Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007234.1 Corchorus capsularis cultivar CVL-1 contig07255, 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: 36140
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1290 original size:40 final size:40
Alignment explanation
Indices: 1236--1386 Score: 162
Period size: 40 Copynumber: 3.8 Consensus size: 40
1226 TAGTAATCAG
* * *
1236 TAATTAAGAAAGGAAGTAAAAAGATTAATCAGTAAATTGA
1 TAATTAAGAGAGAAAGTAAAAAGAGTAATCAGTAAATTGA
* * *
1276 TAATCAAGAGAGGAAGT-AAAAGTAGTAATCAGTAAA-TCA
1 TAATTAAGAGAGAAAGTAAAAAG-AGTAATCAGTAAATTGA
** * * *
1315 GTAATTAAGAGTCAAAGTAAAAGGATTAATTAGTAAATTGA
1 -TAATTAAGAGAGAAAGTAAAAAGAGTAATCAGTAAATTGA
*
1356 TAATTAAGAGAGAAAGTAAAATGAGTAATCA
1 TAATTAAGAGAGAAAGTAAAAAGAGTAATCA
1387 ATAATTAAGA
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 7 0.08
40 77 0.86
41 6 0.07
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.25
Consensus pattern (40 bp):
TAATTAAGAGAGAAAGTAAAAAGAGTAATCAGTAAATTGA
Found at i:1391 original size:32 final size:33
Alignment explanation
Indices: 1355--1428 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
1345 TAGTAAATTG
* * *
1355 ATAATTAAGAGAGAAAGTA-AAATGAGTAATCA
1 ATAATTAAGAAAGAAAGTAGAAAGGACTAATCA
*
1387 ATAATTAAGAAAGGAAGTAGAAAGGACTAATCA
1 ATAATTAAGAAAGAAAGTAGAAAGGACTAATCA
*
1420 GTAAATTAA
1 AT-AATTAA
1429 TAATTAAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 17 0.49
33 12 0.34
34 6 0.17
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.22
Consensus pattern (33 bp):
ATAATTAAGAAAGAAAGTAGAAAGGACTAATCA
Found at i:1423 original size:73 final size:72
Alignment explanation
Indices: 1216--1437 Score: 257
Period size: 80 Copynumber: 3.0 Consensus size: 72
1206 AAGGATTAAA
* * *
1216 AAAGTAAAGGTAGTAATCAGTAATTAAGAAAGGAAGTAAAAAGATTAATCAGTAAATTGATAATC
1 AAAGTAAAAGTAGTAATCAGTAATTAAGAAAGGAAGTAAAAGGATTAATCAGTAAATTGATAATT
1281 AAGAGAG
66 AAGAGAG
* * * *
1288 GAAGTAAAAGTAGTAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAAGGATTAATTAGTAAAT
1 AAAGTAAAAGTAGTAATCAGT-AAT---TAA-GAA-AG--GAAGTAAAAGGATTAATCAGTAAAT
1353 TGATAATTAAGAGAG
58 TGATAATTAAGAGAG
* * *
1368 AAAGTAAAA-TGAGTAATCAATAATTAAGAAAGGAAGTAGAAAGGACTAATCAGTAAATTAATAA
1 AAAGTAAAAGT-AGTAATCAGTAATTAAGAAAGGAAGTA-AAAGGATTAATCAGTAAATTGATAA
1432 TTAAGA
64 TTAAGA
1438 AGGGATTAAT
Statistics
Matches: 126, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
72 24 0.19
73 31 0.25
74 2 0.02
75 2 0.02
76 6 0.05
77 2 0.02
78 2 0.02
79 4 0.03
80 53 0.42
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.24
Consensus pattern (72 bp):
AAAGTAAAAGTAGTAATCAGTAATTAAGAAAGGAAGTAAAAGGATTAATCAGTAAATTGATAATT
AAGAGAG
Found at i:4579 original size:21 final size:21
Alignment explanation
Indices: 4553--4594 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4543 TTCTGGTGTA
* *
4553 ACCCGCGCCTGGGCAATGTTG
1 ACCCGCGCCTGAGCAAGGTTG
4574 ACCCGCGCCTGAGCAAGGTTG
1 ACCCGCGCCTGAGCAAGGTTG
4595 CGGAATAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (21 bp):
ACCCGCGCCTGAGCAAGGTTG
Found at i:6428 original size:29 final size:27
Alignment explanation
Indices: 6396--6449 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
6386 TCCAAATTGC
*
6396 AAGTTCAAGGGGCAAAATGTCCAAAATTA
1 AAGTT-AAGGGGCAAAACGT-CAAAATTA
*
6425 AAGTTTAGGGGCAAAACGTCAAAAT
1 AAGTTAAGGGGCAAAACGTCAAAAT
6450 CATACAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 12 0.52
29 5 0.22
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.20
Consensus pattern (27 bp):
AAGTTAAGGGGCAAAACGTCAAAATTA
Found at i:6461 original size:30 final size:28
Alignment explanation
Indices: 6403--6471 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
6393 TGCAAGTTCA
*
6403 AGGGGCAAAATGTCCAAAATTAAAGTTT
1 AGGGGCAAAACGTCCAAAATTAAAGTTT
6431 AGGGGCAAAACGT-CAAAATCATACAAGTTT
1 AGGGGCAAAACGTCCAAAAT--TA-AAGTTT
6461 AGGGGGCAAAA
1 A-GGGGCAAAA
6472 GGGGTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 6 0.17
28 12 0.33
29 2 0.06
30 7 0.19
31 9 0.25
ACGTcount: A:0.43, C:0.13, G:0.25, T:0.19
Consensus pattern (28 bp):
AGGGGCAAAACGTCCAAAATTAAAGTTT
Found at i:6715 original size:73 final size:74
Alignment explanation
Indices: 6578--6715 Score: 199
Period size: 73 Copynumber: 1.9 Consensus size: 74
6568 GCAGGGGCCA
* * * *
6578 TGGCCCTCCCTAAGTTGGTGAAATTGTCTTTAAGTCCTTGTAAATTTTCATGTGAAATGGAAAAA
1 TGGCCCTCCCTAAGTTGGTGAAATTGTCTTTAAGACATTGTAAATTTTAATGTGAAATGAAAAAA
6643 TTGTTTATT
66 TTGTTTATT
* *
6652 TGGCCC-CCCTTAGTTGGTGAAATTGTCTTTAAAGACATT-TAAATTTTAATGTGGAATGAAAAA
1 TGGCCCTCCCTAAGTTGGTGAAATTGTCTTT-AAGACATTGTAAATTTTAATGTGAAATGAAAAA
6715 A
65 A
6716 ATTTTAATTG
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
73 45 0.79
74 12 0.21
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (74 bp):
TGGCCCTCCCTAAGTTGGTGAAATTGTCTTTAAGACATTGTAAATTTTAATGTGAAATGAAAAAA
TTGTTTATT
Found at i:11140 original size:18 final size:18
Alignment explanation
Indices: 11117--11180 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
11107 AATGGGTAGT
11117 TTTTATTATCCTTGGTGG
1 TTTTATTATCCTTGGTGG
* * * *
11135 TTTTATTTTCAAATAGGTAGT
1 TTTTATTATC--CTTGGT-GG
*
11156 TTTTATTATCCTTGTTGG
1 TTTTATTATCCTTGGTGG
11174 TTTTATT
1 TTTTATT
11181 TTCAAATGGC
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
18 17 0.50
19 3 0.09
20 4 0.12
21 10 0.29
ACGTcount: A:0.17, C:0.08, G:0.16, T:0.59
Consensus pattern (18 bp):
TTTTATTATCCTTGGTGG
Found at i:11147 original size:39 final size:39
Alignment explanation
Indices: 11103--11201 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
11093 AAATTAATTA
11103 TTCAAATGGGTAGTTTTTATTATCCTTGGTGGTTTTATT
1 TTCAAATGGGTAGTTTTTATTATCCTTGGTGGTTTTATT
* *
11142 TTCAAATAGGTAGTTTTTATTATCCTTGTTGGTTTTATT
1 TTCAAATGGGTAGTTTTTATTATCCTTGGTGGTTTTATT
*
11181 TTCAAATGGCTAGTTTTTATT
1 TTCAAATGGGTAGTTTTTATT
11202 TTGTTTTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.20, C:0.08, G:0.17, T:0.55
Consensus pattern (39 bp):
TTCAAATGGGTAGTTTTTATTATCCTTGGTGGTTTTATT
Found at i:11161 original size:21 final size:20
Alignment explanation
Indices: 11103--11203 Score: 66
Period size: 21 Copynumber: 5.1 Consensus size: 20
11093 AAATTAATTA
11103 TTCAAATGGGTAGTTTTTATT
1 TTCAAAT-GGTAGTTTTTATT
* ** *
11124 ATC-CTTGGT-GGTTTTATT
1 TTCAAATGGTAGTTTTTATT
11142 TTCAAATAGGTAGTTTTTATT
1 TTCAAAT-GGTAGTTTTTATT
* * * * *
11163 ATC--CTTGTTGGTTTTATT
1 TTCAAATGGTAGTTTTTATT
11181 TTCAAATGGCTAGTTTTTATT
1 TTCAAATGG-TAGTTTTTATT
11202 TT
1 TT
11204 GTTTTTAATT
Statistics
Matches: 56, Mismatches: 18, Indels: 12
0.65 0.21 0.14
Matches are distributed among these distances:
18 22 0.39
19 5 0.09
20 6 0.11
21 23 0.41
ACGTcount: A:0.20, C:0.08, G:0.17, T:0.55
Consensus pattern (20 bp):
TTCAAATGGTAGTTTTTATT
Found at i:12774 original size:14 final size:13
Alignment explanation
Indices: 12731--12777 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
12721 TTTCCTTAAG
12731 TTTTGTTTTTAT-T
1 TTTTGTTTTT-TGT
* *
12744 TTTCGTATTTTGT
1 TTTTGTTTTTTGT
12757 TTTTGTTTTTGTGT
1 TTTTGTTTTT-TGT
12771 TTTTGTT
1 TTTTGTT
12778 AATTTTGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 1 0.04
13 17 0.61
14 10 0.36
ACGTcount: A:0.04, C:0.02, G:0.15, T:0.79
Consensus pattern (13 bp):
TTTTGTTTTTTGT
Found at i:12777 original size:6 final size:6
Alignment explanation
Indices: 12731--12773 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
12721 TTTCCTTAAG
*
12731 TTTTGT TTTTAT TTTTCGT ATTTTGT TTTTGT TTTTGT GTTTT
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT -TTTT
12774 TGTTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 21 0.66
7 7 0.22
8 4 0.12
ACGTcount: A:0.05, C:0.02, G:0.14, T:0.79
Consensus pattern (6 bp):
TTTTGT
Found at i:14228 original size:18 final size:17
Alignment explanation
Indices: 14205--14253 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
14195 AAAAAAATCT
*
14205 TAATTTTCTTTTCTGCCC
1 TAATTTTCTTTTC-CCCC
14223 TAATTTT-TTTTCCCCC
1 TAATTTTCTTTTCCCCC
*
14239 AAATTCTTCTTTTCC
1 TAATT-TTCTTTTCC
14254 TCGAACCACC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.26
17 7 0.26
18 13 0.48
ACGTcount: A:0.14, C:0.29, G:0.02, T:0.55
Consensus pattern (17 bp):
TAATTTTCTTTTCCCCC
Found at i:16284 original size:16 final size:16
Alignment explanation
Indices: 16260--16292 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16250 CCACCAAGAA
16260 AATTCAAAAAAAAAAG
1 AATTCAAAAAAAAAAG
*
16276 AATTGAAAAAAAAAAG
1 AATTCAAAAAAAAAAG
16292 A
1 A
16293 CACTTGTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (16 bp):
AATTCAAAAAAAAAAG
Found at i:19765 original size:22 final size:22
Alignment explanation
Indices: 19722--19765 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19712 ATTGTTATCA
**
19722 ATAAGAATGGAAAAAATTAAAT
1 ATAAGAATGGAAAAAAAAAAAT
19744 ATAAGAAAT-GAAAAAAAAAAAT
1 ATAAG-AATGGAAAAAAAAAAAT
19766 CATCAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.18
Consensus pattern (22 bp):
ATAAGAATGGAAAAAAAAAAAT
Found at i:22986 original size:21 final size:23
Alignment explanation
Indices: 22943--22989 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
22933 TATTGGAGGG
22943 ATTTTATTATAATTGTTTCCTTA
1 ATTTTATTATAATTGTTTCCTTA
22966 ATTTTATT-T-ATTGCTTT-CTTA
1 ATTTTATTATAATTG-TTTCCTTA
22987 ATT
1 ATT
22990 AGTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.48
22 4 0.17
23 8 0.35
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.64
Consensus pattern (23 bp):
ATTTTATTATAATTGTTTCCTTA
Found at i:25820 original size:74 final size:74
Alignment explanation
Indices: 25730--25886 Score: 242
Period size: 74 Copynumber: 2.1 Consensus size: 74
25720 TGGTCTTTTC
* * * *
25730 ACACTTTTCGGGTGACTAAAAAGTCCCTCTATGAGTTTCCCCTATTCCTTTTCATTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCATTCTACCATTT
25795 TTCGTAATT
66 TTCGTAATT
* * *
25804 ACACTTTTTGGATGACTAAAAAGCCCCTTTATGAGTTTCCCCCATTCCTTTTCCTTCTACCATTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCATTCTACCATTT
25869 TTCGTAATT
66 TTCGTAATT
*
25878 ACACATTTC
1 ACACTTTTC
25887 CCTTCCTTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCATTCTACCATTT
TTCGTAATT
Found at i:27516 original size:84 final size:84
Alignment explanation
Indices: 27417--27586 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
27407 TTTGATATTT
*
27417 TTGGAGATGGAAAATGGAGAATGATCTCCACTATCAATCATAGCCTTAACTTCTCCGTCAACTGG
1 TTGGAGATGAAAAATGGAGAATGATCTCCACTATCAATCATAGCCTTAACTTCTCCGTCAACTGG
27482 GATGTTTTCCGTCTTCTTC
66 GATGTTTTCCGTCTTCTTC
*
27501 TTGGAGATGAAAAATGGAGAATGATCTCCACTATCAATCATAGCCTTAACTTCTCTGTCAACTGG
1 TTGGAGATGAAAAATGGAGAATGATCTCCACTATCAATCATAGCCTTAACTTCTCCGTCAACTGG
27566 GATGTTTTCCGTCTTCTTC
66 GATGTTTTCCGTCTTCTTC
27585 TT
1 TT
27587 CCCTTCCACA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (84 bp):
TTGGAGATGAAAAATGGAGAATGATCTCCACTATCAATCATAGCCTTAACTTCTCCGTCAACTGG
GATGTTTTCCGTCTTCTTC
Found at i:27880 original size:15 final size:15
Alignment explanation
Indices: 27860--27889 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27850 AATGTCTCAA
27860 TTGACGATTTGTACT
1 TTGACGATTTGTACT
27875 TTGACGATTTGTACT
1 TTGACGATTTGTACT
27890 AAAACAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
TTGACGATTTGTACT
Found at i:28064 original size:62 final size:62
Alignment explanation
Indices: 27966--28095 Score: 208
Period size: 62 Copynumber: 2.1 Consensus size: 62
27956 GGTGAGGTCA
* *
27966 ATGGGTATCATTTAATCTGAACCATTCAAATTAATTTTAATACGTATCAACAATCTAAATCT
1 ATGGGTATCATTTAATCTCAACCATTCAAATCAATTTTAATACGTATCAACAATCTAAATCT
*
28028 ATGGGTATCATTTAATCTCAACCA-TCGAAATCAATTTTAATACGTGTCAACAATCTAAATCT
1 ATGGGTATCATTTAATCTCAACCATTC-AAATCAATTTTAATACGTATCAACAATCTAAATCT
*
28090 AAGGGT
1 ATGGGT
28096 GTATTGACAC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 2 0.03
62 61 0.97
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (62 bp):
ATGGGTATCATTTAATCTCAACCATTCAAATCAATTTTAATACGTATCAACAATCTAAATCT
Found at i:28108 original size:27 final size:27
Alignment explanation
Indices: 28077--28128 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
28067 ATACGTGTCA
28077 ACAATCTAAATCTAAGGGTGTATTGAC
1 ACAATCTAAATCTAAGGGTGTATTGAC
28104 ACAATCTAAATCTAAGGGTGTATTG
1 ACAATCTAAATCTAAGGGTGTATTG
28129 GAAACTGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (27 bp):
ACAATCTAAATCTAAGGGTGTATTGAC
Found at i:32090 original size:16 final size:16
Alignment explanation
Indices: 31997--32097 Score: 73
Period size: 16 Copynumber: 6.4 Consensus size: 16
31987 GGCAGTTTTA
*
31997 TCGGGTAATTCGGGTT
1 TCGGGTCATTCGGGTT
*
32013 TCGGGTCA-TC-TGTGT
1 TCGGGTCATTCGGGT-T
* *
32028 TAGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
32044 TCGGGTCATAT-GAGTC
1 TCGGGTCAT-TCGGGTT
* *
32060 TCAGGTCATTTGGGTT
1 TCGGGTCATTCGGGTT
* *
32076 TCGGGTCATCCGGGTC
1 TCGGGTCATTCGGGTT
32092 TCGGGT
1 TCGGGT
32098 TGGGCGGGTT
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
14 2 0.03
15 10 0.16
16 49 0.77
17 3 0.05
ACGTcount: A:0.11, C:0.17, G:0.36, T:0.37
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:32093 original size:32 final size:33
Alignment explanation
Indices: 31999--32085 Score: 108
Period size: 31 Copynumber: 2.7 Consensus size: 33
31989 CAGTTTTATC
* *
31999 GGGTAATTCGGGTTTCGGGTCATCTGTGT-T-A
1 GGGTCATTCGGGTTTCGGGTCATCTGAGTCTCA
* *
32030 GGGTTATTCGGGTTTCGGGTCATATGAGTCTCA
1 GGGTCATTCGGGTTTCGGGTCATCTGAGTCTCA
*
32063 -GGTCATTTGGGTTTCGGGTCATC
1 GGGTCATTCGGGTTTCGGGTCATC
32086 CGGGTCTCGG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 26 0.54
32 21 0.44
33 1 0.02
ACGTcount: A:0.13, C:0.15, G:0.34, T:0.38
Consensus pattern (33 bp):
GGGTCATTCGGGTTTCGGGTCATCTGAGTCTCA
Found at i:32796 original size:167 final size:165
Alignment explanation
Indices: 32558--33001 Score: 602
Period size: 166 Copynumber: 2.7 Consensus size: 165
32548 ATGAGGAGCG
* * * *
32558 AGAGAACAAATTTTTTTCGTCTTTTCCAACTTGACAGATTACTTAGATG-TCATAACTTTTAATT
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGACAGATTACTTAAATGTTC-TAACTTTTGATT
* * * *
32622 TTTGAGGGGATTAAATAACTAGACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAA
65 CTTGAGGGGATTAAATAACTA-ATTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAATGGAA
* ** ** * **
32687 TTACTAAAAGATCCCTGTCAAGGCTTGTTTTTGCAGTT
129 TTAATAAAAGATCCCCATCAAGAATTGATGATG-AGTT
* *
32725 AGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTTCTAACTTTTGATTC
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGACAGATTACTTAAATGTTCTAACTTTTGATTC
* *
32790 TTGAGGGGATTAAATAAGTAATTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAATGGAATT
66 TTGAGGGGATTAAATAACTAATTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAATGGAATT
32855 AATAAAAGATCCCCATCAAGAATTGATGATGAGTT
131 AATAAAAGATCCCCATCAAGAATTGATGATGAGTT
* * * *
32890 AGAGAACTAATATTTTTCGTCTTTGCCTACTTGACAGATTACTTAAAATGTCCTATCTTTTGATT
1 AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGACAGATTACTT-AAATGTTCTAACTTTTGATT
* *
32955 CTTGTGGAGATTAAATAACTAAATTTTTTGGTCATTTCTCAATTGAC
65 CTTGAGGGGATTAAATAACT-AATTTTTTGGTCATTTCTCAATTGAC
33002 AAATGACTCA
Statistics
Matches: 244, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
165 44 0.18
166 99 0.41
167 99 0.41
168 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (165 bp):
AGAGAACTAATTTTTTTCGTCTTTTCCTACTTGACAGATTACTTAAATGTTCTAACTTTTGATTC
TTGAGGGGATTAAATAACTAATTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAATGGAATT
AATAAAAGATCCCCATCAAGAATTGATGATGAGTT
Done.