Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013644.1 Corchorus olitorius cultivar O-4 contig13677, 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: 49131
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3523 original size:13 final size:14
Alignment explanation
Indices: 3507--3543 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3497 TTTTCATTAC
*
3507 TATTTTATTAAT-A
1 TATTTTATAAATGA
3520 TATTTTATAAATGA
1 TATTTTATAAATGA
3534 T-TTTTATAAA
1 TATTTTATAAA
3544 AAAATTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TATTTTATAAATGA
Found at i:11251 original size:11 final size:11
Alignment explanation
Indices: 11235--11264 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
11225 TGATCTTCAA
11235 ATCTTCAAATT
1 ATCTTCAAATT
11246 ATCTTCAAATT
1 ATCTTCAAATT
11257 ATCTTCAA
1 ATCTTCAA
11265 TAAGTCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (11 bp):
ATCTTCAAATT
Found at i:18558 original size:14 final size:14
Alignment explanation
Indices: 18541--18594 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
18531 AAACAAGATT
18541 TGTTTTTCAAAAAA
1 TGTTTTTCAAAAAA
18555 TG-TTTTCAAGAAAA
1 TGTTTTTCAA-AAAA
*
18569 AGTTTTT--AAAAA
1 TGTTTTTCAAAAAA
*
18581 TGAGTTTTCAAAAA
1 TG-TTTTTCAAAAA
18595 TGTCTTGAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
12 5 0.16
13 12 0.38
14 7 0.22
15 8 0.25
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (14 bp):
TGTTTTTCAAAAAA
Found at i:18596 original size:14 final size:13
Alignment explanation
Indices: 18544--18594 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
18534 CAAGATTTGT
18544 TTTTCAAAAA-ATG
1 TTTTCAAAAAGA-G
*
18557 TTTTCAAGAAAAAG
1 TTTTCAA-AAAGAG
*
18571 TTTTTAAAAATGAG
1 TTTTCAAAAA-GAG
18585 TTTTCAAAAA
1 TTTTCAAAAA
18595 TGTCTTGAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 10 0.31
14 21 0.66
15 1 0.03
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAAGAG
Found at i:19255 original size:20 final size:20
Alignment explanation
Indices: 19211--19247 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19201 GATTGTTCCT
*
19211 AAAATAAAAATTGTTTTTGC
1 AAAAGAAAAATTGTTTTTGC
19231 AAAAGAAAAA-TGTTTTT
1 AAAAGAAAAATTGTTTTT
19248 CTCAAAAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.38
Consensus pattern (20 bp):
AAAAGAAAAATTGTTTTTGC
Found at i:20698 original size:105 final size:105
Alignment explanation
Indices: 20574--20894 Score: 448
Period size: 105 Copynumber: 3.1 Consensus size: 105
20564 CAGTTAATCA
* * *
20574 TGATCCAGGGTGGTCTCTATTAAGTTAATTTTGGATGATCCAGGGCGATCTTTTTTCAGACTTTC
1 TGATCCAAGGTGGTCTCTATTCAGTCAATTTTGGATGATCCAGGGCGATCTTTTTTCAGACTTTC
*
20639 AGGTTGACCCAGGGCGGTCCTTCTCCATTTGTTTTCAAGT
66 AGGTTGACCCAGGGCGGTCATTCTCCATTTGTTTTCAAGT
* * * *
20679 TGATCCAAGGTGGTATCTATTCAGTCAATATTGGATGATCCAAGGCGATCTTTCTTCAGACTTTC
1 TGATCCAAGGTGGTCTCTATTCAGTCAATTTTGGATGATCCAGGGCGATCTTTTTTCAGACTTTC
* * *
20744 AGGTTGACCTAGGGCAGTCATTCTCCATTTTTTTTCAAGT
66 AGGTTGACCCAGGGCGGTCATTCTCCATTTGTTTTCAAGT
* * ** *
20784 TGATCCAAGGTGGTCTCTATTCAGTCAATTTCGGATCAT-TTGAAGCGAT-TTTTCTTCAGACTT
1 TGATCCAAGGTGGTCTCTATTCAGTCAATTTTGGATGATCCAG-GGCGATCTTTT-TTCAGACTT
* *
20847 TCAGGTTGACCCGGGGCGGTCTTTCTCCATTTGTTTTCAAGT
64 TCAGGTTGACCCAGGGCGGTCATTCTCCATTTGTTTTCAAGT
20889 TGATCC
1 TGATCC
20895 TGGGCAATCT
Statistics
Matches: 189, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
104 3 0.02
105 186 0.98
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (105 bp):
TGATCCAAGGTGGTCTCTATTCAGTCAATTTTGGATGATCCAGGGCGATCTTTTTTCAGACTTTC
AGGTTGACCCAGGGCGGTCATTCTCCATTTGTTTTCAAGT
Found at i:21344 original size:35 final size:35
Alignment explanation
Indices: 21328--22347 Score: 1214
Period size: 35 Copynumber: 29.1 Consensus size: 35
21318 ACGATGATCA
*
21328 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-T
* * * *
21364 TTCTTCAGTTTTTTTCAGTTGACCTAGGGCGGTGT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* *
21399 TTCTTCAGTTTATTTTAGTTGA-CTAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* * * * *
21433 TTCTTCAGTTTATTTCAATTGATCCATGGTGATCA
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
*
21468 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-T
* * *
21504 TTCTTCAGTTT-TTTCAGTTGACCTAGGGCGGTAT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* *
21538 TTCTTCAGTTTATTTTAGTTGA-CTAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
*
21572 TTCTTCAGTTTATTTCAGTTGACCCAGGATGGTCTT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-T
21608 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* * ***
21643 TTCTTCAGTTTATTTCAGTTCACCTAGGACAGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
21678 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* *
21713 TTCGTT-AGTTTATTTCATTTGACCTAGGGTGGT-T
1 TTC-TTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* * *
21747 TTCTTCAATTTATTTCACTTGACCCAAGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* *
21782 TTTTTCAGTTTATTTCAGTTGACCGAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* **
21817 GTC-TCTAGTTTATTT-AGTTGACCCAGGCCGGTCT
1 TTCTTC-AGTTTATTTCAGTTGACCCAGGGTGGTCT
* *
21851 TTCTTCAGCTTATTTCAGTTGACCCAGGGTGTTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
*
21886 TTCTTCAGTTTACTTCAGTTGACCCA-GGTCGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGT-GGTCT
*
21921 TTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* * * *
21956 TTCTTCAGTTCATTTTAGTTGACCTAGTGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
*
21991 TTCTTCAGTTTACTTCAGTTGACCCAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
22026 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* *
22061 TTCTTCAGTTTATTTCAGTTGACCTAGGATGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* * * *
22096 TTCTTTAGTTTATTTAAGTTGACTCAGGGCGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* *
22131 TTCTTCAGTTTATTTCAGTTGACCAAGGGGGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* * * * * * *
22166 TTTTTCAGTTTATGTCAGAATGATCGAGGGTGTTCG
1 TTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCT
* ** * * *** *
22202 TTCTTCAGTTCAGCTCGGAATGATTGAGGGTGGTCA
1 TTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCT
*
22238 TTCTTCAGTTTATTTCAGTTGACCTAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
* * * * *
22273 TTAC-TCAGTTTATGTCCGTATGATCGAGGGTGGTCG
1 TT-CTTCAGTTTATTTCAGT-TGACCCAGGGTGGTCT
*
22309 TTCTTCAGTTTATTTCAGTTG-TCCAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
22343 TTCTT
1 TTCTT
22348 TAATTTTACC
Statistics
Matches: 845, Mismatches: 122, Indels: 36
0.84 0.12 0.04
Matches are distributed among these distances:
33 2 0.00
34 147 0.17
35 533 0.63
36 163 0.19
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (35 bp):
TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCT
Found at i:27786 original size:21 final size:20
Alignment explanation
Indices: 27746--27785 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27736 CAAAATTAAC
27746 CCTATTTTTATGGTCATTTT
1 CCTATTTTTATGGTCATTTT
*
27766 CCTATGTTTTTTGGT-ATTTT
1 CCTAT-TTTTATGGTCATTTT
27786 TATGTGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (20 bp):
CCTATTTTTATGGTCATTTT
Found at i:29388 original size:21 final size:21
Alignment explanation
Indices: 29364--29412 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
29354 ATAGTTTAGA
29364 TTTAATTTAATTTGC-TTTATT
1 TTTAATTTAA-TTGCTTTTATT
*
29385 TTTAGA-TTAATTGCTTTTCTT
1 TTTA-ATTTAATTGCTTTTATT
29406 TTTAATT
1 TTTAATT
29413 GTTCTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 5 0.21
21 18 0.75
22 1 0.04
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.65
Consensus pattern (21 bp):
TTTAATTTAATTGCTTTTATT
Found at i:30637 original size:36 final size:36
Alignment explanation
Indices: 30585--30905 Score: 368
Period size: 36 Copynumber: 9.0 Consensus size: 36
30575 ACTCATGCAC
30585 AAGTCAGTTAGTAACTTAATTCAGGGTAATTAAGTA
1 AAGTCAGTTAGTAACTTAATTCAGGGTAATTAAGTA
* *
30621 GAGTCAGTTAGGAACTTAATTCAGGGTAATTAAGTA
1 AAGTCAGTTAGTAACTTAATTCAGGGTAATTAAGTA
* * * *
30657 GAGTCAGTTATTAGCAACTTAATCCAGGGTAATTCAAATA
1 AAGTCAG---TTAGTAACTTAATTCAGGGTAATT-AAGTA
30697 AAGT---TT-GTAACTTAATTCAGGGTAATTAAGTA
1 AAGTCAGTTAGTAACTTAATTCAGGGTAATTAAGTA
* *
30729 AACTCAGTTAGTAACTTAATTCATGGTAATTAAGTA
1 AAGTCAGTTAGTAACTTAATTCAGGGTAATTAAGTA
* *
30765 AAATCAATTAGTAACTTAATTCAGGGTAATTAAGTA
1 AAGTCAGTTAGTAACTTAATTCAGGGTAATTAAGTA
* * *
30801 AAGTCAGTTAGTAACTTAATTTATGGTAATTAAG-C
1 AAGTCAGTTAGTAACTTAATTCAGGGTAATTAAGTA
* *
30836 AAGTCAG-TAATCAACTTAATTCAGGGTAAATAAGT-
1 AAGTCAGTTAGT-AACTTAATTCAGGGTAATTAAGTA
* * * * *
30871 GAGTCCGTAAGTAACTCAATCCAGGGTAATTAAGT
1 AAGTCAGTTAGTAACTTAATTCAGGGTAATTAAGT
30906 TAGTTAAGAA
Statistics
Matches: 244, Mismatches: 30, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
32 7 0.03
33 19 0.08
34 5 0.02
35 53 0.22
36 131 0.54
39 22 0.09
40 7 0.03
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (36 bp):
AAGTCAGTTAGTAACTTAATTCAGGGTAATTAAGTA
Found at i:42200 original size:2 final size:2
Alignment explanation
Indices: 42179--42220 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
42169 CTATGGCTGT
42179 TA TA T- TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42218 TA T
1 TA T
42221 CATTGTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47638 original size:154 final size:154
Alignment explanation
Indices: 47358--49131 Score: 2861
Period size: 154 Copynumber: 11.5 Consensus size: 154
47348 GCCGCAGGGG
* * *
47358 TTAGCTCATTTGGAGCACCTGTTATTTTGGGCCTATCAGGGCCCATCAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
*
47423 CTTCGATTTGGCAAACCTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
*
47488 TAAGATTAGTCCACTGTAAAGTTT
131 TGAGATTAGTCCACTGTAAAGTTT
*
47512 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATTAGGGCCCATTAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* *
47577 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATCATTTTAG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
* *
47642 TGAGATCAGTCCATTGTGAAAGTTT
131 TGAGATTAGTCCACTGT-AAAGTTT
* * *
47667 TTAGCTCATTTGGAACACCTATTATTTTGGGCCTATCAGGGCCCATTGGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
*
47732 CTTCGATTTGGCAAACCTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
* *
47797 TAAGATTAGTCCACTGTGAAGTTT
131 TGAGATTAGTCCACTGTAAAGTTT
*
47821 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAACCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* * *
47886 CTTCGATTTCGCAAACTTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
* *
47951 TGAGATTAGTCCACTGTGAAGGTT
131 TGAGATTAGTCCACTGTAAAGTTT
* * * **
47975 TTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* * *
48040 CTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
* *
48105 TGAGATTAGTCCACTATGAAGTTT
131 TGAGATTAGTCCACTGTAAAGTTT
* * * * *
48129 TTAGCTCAGTATGGAATACCTGTTATTTTGGGCCTATCAGGGCCCATCACTGACGTTTTGAATCG
1 TTAGCTCA-TTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCG
*
48194 TCTTCGATTTGGCAAACCTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
65 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
* *
48259 GTAAGATTACTCCACTGTAAAGTTT
130 GTGAGATTAGTCCACTGTAAAGTTT
*
48284 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAAGGCCCATTAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* *
48349 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATCA-TTTAG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
* * *
48413 TGAGATCAGCCCATTGTGAAAGTTT
131 TGAGATTAGTCCACTGT-AAAGTTT
* *
48438 TTAGCTCATTTGGAATACCTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* *
48503 CTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
*
48568 TAAGATTAGTCCACTGTAAAGTTT
131 TGAGATTAGTCCACTGTAAAGTTT
48592 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* * *
48657 CTTCGATTTGGGAAACCTTAATGGTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
48722 TGAGATTAGTCCACTGTAAAGTTT
131 TGAGATTAGTCCACTGTAAAGTTT
*
48746 TTAGCTCATTTGGAACACTTGTTATTTTGGGCTTATCAGGGCCCATTAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
*
48811 CTTCGATTTGGCAAACCTCAATGCTATTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
*
48876 TGAGATTAGTCCACTGTGAAGTTT
131 TGAGATTAGTCCACTGTAAAGTTT
* *
48900 TTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATTAGGGCCCATTAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* * *
48965 CTTCGATTTGGCATACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA-AATCATTTAGT
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
*
49029 TGAGATTAGTCCACTGTGAAG-TT
131 TGAGATTAGTCCACTGTAAAGTTT
* *
49052 TTAGTATCATTTGGTAACACTTGTTATTTTGGGTCCGTATCAAGGCCCACTTAGTGACGTTTTGT
1 TTAG-CTCATTTGG-AACACTTGTTATTTTGGG-CC-TATCAGGGCCCA-TTAGTGACGTTTTG-
49117 AATCGTCTTCGATTT
60 AATCGTCTTCGATTT
Statistics
Matches: 1499, Mismatches: 111, Indels: 16
0.92 0.07 0.01
Matches are distributed among these distances:
152 6 0.00
153 54 0.04
154 1101 0.73
155 299 0.20
156 10 0.01
157 14 0.01
158 15 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
TGAGATTAGTCCACTGTAAAGTTT
Found at i:48223 original size:463 final size:462
Alignment explanation
Indices: 47358--49131 Score: 2914
Period size: 463 Copynumber: 3.8 Consensus size: 462
47348 GCCGCAGGGG
* * *
47358 TTAGCTCATTTGGAGCACCTGTTATTTTGGGCCTATCAGGGCCCATCAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* *
47423 CTTCGATTTGGCAAACCTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG
* * *
47488 TAAGATTAGTCCACTGTAAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATTAGGG
131 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATTAGGG
*
47553 CCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTT
196 CCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTT
* * *
47618 ATGGCCTAAGTATAATCATTTTAGTGAGATCAGTCCATTGTGAAAGTTTTTAGCTCATTTGGAAC
261 ATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTG-AAGTTTTTAGCTCATTTGGAAC
* *
47683 ACCTATTATTTTGGGCCTATCAGGGCCCATTGGTGACGTTTTGAATCGTCTTCGATTTGGCAAAC
325 ACCTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAAC
47748 CTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTG
390 CTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTG
*
47813 TGAAGTTT
455 TAAAGTTT
*
47821 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAACCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* *
47886 CTTCGATTTCGCAAACTTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG
* * * *
47951 TGAGATTAGTCCACTGTGAAGGTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCT-TTCGGG
131 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATT-AGG
** *
48015 GCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTT
195 GCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTT
* *
48080 TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTATGAAGTTTTTAGCTCAGTATGGAA
260 TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA-TTTGGAA
* * *
48145 TACCTGTTATTTTGGGCCTATCAGGGCCCATCACTGACGTTTTGAATCGTCTTCGATTTGGCAAA
324 CACCTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
*
48210 CCTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTACTCCACT
389 CCTCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACT
48275 GTAAAGTTT
454 GTAAAGTTT
*
48284 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAAGGCCCATTAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
*
48349 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATCA-TTTAG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG
* * * * *
48413 TGAGATCAGCCCATTGTGAAAGTTTTTAGCTCATTTGGAATACCTGTTATTTTGGGCCTATCAGG
131 TGAGATTAGTCCACTGTG-AAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATTAGG
*
48478 GCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTT
195 GCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTT
* * *
48543 TATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTAAAGTTTTTAGCTCATTTGGAAC
260 TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
* *
48608 ACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGGAAAC
325 ACCTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAAC
* *
48673 CTTAATG-GTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
390 CTCAATGCG-TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACT
48737 GTAAAGTTT
454 GTAAAGTTT
*
48746 TTAGCTCATTTGGAACACTTGTTATTTTGGGCTTATCAGGGCCCATTAGTGACGTTTTGAATCGT
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
* *
48811 CTTCGATTTGGCAAACCTCAATGCTATTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG
48876 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATTAGGG
131 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATTAGGG
48941 CCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCATA-CCTCAATGCTTTTCTTTCCATTGTT
196 CCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA-ACCCTCAATGCTTTTCTTTCCATTGTT
*
49005 TATGGCCTAACTA-AATCA-TTTAGTTGAGATTAGTCCACTGTGAAG-TTTTAGTATCATTTGGT
260 TATGGCCTAACTATAATCATTTTAG-TGAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGG-
* *
49067 AACACTTGTTATTTTGGGTCCGTATCAAGGCCCACTTAGTGACGTTTTGTAATCGTCTTCGATTT
322 AACACCTGTTATTTTGGG-CC-TATCAGGGCCCA-TTAGTGACGTTTTG-AATCGTCTTCGATTT
Statistics
Matches: 1223, Mismatches: 74, Indels: 25
0.93 0.06 0.02
Matches are distributed among these distances:
460 10 0.01
461 33 0.03
462 428 0.35
463 711 0.58
464 12 0.01
465 14 0.01
466 15 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (462 bp):
TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGT
CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG
TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGGGCCTATTAGGG
CCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTT
ATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
CCTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC
TCAATGCGTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGT
AAAGTTT
Done.