Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012242.1 Corchorus olitorius cultivar O-4 contig12275, 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: 53472
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:3300 original size:32 final size:32
Alignment explanation
Indices: 3259--3333 Score: 150
Period size: 32 Copynumber: 2.3 Consensus size: 32
3249 CACAATTATT
3259 AGTTCAGGGGGTAAACTGACCTAAAATTGCAA
1 AGTTCAGGGGGTAAACTGACCTAAAATTGCAA
3291 AGTTCAGGGGGTAAACTGACCTAAAATTGCAA
1 AGTTCAGGGGGTAAACTGACCTAAAATTGCAA
3323 AGTTCAGGGGG
1 AGTTCAGGGGG
3334 CAATGGGGGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (32 bp):
AGTTCAGGGGGTAAACTGACCTAAAATTGCAA
Found at i:7801 original size:14 final size:14
Alignment explanation
Indices: 7782--7829 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
7772 GTGTGTGGTG
7782 TGTTGTTATCTTGT
1 TGTTGTTATCTTGT
*
7796 TGTTG-T-TGTTG-
1 TGTTGTTATCTTGT
7807 TGTTGTTATCTTGT
1 TGTTGTTATCTTGT
7821 TGTTGTTAT
1 TGTTGTTAT
7830 TGTTTGAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 5 0.17
14 14 0.48
ACGTcount: A:0.06, C:0.04, G:0.25, T:0.65
Consensus pattern (14 bp):
TGTTGTTATCTTGT
Found at i:7808 original size:25 final size:25
Alignment explanation
Indices: 7780--7832 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
7770 TGGTGTGTGG
*
7780 TGTGTTGTTATCTTGTTGTTGTTGT
1 TGTGTTGTTATCTTGTTGTTGTTAT
7805 TGTGTTGTTATCTTGTTGTTGTTAT
1 TGTGTTGTTATCTTGTTGTTGTTAT
7830 TGT
1 TGT
7833 TTGAATGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.06, C:0.04, G:0.26, T:0.64
Consensus pattern (25 bp):
TGTGTTGTTATCTTGTTGTTGTTAT
Found at i:8891 original size:3 final size:3
Alignment explanation
Indices: 8874--8913 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
8864 AAGGAAAATC
*
8874 AAG AAA AAG -AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
8914 AATGGTGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9067 original size:24 final size:24
Alignment explanation
Indices: 9040--9097 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
9030 AGAAATAAAT
* *
9040 TTCAAAAAGTAAAATGGTAATTAG
1 TTCAAAAAGTAAAATAGTAATCAG
*
9064 TTCAAAGAGTAAAATAGTAATCAG
1 TTCAAAAAGTAAAATAGTAATCAG
9088 -T-AAAAAGTAA
1 TTCAAAAAGTAA
9098 TGGTAAAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 8 0.27
23 1 0.03
24 21 0.70
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (24 bp):
TTCAAAAAGTAAAATAGTAATCAG
Found at i:9108 original size:35 final size:35
Alignment explanation
Indices: 9067--9173 Score: 169
Period size: 35 Copynumber: 3.1 Consensus size: 35
9057 TAATTAGTTC
9067 AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGT
1 AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGT
* *
9102 AAAGAGTAAAATAGTAATCAATGAAAAGTAATGGT
1 AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGT
* * *
9137 AAAGAGTGAAATAGTAATAAGTAAAAAGTAACGGT
1 AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGT
9172 AA
1 AA
9174 TCAGTAAAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (35 bp):
AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGT
Found at i:9142 original size:70 final size:69
Alignment explanation
Indices: 9067--9294 Score: 186
Period size: 70 Copynumber: 3.4 Consensus size: 69
9057 TAATTAGTTC
9067 AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGTAAAGAGTAAAATAGTAATCAATGAAAAGTA
1 AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGTAAA-AGTAAAATAGTAATCAATGAAAAGTA
9132 ATGGT
65 ATGGT
* * * * * **
9137 AAAGAGTGAAATAGTAATAAGTAAAAAGTAACGGTAATCAGT-AAAGAGTAA--AATGGTAATGG
1 AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGTAA-AAGTAAAATAGTAATCAAT-G-AAAAG
9199 TAAATGGT
63 T-AATGGT
* * * * ** * *
9207 AAAAAGTAAAATGGTTAT-GGTAATCAG---T-G-AAAAGTAAAATAGTAATCAGTAAAAAGTAA
1 AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGTAAAAGTAAAATAGTAATCAATGAAAAGTAA
9266 TGGT
66 TGGT
* * *
9270 AATGAATAAAATGGTAATCAGTAAA
1 AAAGAGTAAAATAGTAATCAGTAAA
9295 GAATAAAATG
Statistics
Matches: 123, Mismatches: 27, Indels: 22
0.72 0.16 0.13
Matches are distributed among these distances:
63 23 0.19
64 18 0.15
65 1 0.01
66 2 0.02
67 3 0.02
68 1 0.01
69 18 0.15
70 57 0.46
ACGTcount: A:0.52, C:0.03, G:0.21, T:0.24
Consensus pattern (69 bp):
AAAGAGTAAAATAGTAATCAGTAAAAAGTAATGGTAAAAGTAAAATAGTAATCAATGAAAAGTAA
TGGT
Found at i:9239 original size:28 final size:27
Alignment explanation
Indices: 9149--9252 Score: 104
Period size: 28 Copynumber: 3.7 Consensus size: 27
9139 AGAGTGAAAT
* *
9149 AGTAATAAGTAAAA-AGTAACGGTAATC
1 AGTAA-AAGTAAAATGGTAATGGTAATC
9176 AGTAAAGAGTAAAATGGTAATGGTAAAT-
1 AGTAAA-AGTAAAATGGTAATGGT-AATC
* *
9204 GGTAAAAAGTAAAATGGTTATGGTAATC
1 AGT-AAAAGTAAAATGGTAATGGTAATC
*
9232 AGTGAAAAGTAAAATAGTAAT
1 AGT-AAAAGTAAAATGGTAAT
9253 CAGTAAAAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
26 1 0.02
27 15 0.23
28 42 0.66
29 6 0.09
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (27 bp):
AGTAAAAGTAAAATGGTAATGGTAATC
Found at i:9298 original size:22 final size:22
Alignment explanation
Indices: 9268--9459 Score: 174
Period size: 22 Copynumber: 9.0 Consensus size: 22
9258 AAAAGTAATG
*
9268 GTAATGAATAAAATGGTAATCA
1 GTAAAGAATAAAATGGTAATCA
9290 GTAAAGAATAAAATGGTTAA--A
1 GTAAAGAATAAAATGG-TAATCA
* *
9311 CTAAA-AGTAAAATGGTAATC-
1 GTAAAGAATAAAATGGTAATCA
9331 -T---G--TAAAATGGTAATCTA
1 GTAAAGAATAAAATGGTAATC-A
*
9348 -TAAAGAATAAACTGGTAATCA
1 GTAAAGAATAAAATGGTAATCA
9369 GTAAA-AAGTAAAATGGTAATCA
1 GTAAAGAA-TAAAATGGTAATCA
9391 GTAAAGAAGTAAAATGGTAATCA
1 GTAAAGAA-TAAAATGGTAATCA
* * **
9414 ATAAAAAAATGTAATGGTAATCA
1 GT-AAAGAATAAAATGGTAATCA
*
9437 GTAAAGAATAAAACGGTAATCA
1 GTAAAGAATAAAATGGTAATCA
9459 G
1 G
9460 AAATTAAATT
Statistics
Matches: 141, Mismatches: 14, Indels: 30
0.76 0.08 0.16
Matches are distributed among these distances:
15 13 0.09
17 1 0.01
19 4 0.03
20 10 0.07
21 8 0.06
22 66 0.47
23 34 0.24
24 5 0.04
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (22 bp):
GTAAAGAATAAAATGGTAATCA
Found at i:9302 original size:57 final size:58
Alignment explanation
Indices: 9223--9395 Score: 187
Period size: 57 Copynumber: 3.0 Consensus size: 58
9213 TAAAATGGTT
* * *
9223 ATGGTAATCAGTGAAA-AGTAAAATAGTAATCAGTAAAAAGT-AATGGTAATGAATAAA
1 ATGGTAATCAGT-AAAGAATAAAATGGTAATCAGTAAAAAGTAAATGGTAATCAATAAA
* **
9280 ATGGTAATCAGTAAAGAATAAAATGGTTAA--ACT-AAAAGTAAAATGGTAATCTGTAAA
1 ATGGTAATCAGTAAAGAATAAAATGG-TAATCAGTAAAAAGT-AAATGGTAATCAATAAA
* *
9337 ATGGTAATCTA-TAAAGAATAAACTGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAAA
1 ATGGTAATC-AGTAAAGAATAAAATGGTAATCAGTAAAAAGT-AAATGGTAATCAATAAA
9396 GAAGTAAAAT
Statistics
Matches: 99, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
55 6 0.06
56 8 0.08
57 56 0.57
58 6 0.06
59 23 0.23
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.25
Consensus pattern (58 bp):
ATGGTAATCAGTAAAGAATAAAATGGTAATCAGTAAAAAGTAAATGGTAATCAATAAA
Found at i:9337 original size:15 final size:15
Alignment explanation
Indices: 9317--9351 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
9307 TAAACTAAAA
9317 GTAAAATGGTAATCT
1 GTAAAATGGTAATCT
9332 GTAAAATGGTAATCT
1 GTAAAATGGTAATCT
*
9347 ATAAA
1 GTAAA
9352 GAATAAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (15 bp):
GTAAAATGGTAATCT
Found at i:9373 original size:37 final size:35
Alignment explanation
Indices: 9298--9374 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 35
9288 CAGTAAAGAA
*
9298 TAAAATGGTTAAACTAAAAGTAAAATGGTAATCTG
1 TAAAATGGTTAAACTAAAAGTAAAATGGTAATCAG
* *
9333 TAAAATGG-TAATCTATAAAGAATAAACTGGTAATCAG
1 TAAAATGGTTAAACTA-AAAG--TAAAATGGTAATCAG
9370 TAAAA
1 TAAAA
9375 AGTAAAATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 6 0.17
35 12 0.33
37 18 0.50
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (35 bp):
TAAAATGGTTAAACTAAAAGTAAAATGGTAATCAG
Found at i:9449 original size:68 final size:67
Alignment explanation
Indices: 9332--9459 Score: 179
Period size: 68 Copynumber: 1.9 Consensus size: 67
9322 ATGGTAATCT
* * *
9332 GTAAAATGGTAATCTATAAAGAATAAACTGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAAAG
1 GTAAAATGGTAATCAATAAAAAATAAACTGGTAATCAGTAAAAAGTAAAACGGTAATCAGTAAAG
9397 AA
66 AA
*
9399 GTAAAATGGTAATCAATAAAAAAATGTAA-TGGTAATCAGTAAAGAA-TAAAACGGTAATCAG
1 GTAAAATGGTAATCAAT-AAAAAAT-AAACTGGTAATCAGTAAA-AAGTAAAACGGTAATCAG
9460 AAATTAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
67 16 0.30
68 34 0.63
69 4 0.07
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.23
Consensus pattern (67 bp):
GTAAAATGGTAATCAATAAAAAATAAACTGGTAATCAGTAAAAAGTAAAACGGTAATCAGTAAAG
AA
Found at i:9531 original size:20 final size:22
Alignment explanation
Indices: 9496--9539 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
9486 AATCAAACTC
9496 AAAAAGTAATATGGTAATCAGT
1 AAAAAGTAATATGGTAATCAGT
*
9518 AAAAAG-AA-ATGGTAGTCAGT
1 AAAAAGTAATATGGTAATCAGT
9538 AA
1 AA
9540 TTTAAAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (22 bp):
AAAAAGTAATATGGTAATCAGT
Found at i:10521 original size:10 final size:10
Alignment explanation
Indices: 10506--10536 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
10496 GTTCATCAAA
10506 TTCTTACTTG
1 TTCTTACTTG
10516 TTCTTACTTG
1 TTCTTACTTG
10526 TTCTT-CTTG
1 TTCTTACTTG
10535 TT
1 TT
10537 TTCCTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.06, C:0.19, G:0.10, T:0.65
Consensus pattern (10 bp):
TTCTTACTTG
Found at i:13752 original size:15 final size:15
Alignment explanation
Indices: 13734--13762 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13724 GTCTAGTTAG
13734 TCTTAGTTTTTGTAT
1 TCTTAGTTTTTGTAT
13749 TCTTAGTTTTTGTA
1 TCTTAGTTTTTGTA
13763 CACTAGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.66
Consensus pattern (15 bp):
TCTTAGTTTTTGTAT
Found at i:15015 original size:20 final size:20
Alignment explanation
Indices: 14967--15016 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
14957 AAAGTTCGTG
*
14967 ATTGAAGACCTTTTGTAGTC
1 ATTGAAGATCTTTTGTAGTC
14987 ATTGAAGATCTTTTGTAGTC
1 ATTGAAGATCTTTTGTAGTC
15007 ATTGAAGATC
1 ATTGAAGATC
15017 ATTAAAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTGAAGATCTTTTGTAGTC
Found at i:18482 original size:29 final size:29
Alignment explanation
Indices: 18402--18489 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
18392 CAAAGATTTG
* * *
18402 ACACGAGTGCA-AACCCACACTCAAAACAA
1 ACACAAGTGCACAACCCAAACT-TAAACAA
* * * * *
18431 TCCCAAGTGTACAACCCACACTTGAACAA
1 ACACAAGTGCACAACCCAAACTTAAACAA
*
18460 ACACAAGTGCACAACCTAAACTTAAACAA
1 ACACAAGTGCACAACCCAAACTTAAACAA
18489 A
1 A
18490 ATCAGAAAAA
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
29 36 0.78
30 10 0.22
ACGTcount: A:0.47, C:0.32, G:0.09, T:0.12
Consensus pattern (29 bp):
ACACAAGTGCACAACCCAAACTTAAACAA
Found at i:28037 original size:21 final size:21
Alignment explanation
Indices: 28011--28052 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28001 GCACAAAGAA
28011 GTTTCAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
28032 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
28053 ACTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Found at i:29010 original size:8 final size:8
Alignment explanation
Indices: 28986--29020 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
28976 TTCTTTTTTC
28986 CAAAAATT
1 CAAAAATT
*
28994 CCGAAAATT
1 -CAAAAATT
29003 CAAAAATT
1 CAAAAATT
29011 CAAAAATT
1 CAAAAATT
29019 CA
1 CA
29021 TTGTGCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (8 bp):
CAAAAATT
Found at i:30632 original size:33 final size:32
Alignment explanation
Indices: 30531--30668 Score: 116
Period size: 33 Copynumber: 4.2 Consensus size: 32
30521 TTGCAAAGAG
* * * *
30531 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATC
** *
30564 TAATTT-GAGTGTTGTTTGTGATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGTGATGAAAC-AAATC
30597 TGTTTTAGGTGTTGTTTGTGATGAAACAAATTC
1 TGTTTTAGGTGTTGTTTGTGATGAAACAAA-TC
* * * **
30630 TGTTTTTGATGCTAATTGTGATGAAAACAAATC
1 TGTTTTAGGTGTTGTTTGTGATG-AAACAAATC
30663 TGTTTT
1 TGTTTT
30669 GGTTGATCAT
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
32 4 0.05
33 75 0.86
34 8 0.09
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (32 bp):
TGTTTTAGGTGTTGTTTGTGATGAAACAAATC
Found at i:32514 original size:21 final size:21
Alignment explanation
Indices: 32488--32529 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
32478 GCACAAAGAA
32488 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
32509 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
32530 CCTAAGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:42351 original size:11 final size:10
Alignment explanation
Indices: 42335--42381 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
42325 AAGTTCGTGT
42335 TTGAAGACTCA
1 TTGAAGA-TCA
*
42346 TTGAAGATAA
1 TTGAAGATCA
42356 TTTGAAGAT--
1 -TTGAAGATCA
42365 TTGAAGATCA
1 TTGAAGATCA
42375 TTGAAGA
1 TTGAAGA
42382 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:42370 original size:19 final size:18
Alignment explanation
Indices: 42346--42381 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42336 TGAAGACTCA
42346 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
42365 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
42382 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:43933 original size:5 final size:6
Alignment explanation
Indices: 43918--43942 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43908 TTGTGAATTA
43918 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
43943 ATTTAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:46880 original size:11 final size:12
Alignment explanation
Indices: 46851--46882 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
46841 GGATTTTACA
46851 AAAGA-TTCATC
1 AAAGATTTCATC
46862 AAAGATTTC-TC
1 AAAGATTTCATC
46873 AAAGATTTCA
1 AAAGATTTCA
46883 GCACCTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 16 0.84
12 3 0.16
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (12 bp):
AAAGATTTCATC
Done.