAAAATAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTAAGTAAAAAATAGA
1638 ATGTATCGATA
1 ATGTATCGATA
1649 TATGTATGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 7 0.13
50 48 0.87
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATATATCGATACATCTAAGTAAAAAATAGA
Found at i:2933 original size:28 final size:28
Alignment explanation
Indices: 2888--3472 Score: 222
Period size: 28 Copynumber: 19.9 Consensus size: 28
2878 GAGAAGAGGT
*
2888 CACTTACTTGTGGGCTTTAAAAGGATGC
1 CACTGACTTGTGGGCTTTAAAAGGATGC
* *
2916 CACTGACTTGTAGACTTTGAAAA-GATGC
1 CACTGACTTGTGGGCTTT-AAAAGGATGC
*
2944 CACTGACTTGTGGGCTTTGAAAGGATGC
1 CACTGACTTGTGGGCTTTAAAAGGATGC
*
2972 CACTGACTTGTGGGCTTTGAAAGGATGC
1 CACTGACTTGTGGGCTTTAAAAGGATGC
* **
3000 CACTAACTTGTGGGCTTTTGAAAAAAAAAATGC
1 CACTGACTTGTGGGC-TTT----AAAAGGATGC
**
3033 CACT-AGCTTGTGTGGGCTTTGAAGGGGATTGC
1 CACTGA-C-T-TGTGGGCTTT-AAAAGGA-TGC
* * ** *
3065 CACAGAATTATGTGCACTTTAGAATGG-TGC
1 CACTG-ACT-TGTGGGCTTTA-AAAGGATGC
*
3095 CACTGACTTGTGGGCTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTT-AAAAGGATGC
* *
3124 CACTGACTTGTGGGCCTTGAAA-GAGTGC
1 CACTGACTTGTGGGCTTTAAAAGGA-TGC
* * *
3152 CACTAACTTAT-GGCTTTGAAAAAAAGATGC
1 CACTGACTTGTGGGCTTT---AAAAGGATGC
** *
3182 CACCAACTTGTGTAGGCTTTGAAAGGATG-
1 CACTGACTTGTG--GGCTTTAAAAGGATGC
* * *
3211 CATTGACTTATGGGCTTTGAAAAAAAAGATGC
1 CACTGACTTGTGGGCTTT----AAAAGGATGC
** **
3243 CACCAACTTGTGTGGGCTTTGAAGGGGGATGC
1 CACTGAC-T-TGTGGGCTTT-AA-AAGGATGC
* * * *
3275 CACAGACTTGTATGGACTTTAGAAAGGGTTGT
1 CACTGACTTG--TGGGCTTTA-AAA-GGATGC
** * *
3307 CACCAATTTGTGTAGGCTTTAATGAAGGGTGC
1 CACTGACTTGTG--GGCTTTAA--AAGGATGC
* *
3339 CACTAACTTGTGAGCTTTAAAAGGATGC
1 CACTGACTTGTGGGCTTTAAAAGGATGC
* * *
3367 CACAT-AGTTGTGGAC-TTAAAAGGGTTGC
1 CAC-TGACTTGTGGGCTTTAAAA-GGATGC
* * *
3395 CAC-GAAGTTGTGGAC-TTAAAAGGGTGC
1 CACTG-ACTTGTGGGCTTTAAAAGGATGC
* * * * *
3422 CACAGAGTTGTAGAC-TTAAAAGGGTGC
1 CACTGACTTGTGGGCTTTAAAAGGATGC
* * *
3449 CA-TAGAGTTGTGGACTTAAAAAGG
1 CACT-GACTTGTGGGCTTTAAAAGG
3473 GAAGGTGCCA
Statistics
Matches: 432, Mismatches: 78, Indels: 94
0.72 0.13 0.16
Matches are distributed among these distances:
27 62 0.14
28 159 0.37
29 39 0.09
30 40 0.09
31 18 0.04
32 72 0.17
33 21 0.05
34 14 0.03
35 7 0.02
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (28 bp):
CACTGACTTGTGGGCTTTAAAAGGATGC
Found at i:3124 original size:29 final size:29
Alignment explanation
Indices: 2888--3233 Score: 266
Period size: 28 Copynumber: 11.8 Consensus size: 29
2878 GAGAAGAGGT
*
2888 CACTTACTTGTGGGCTTT-AAAAGGATGC
1 CACTGACTTGTGGGCTTTGAAAAGGATGC
* *
2916 CACTGACTTGTAGACTTTGAAAA-GATGC
1 CACTGACTTGTGGGCTTTGAAAAGGATGC
2944 CACTGACTTGTGGGCTTTG-AAAGGATGC
1 CACTGACTTGTGGGCTTTGAAAAGGATGC
2972 CACTGACTTGTGGGCTTTG-AAAGGATGC
1 CACTGACTTGTGGGCTTTGAAAAGGATGC
* **
3000 CACTAACTTGTGGGCTTTTGAAAAAAAAAATGC
1 CACTGACTTGTGGGC-TTTG---AAAAGGATGC
**
3033 CACT-AGCTTGTGTGGGCTTTGAAGGGGATTGC
1 CACTGA-C-T-TGTGGGCTTTGAAAAGGA-TGC
* * ** *
3065 CACAGAATTATGTGCACTTT-AGAATGG-TGC
1 CACTG-ACT-TGTGGGCTTTGA-AAAGGATGC
*
3095 CACTGACTTGTGGGCTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTGAAAAGGATGC
*
3124 CACTGACTTGTGGGCCTTG-AAA-GAGTGC
1 CACTGACTTGTGGGCTTTGAAAAGGA-TGC
* * *
3152 CACTAACTTAT-GGCTTTGAAAAAAAGATGC
1 CACTGACTTGTGGGCTTTG--AAAAGGATGC
**
3182 CACCAACTTGTGTAGGCTTTG-AAAGGATG-
1 CACTGACTTGTG--GGCTTTGAAAAGGATGC
* *
3211 CATTGACTTATGGGCTTTGAAAA
1 CACTGACTTGTGGGCTTTGAAAA
3234 AAAAGATGCC
Statistics
Matches: 257, Mismatches: 36, Indels: 50
0.75 0.10 0.15
Matches are distributed among these distances:
27 17 0.07
28 114 0.44
29 40 0.16
30 29 0.11
31 6 0.02
32 19 0.07
33 19 0.07
34 6 0.02
35 7 0.03
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (29 bp):
CACTGACTTGTGGGCTTTGAAAAGGATGC
Found at i:3177 original size:59 final size:59
Alignment explanation
Indices: 3095--3254 Score: 168
Period size: 61 Copynumber: 2.7 Consensus size: 59
3085 AGAATGGTGC
* * * * **
3095 CACTGACTTGTGGGCTTTG--AAAAGGGTGCCACTGACTTGTG-GGCCTTGAAA-GAGTG
1 CACTAACTTATGGGCTTTGAAAAAAAGATGCCACCAACTTGTGAGGCCTTGAAAGGA-TG
*
3151 CCACTAACTTAT-GGCTTTGAAAAAAAGATGCCACCAACTTGTGTAGGCTTTGAAAGGATG
1 -CACTAACTTATGGGCTTTGAAAAAAAGATGCCACCAACTTGTG-AGGCCTTGAAAGGATG
* *
3211 CATTGACTTATGGGCTTTGAAAAAAAAGATGCCACCAACTTGTG
1 CACTAACTTATGGGCTTTG-AAAAAAAGATGCCACCAACTTGTG
3255 TGGGCTTTGA
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
56 7 0.08
57 9 0.10
58 18 0.21
59 9 0.10
60 18 0.21
61 26 0.30
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (59 bp):
CACTAACTTATGGGCTTTGAAAAAAAGATGCCACCAACTTGTGAGGCCTTGAAAGGATG
Found at i:3184 original size:30 final size:31
Alignment explanation
Indices: 3143--3251 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 31
3133 GTGGGCCTTG
*
3143 AAAGAGTGCCACTAACTTAT-GGCTTTGAAAA
1 AAAGA-TGCCACCAACTTATAGGCTTTGAAAA
*
3174 AAAGATGCCACCAACTTGTGTAGGCTTTG---A
1 AAAGATGCCACCAAC-T-TATAGGCTTTGAAAA
* *** *
3204 AAGGATG-CATTGACTTATGGGCTTTGAAAAA
1 AAAGATGCCACCAACTTATAGGCTTTG-AAAA
3235 AAAGATGCCACCAACTT
1 AAAGATGCCACCAACTT
3252 GTGTGGGCTT
Statistics
Matches: 58, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
27 9 0.16
28 1 0.02
29 4 0.07
30 16 0.28
31 13 0.22
32 8 0.14
33 7 0.12
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (31 bp):
AAAGATGCCACCAACTTATAGGCTTTGAAAA
Found at i:3257 original size:210 final size:207
Alignment explanation
Indices: 2888--3298 Score: 535
Period size: 210 Copynumber: 2.0 Consensus size: 207
2878 GAGAAGAGGT
* * *
2888 CACTTACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTAGACTTTGAAAAGATGCCACTGACTT
1 CACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTAGACCTTGAAAAGATGCCACTAACTT
* * ** *
2953 GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTT
66 ATGGGCTTTGAAAAGATGCCACCAACTTGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTT
* * *
3018 TGAAAAAAAAAATGCCACTAGCTTGTGTGGGCTTTGAA-GGGGATTGCCACAGAATTATGTGCAC
131 TGAAAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAGGGGGA-TGCCACAGAATTATATGCAC
3082 TTTAGAATGGTGC
195 TTTAGAATGGTGC
* * *
3095 CACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCCTTG-AAAGAGTGCCACTAAC
1 CACTGACTTGTGGGCTTT-AAAAGGATGCCACTGACTTGTAGACCTTGAAAAGA-TGCCACTAAC
* *
3159 TTAT-GGCTTTGAAAAAAAGATGCCACCAACTTGTGTAGGCTTTGAAAGGATG-CATTGACTTAT
64 TTATGGGCTTTG---AAAAGATGCCACCAACTTGTG--GGCTTTGAAAGGATGCCACTAACTTAT
* * *
3222 GGGC-TTTGAAAAAAAAGATGCCACCAACTTGTGTGGGCTTTGAAGGGGGATGCCACAGACTTGT
124 GGGCTTTTGAAAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAGGGGGATGCCACAGAATTAT
*
3286 ATGGACTTTAGAA
189 ATGCACTTTAGAA
3299 AGGGTTGTCA
Statistics
Matches: 176, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
207 29 0.16
208 37 0.21
210 78 0.44
211 17 0.10
212 15 0.09
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (207 bp):
CACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTAGACCTTGAAAAGATGCCACTAACTT
ATGGGCTTTGAAAAGATGCCACCAACTTGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTT
TGAAAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAGGGGGATGCCACAGAATTATATGCACT
TTAGAATGGTGC
Found at i:3430 original size:27 final size:27
Alignment explanation
Indices: 3355--3529 Score: 172
Period size: 27 Copynumber: 6.2 Consensus size: 27
3345 CTTGTGAGCT
* *
3355 TTAAAAGGATGCCACATAGTTGTGGAC
1 TTAAAAGGGTGCCACAGAGTTGTGGAC
3382 TTAAAAGGGTTGCCAC-GAAGTTGTGGAC
1 TTAAAAGGG-TGCCACAG-AGTTGTGGAC
*
3410 TTAAAAGGGTGCCACAGAGTTGTAGAC
1 TTAAAAGGGTGCCACAGAGTTGTGGAC
*
3437 TTAAAAGGGTGCCATAGAGTTGTGGAC
1 TTAAAAGGGTGCCACAGAGTTGTGGAC
* *
3464 TTAAAAAGGGAAGGTGCCACGGAGTTGTGGATT
1 TT-AAAA--G--GGTGCCACAGAGTTGTGGA-C
* * * * *
3497 TTAATAGGTTGCCACAAAATTATGGAC
1 TTAAAAGGGTGCCACAGAGTTGTGGAC
3524 TTAAAA
1 TTAAAA
3530 AGGGAAAGTG
Statistics
Matches: 123, Mismatches: 16, Indels: 18
0.78 0.10 0.11
Matches are distributed among these distances:
27 55 0.45
28 44 0.36
30 2 0.02
32 20 0.16
33 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (27 bp):
TTAAAAGGGTGCCACAGAGTTGTGGAC
Found at i:3473 original size:55 final size:54
Alignment explanation
Indices: 3355--3469 Score: 169
Period size: 55 Copynumber: 2.1 Consensus size: 54
3345 CTTGTGAGCT
* * * *
3355 TTAAAAGGATGCCACATAGTTGTGGACTTAAAAGGGTTGCCA-CGAAGTTGTGGAC
1 TTAAAAGGGTGCCACAGAGTTGTAGACTTAAAAGGG-TGCCATAG-AGTTGTGGAC
3410 TTAAAAGGGTGCCACAGAGTTGTAGACTTAAAAGGGTGCCATAGAGTTGTGGAC
1 TTAAAAGGGTGCCACAGAGTTGTAGACTTAAAAGGGTGCCATAGAGTTGTGGAC
3464 TTAAAA
1 TTAAAA
3470 AGGGAAGGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
54 21 0.38
55 34 0.62
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (54 bp):
TTAAAAGGGTGCCACAGAGTTGTAGACTTAAAAGGGTGCCATAGAGTTGTGGAC
Found at i:3482 original size:32 final size:31
Alignment explanation
Indices: 3359--3654 Score: 158
Period size: 32 Copynumber: 9.8 Consensus size: 31
3349 TGAGCTTTAA
*
3359 AAGGATGCCACATAGTTGTGGACTTAAAA-GG
1 AAGG-TGCCACAGAGTTGTGGACTTAAAAGGG
*
3390 --GTTGCCAC-GAAGTTGTGGACTTAAAA--G
1 AAGGTGCCACAG-AGTTGTGGACTTAAAAGGG
*
3417 --GGTGCCACAGAGTTGTAGACTTAAAA--G
1 AAGGTGCCACAGAGTTGTGGACTTAAAAGGG
*
3444 --GGTGCCATAGAGTTGTGGACTTAAAAAGGG
1 AAGGTGCCACAGAGTTGTGGACTT-AAAAGGG
* * *
3474 AAGGTGCCACGGAGTTGTGGATTTTAATA--G
1 AAGGTGCCACAGAGTTGTGGA-CTTAAAAGGG
* * * *
3504 --GTTGCCACAAAATTATGGACTTAAAAAGGG
1 AAGGTGCCACAGAGTTGTGGACTT-AAAAGGG
* * * * * **
3534 AAAGTGCCATAAAGTTGTGGGCTTTAACAGAA
1 AAGGTGCCACAGAGTTGTGGAC-TTAAAAGGG
3566 AAGGTTGCCAC-GAGTTGTGGACTTAAAAGGG
1 AAGG-TGCCACAGAGTTGTGGACTTAAAAGGG
* * * * **
3597 AAGGTGTCACGGAGTTATGGACTTTAATAGAAA
1 AAGGTGCCACAGAGTTGTGGAC-TTAAAAG-GG
*
3630 AAGGTTGCCACGGAGTTGTGGACTT
1 AAGG-TGCCACAGAGTTGTGGACTT
3655 TGAAAAGAAA
Statistics
Matches: 206, Mismatches: 40, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
27 46 0.22
28 44 0.21
29 1 0.00
30 8 0.04
31 20 0.10
32 56 0.27
33 15 0.07
34 16 0.08
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.25
Consensus pattern (31 bp):
AAGGTGCCACAGAGTTGTGGACTTAAAAGGG
Found at i:3528 original size:60 final size:59
Alignment explanation
Indices: 3459--3626 Score: 158
Period size: 60 Copynumber: 2.8 Consensus size: 59
3449 CATAGAGTTG
3459 TGGACTTAAAAAGGGAAGGTGCCACGGAGTTGTGGATTTTAATAGGTTGCCACAAAATTA
1 TGGACTTAAAAAGGGAAGGTGCCACGGAGTTGTGGATTTTAATAGGTTGCCAC-AAATTA
* *** * * * * * *
3519 TGGACTTAAAAAGGGAAAGTGCCATAAAGTTGTGGGCTTTAACAGAAAAGGTTGCCACGAGTTG
1 TGGACTTAAAAAGGGAAGGTGCCACGGAGTTGT-GGATTT----TAATAGGTTGCCACAAATTA
* * *
3583 TGGACTT-AAAAGGGAAGGTGTCACGGAGTTATGGACTTTAATAG
1 TGGACTTAAAAAGGGAAGGTGCCACGGAGTTGTGGATTTTAATAG
3627 AAAAAGGTTG
Statistics
Matches: 83, Mismatches: 20, Indels: 12
0.72 0.17 0.10
Matches are distributed among these distances:
58 4 0.05
60 29 0.35
61 5 0.06
62 4 0.05
63 19 0.23
64 10 0.12
65 12 0.14
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (59 bp):
TGGACTTAAAAAGGGAAGGTGCCACGGAGTTGTGGATTTTAATAGGTTGCCACAAATTA
Found at i:3644 original size:34 final size:33
Alignment explanation
Indices: 3546--3664 Score: 136
Period size: 34 Copynumber: 3.6 Consensus size: 33
3536 AGTGCCATAA
* *
3546 AGTTGTGGGCTTTAACAGAAAAGGTTGCCAC-G
1 AGTTGTGGACTTTAAAAGAAAAGGTTGCCACGG
** *
3578 AGTTGTGGAC-TTAAAAGGGAAGG-TGTCACGG
1 AGTTGTGGACTTTAAAAGAAAAGGTTGCCACGG
* *
3609 AGTTATGGACTTTAATAGAAAAAGGTTGCCACGG
1 AGTTGTGGACTTTAAAAG-AAAAGGTTGCCACGG
3643 AGTTGTGGACTTTGAAAAGAAA
1 AGTTGTGGACTTT-AAAAGAAA
3665 TGCCACTGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
30 5 0.07
31 20 0.29
32 15 0.21
33 4 0.06
34 22 0.31
35 4 0.06
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.25
Consensus pattern (33 bp):
AGTTGTGGACTTTAAAAGAAAAGGTTGCCACGG
Found at i:3682 original size:64 final size:62
Alignment explanation
Indices: 3550--3685 Score: 141
Period size: 64 Copynumber: 2.1 Consensus size: 62
3540 CCATAAAGTT
* * * * *
3550 GTGGGCTTTAACAGAAAAGGTTGCCACGAGTTGTGGACTTAAAAGGGAAGGTGTCACGGAGTT
1 GTGGACTTTAACAGAAAAGGTTGCCACGAGTTGTGGACTTAAAA-GGAAGATGCCACGGAATC
* * *
3613 ATGGACTTTAATAGAAAAAGGTTGCCACGGAGTTGTGGACTTTGAAAA-GAA-ATGCCACTGAAT
1 GTGGACTTTAACAG-AAAAGGTTGCCAC-GAGTTGTGGAC-TT-AAAAGGAAGATGCCACGGAAT
3676 C
62 C
3677 GTGGACTTT
1 GTGGACTTT
3686 GAAGAGGTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
63 11 0.18
64 29 0.48
65 14 0.23
66 2 0.03
67 4 0.07
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (62 bp):
GTGGACTTTAACAGAAAAGGTTGCCACGAGTTGTGGACTTAAAAGGAAGATGCCACGGAATC
Found at i:4749 original size:211 final size:213
Alignment explanation
Indices: 4385--4792 Score: 653
Period size: 210 Copynumber: 1.9 Consensus size: 213
4375 ATTTGGTTTA
*
4385 TTTCTGACGAACAGACTGCTTGACAAGAAATGTGATATAATTCAATTTTTTTTGACAAGAAAAGT
1 TTTCTGACGAACAGACTGCTTGACAAGAAATGTGATACAATTCAATTTTTTTTGACAAGAAAAGT
* *
4450 GATGGTTTACTTCCAACAAAATGATTTGATGGCTAGAAGGGTGATGCAATTTGGGCTATTGATGT
66 GATGGTTTACTTCCAACAAAATGATTTGATGGCTACAAGGGTGATGCAATTTGGGCTATTCATGT
* *
4515 CCCTGATATCATGACACAAATG-TTTTTCTGATGCATCTCGAGATC-TTCTCGAATAATCAACCT
131 CCCTGATATCATGACACAAATGTTTTTTCTGATGCATCTCGAGATCTTTCTCAAACAATCAACCT
4578 AATAGGTATAGTAATGTT
196 AATAGGTATAGTAATGTT
* *
4596 TTTCTGACGAA-AGGCCTGCTTGACAAGAAATGTGATACAATTCAA-TTTTTTTGACAAGAAAGG
1 TTTCTGACGAACA-GACTGCTTGACAAGAAATGTGATACAATTCAATTTTTTTTGACAAGAAAAG
* *
4659 TGATGGTTTACTTCTAACAAAATGGTTTGATGGCTACAAGGGTGATGCAATTTGGGCTATTCATG
65 TGATGGTTTACTTCCAACAAAATGATTTGATGGCTACAAGGGTGATGCAATTTGGGCTATTCATG
* * * *
4724 TCCCTGATAATCATGATACAAATGTTTTTTTTTATGCATCTCGAGATCTTTCTCAAACAATTAAC
130 TCCCTGAT-ATCATGACACAAATGTTTTTTCTGATGCATCTCGAGATCTTTCTCAAACAATCAAC
4789 CTAA
194 CTAA
4793 CCGGTATGAG
Statistics
Matches: 180, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
210 87 0.48
211 55 0.31
212 21 0.12
213 17 0.09
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (213 bp):
TTTCTGACGAACAGACTGCTTGACAAGAAATGTGATACAATTCAATTTTTTTTGACAAGAAAAGT
GATGGTTTACTTCCAACAAAATGATTTGATGGCTACAAGGGTGATGCAATTTGGGCTATTCATGT
CCCTGATATCATGACACAAATGTTTTTTCTGATGCATCTCGAGATCTTTCTCAAACAATCAACCT
AATAGGTATAGTAATGTT
Found at i:5230 original size:18 final size:19
Alignment explanation
Indices: 5207--5244 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5197 TGATTTTGCC
*
5207 TTTTTAT-TTTTGTGTTTT
1 TTTTTATCTTTTATGTTTT
5225 TTTTTATCTTTTATGTTTT
1 TTTTTATCTTTTATGTTTT
5244 T
1 T
5245 GGCTTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.08, C:0.03, G:0.08, T:0.82
Consensus pattern (19 bp):
TTTTTATCTTTTATGTTTT
Found at i:9707 original size:13 final size:14
Alignment explanation
Indices: 9686--9715 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9676 TATTACCTCT
9686 ACAA-TTTTTGTAA
1 ACAACTTTTTGTAA
9699 ACAACTTTTTGTAA
1 ACAACTTTTTGTAA
9713 ACA
1 ACA
9716 TGAATGCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (14 bp):
ACAACTTTTTGTAA
Found at i:11406 original size:20 final size:19
Alignment explanation
Indices: 11362--11416 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
11352 ATATCAATAC
*
11362 ATTGTATCGATA-ACTGTTC
1 ATTGTATCGATACA-TGTTA
11381 ATTGTATCGATACATGTATA
1 ATTGTATCGATACATGT-TA
11401 ATTGTATCGATACATG
1 ATTGTATCGATACATG
11417 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (19 bp):
ATTGTATCGATACATGTTA
Found at i:12574 original size:299 final size:299
Alignment explanation
Indices: 12037--12936 Score: 1707
Period size: 299 Copynumber: 3.0 Consensus size: 299
12027 TAATCAATTC
*
12037 TTGTAGTGAATTGGATAACCACTCGACGAAGAAGTGTCGAAGAGAGAGGATGTAGGTACTGAA-T
1 TTGTAGTAAATTGGATAACCACTCGACGAAGAAGTGTCGAAGAGAGAGGATGTAGGTACTGAATT
12101 AGACCGAACCTCTATAAACTCTGGTGTCGAGCATTTCTTCCTTAATCTTTTTATCTTTGGAATTG
66 AGACCGAACCTCTATAAACTCTGGTGTCGAGCATTTCTTCCTTAATCTTTTTATCTTTGGAATTG
*
12166 TTTTTTACCAAATCTTTCAAAACACTCAAAATTCGAAAAGAACCAATTAACCCCCTCTTGGTTCA
131 TTTTGTACCAAATCTTTCAAAACACTCAAAATTCGAAAAGAACCAATTAACCCCCTCTTGGTTCA
12231 TTATTCCTTGAGCTTTCAATAGCCAAAATGTTGGTGTCAAATAGGAGGTGTTTTGGGTCATTTCC
196 TTATTCCTTGAGCTTTCAATAGCCAAAATGTTGGTGTCAAATAGGAGGTGTTTTGGGTCATTTCC
12296 CTCAACCAATTTGCAAGACAAGGTGCTAACAACATGATG
261 CTCAACCAATTTGCAAGACAAGGTGCTAACAACATGATG
12335 TTGTAGTAAATTGGATAACCACTCGACGAAGAAGTGTCGAAGAGAGAGGATGTAGGTACTGAATT
1 TTGTAGTAAATTGGATAACCACTCGACGAAGAAGTGTCGAAGAGAGAGGATGTAGGTACTGAATT
12400 AGACCGAACCTCTATAAACTCTGGTGTCGAGCATTTTCTTTCCTTAATCTTTTTATCTTTGGAAT
66 AGACCGAACCTCTATAAACTCTGGTGTCGAGCA-TTTC-TTCCTTAATCTTTTTATCTTTGGAAT
12465 TGTTTTGTACCAAATCTTTCAAAACACTCAAAATTCG-AAAGAACCAATTAACCCCCTC-TGGTT
129 TGTTTTGTACCAAATCTTTCAAAACACTCAAAATTCGAAAAGAACCAATTAACCCCCTCTTGGTT
*
12528 CATTATTCCTTGAGCTTTCAATAGCCAAAATATTGGTGTCAAATAGGAGGTGTTTTGGGTCATTT
194 CATTATTCCTTGAGCTTTCAATAGCCAAAATGTTGGTGTCAAATAGGAGGTGTTTTGGGTCATTT
12593 CCCTCAACCAATTTGCAAGACAAGGTGCTAACAACATGATG
259 CCCTCAACCAATTTGCAAGACAAGGTGCTAACAACATGATG
12634 TTGTAGTAAATTGGATAACCACTCGACGAAGAAGTGTCGAAGAGAGAGGATGTAGGTACTGAATT
1 TTGTAGTAAATTGGATAACCACTCGACGAAGAAGTGTCGAAGAGAGAGGATGTAGGTACTGAATT
*
12699 AGACCGAACCTCTATAAACTCTGGTGTTGAGCATTTCTTCCTTAATCTTTTTATCTTTGGAATTG
66 AGACCGAACCTCTATAAACTCTGGTGTCGAGCATTTCTTCCTTAATCTTTTTATCTTTGGAATTG
12764 TTTTGTACCAAATCTTTCAAAACACTCAAAATTCGAAAAGAACCAATTAACCCCCTCTTGGTTCA
131 TTTTGTACCAAATCTTTCAAAACACTCAAAATTCGAAAAGAACCAATTAACCCCCTCTTGGTTCA
*
12829 TTATTCCTTGAGCTTTCAATAGCCAAAATGTTGGTGTCAAATAGGAGGTATTTTGGGTCATTTCC
196 TTATTCCTTGAGCTTTCAATAGCCAAAATGTTGGTGTCAAATAGGAGGTGTTTTGGGTCATTTCC
*
12894 CTCAACCAATTTGCAAGACAAGGTGCTGACAACATGATG
261 CTCAACCAATTTGCAAGACAAGGTGCTAACAACATGATG
12933 TTGT
1 TTGT
12937 TTAGCTGATA
Statistics
Matches: 590, Mismatches: 7, Indels: 9
0.97 0.01 0.01
Matches are distributed among these distances:
297 63 0.11
298 87 0.15
299 353 0.60
300 25 0.04
301 62 0.11
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (299 bp):
TTGTAGTAAATTGGATAACCACTCGACGAAGAAGTGTCGAAGAGAGAGGATGTAGGTACTGAATT
AGACCGAACCTCTATAAACTCTGGTGTCGAGCATTTCTTCCTTAATCTTTTTATCTTTGGAATTG
TTTTGTACCAAATCTTTCAAAACACTCAAAATTCGAAAAGAACCAATTAACCCCCTCTTGGTTCA
TTATTCCTTGAGCTTTCAATAGCCAAAATGTTGGTGTCAAATAGGAGGTGTTTTGGGTCATTTCC
CTCAACCAATTTGCAAGACAAGGTGCTAACAACATGATG
Found at i:13279 original size:19 final size:20
Alignment explanation
Indices: 13255--13304 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
13245 AAATAGAATA
*
13255 TATCGATACATTGA-AAATG
1 TATCGATACATTCATAAATG
*
13274 TATCGATACATTCATACATG
1 TATCGATACATTCATAAATG
*
13294 TATTGATACAT
1 TATCGATACAT
13305 CTAGGTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (20 bp):
TATCGATACATTCATAAATG
Found at i:13325 original size:30 final size:30
Alignment explanation
Indices: 13291--13362 Score: 112
Period size: 28 Copynumber: 2.5 Consensus size: 30
13281 ACATTCATAC
*
13291 ATGTATTGATACATCTAGGTAAAAAACAGA
1 ATGTATCGATACATCTAGGTAAAAAACAGA
*
13321 ATGTATCGAT--ATCTAGGTAAAAAATAGA
1 ATGTATCGATACATCTAGGTAAAAAACAGA
13349 ATGTATCGATACAT
1 ATGTATCGATACAT
13363 GTCCTATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 27 0.71
30 11 0.29
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (30 bp):
ATGTATCGATACATCTAGGTAAAAAACAGA
Done.