Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2649_ERROPOS42313
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: 42313
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1445 original size:43 final size:44
Alignment explanation
Indices: 1384--1467 Score: 143
Period size: 43 Copynumber: 1.9 Consensus size: 44
1374 TATGCCTAAA
*
1384 AAAAAGAGATCAAGGTGAAAACCCGAAAAGGGCATCTTGATAAT
1 AAAAAGAGATCAAGGTGAAAACCCGAAAAAGGCATCTTGATAAT
*
1428 AAAAAG-GATCAAGGTGAAAACCCGAAAAAGGCGTCTTGAT
1 AAAAAGAGATCAAGGTGAAAACCCGAAAAAGGCATCTTGAT
1468 TAACACAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 32 0.84
44 6 0.16
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.15
Consensus pattern (44 bp):
AAAAAGAGATCAAGGTGAAAACCCGAAAAAGGCATCTTGATAAT
Found at i:1492 original size:44 final size:43
Alignment explanation
Indices: 1384--1478 Score: 118
Period size: 43 Copynumber: 2.1 Consensus size: 43
1374 TATGCCTAAA
* * *
1384 AAAAAGAGATCAAGGTGAAAACCCGAAAAGGGCATCTTGATAAT
1 AAAAAG-GATCAAGATGAAAACCCGAAAAAGGCATCTTGATAAC
* *
1428 AAAAAGGATCAAGGTGAAAACCCGAAAAAGGCGTCTTGATTAAC
1 AAAAAGGATCAAGATGAAAACCCGAAAAAGGCATCTTGA-TAAC
1472 ACAAAAG
1 A-AAAAG
1479 ATTAGAATGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 31 0.67
44 10 0.22
45 5 0.11
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (43 bp):
AAAAAGGATCAAGATGAAAACCCGAAAAAGGCATCTTGATAAC
Found at i:2420 original size:14 final size:14
Alignment explanation
Indices: 2401--2435 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
2391 TGCTGAGCTG
2401 TTTTCAATTTATGT
1 TTTTCAATTTATGT
2415 TTTTCAATTTATGT
1 TTTTCAATTTATGT
2429 TTTTCAA
1 TTTTCAA
2436 AAATCAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.06, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTATGT
Found at i:2520 original size:167 final size:165
Alignment explanation
Indices: 2273--2913 Score: 541
Period size: 167 Copynumber: 3.9 Consensus size: 165
2263 TTCTGTTTTC
* * * * * * *
2273 AAAAATCAATTCATGTTGCTAGAGGTGAG-T-AGCCTCGGGACACGCTGAGGTATCTTTAACTCC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTTAATTCC
* ** * *
2336 TATTTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGGGCCTTGGCTCACGTGCTGAGCTG
66 TGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTA
2401 TTTTCAATTTATGTTTTTCAATTTATGTTTTTCAA
131 TTTTCAATTTATGTTTTTCAATTTATGTTTTTCAA
2436 AAATCAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTTAATT
1 AAA--AATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTTAATT
* *
2501 CCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTAAG
64 CCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGTGCTGAG
* *
2563 GTATTTTC-A---A----TTTC------TGTTTGTC--
128 CTATTTTCAATTTATGTTTTTCAATTTATGTTTTTCAA
* * * * **
2585 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGGCACGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTTAATTCC
* * *
2650 TGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-C----CTCAGGATGCTGAGG
66 TGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACG-TGCTGAGC
* *
2710 TATTTTCAATTTCTATTTTTTTCAATTTATATTTTTCAAAAA
129 TATTTTCAA-TT-TATGTTTTTCAATTTATGTTTTTC---AA
* * *
2752 AAAAATCAACTCATATTG-AGAGAGGTGAGTTGAGGCTCGGGTCACATGCTGAGGTATTTTCAAA
1 AAAAATCAACTCATATTGCA-AGAGGTGAGTTGAGCCTCAGGTCAC--GCTGAGGTATTTT--TA
2816 ATCTGTTTTGCAAATTCTG-TTTTC-AAAAATCAACTCATATTGCGAG-GAGTGAGTTGAGCCTT
61 A------TT-C-----CTGTTTTTCAAAAAATCAACTCATATTGCGAGAG-GTGAGTTGAGCCTT
*
2878 GGCTCACGTGCTGAGCTATTTTCAATTTCTGTTTTT
113 GGCTCACGTGCTGAGCTATTTTCAATTTATGTTTTT
2914 AATGTCTGTA
Statistics
Matches: 385, Mismatches: 39, Indels: 89
0.75 0.08 0.17
Matches are distributed among these distances:
143 3 0.01
146 13 0.03
147 65 0.17
148 35 0.09
149 3 0.01
151 7 0.02
152 1 0.00
156 4 0.01
157 4 0.01
161 1 0.00
162 6 0.02
163 3 0.01
164 1 0.00
165 34 0.09
166 1 0.00
167 114 0.30
168 2 0.01
169 13 0.03
171 2 0.01
177 2 0.01
179 1 0.00
180 32 0.08
181 1 0.00
182 12 0.03
183 4 0.01
184 16 0.04
185 5 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (165 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTTAATTCC
TGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTA
TTTTCAATTTATGTTTTTCAATTTATGTTTTTCAA
Found at i:2523 original size:74 final size:75
Alignment explanation
Indices: 2415--2729 Score: 469
Period size: 73 Copynumber: 4.2 Consensus size: 75
2405 CAATTTATGT
* *
2415 TTTTCAATTTATGTTTTTCAAAAATCAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGT
1 TTTTCAATTTCTGTTTTTCAAAAA--AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
2480 CACGCTGAGGTA
64 CACGCTGAGGTA
* *
2492 TTTTTAATTCCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
*
2556 CGCTAAGGTA
66 CGCTGAGGTA
* * *
2566 TTTTCAATTTCTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGGCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
2629 CGCTGAGGTA
66 CGCTGAGGTA
* *
2639 TTTTCAATTTTTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--A
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
*
2702 TGCTGAGGTA
66 CGCTGAGGTA
*
2712 TTTTCAATTTCTATTTTT
1 TTTTCAATTTCTGTTTTT
2730 TTCAATTTAT
Statistics
Matches: 217, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
73 92 0.42
74 65 0.30
75 40 0.18
76 4 0.02
77 16 0.07
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
CGCTGAGGTA
Found at i:2733 original size:16 final size:16
Alignment explanation
Indices: 2712--2745 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2702 TGCTGAGGTA
*
2712 TTTTCAATTTCTATTT
1 TTTTCAATTTATATTT
2728 TTTTCAATTTATATTT
1 TTTTCAATTTATATTT
2744 TT
1 TT
2746 CAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCAATTTATATTT
Found at i:2744 original size:14 final size:16
Alignment explanation
Indices: 2712--2748 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
2702 TGCTGAGGTA
*
2712 TTTTCAATTTCTATTT
1 TTTTCAATTTCTATAT
2728 TTTTCAA-TT-TATAT
1 TTTTCAATTTCTATAT
2742 TTTTCAA
1 TTTTCAA
2749 AAAAAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 11 0.55
15 2 0.10
16 7 0.35
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTCAATTTCTATAT
Found at i:2834 original size:14 final size:13
Alignment explanation
Indices: 2808--2843 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
2798 TGCTGAGGTA
2808 TTTTCAAAATCTG
1 TTTTCAAAATCTG
*
2821 TTTTGCAAATTCTG
1 TTTT-CAAAATCTG
2835 TTTTCAAAA
1 TTTTCAAAA
2844 ATCAACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (13 bp):
TTTTCAAAATCTG
Found at i:2844 original size:92 final size:92
Alignment explanation
Indices: 2653--2912 Score: 279
Period size: 88 Copynumber: 2.9 Consensus size: 92
2643 CAATTTTTGC
*
2653 TTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG----ATGCTGAGGTAT
1 TTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTAT
* * * *
2713 TTTCAATTTCTATTTTTTTCAATTTATAT
66 TTTCAATTTC--TGTTTTGCAAATTATAG
* *
2742 TTTTCAAAAAAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGGCTCGGGTCACATGCTGAGGT
1 TTTTC--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGT
** *
2807 ATTTTCAAAATCTGTTTTGCAAATTCT-G
64 ATTTTCAATTTCTGTTTTGCAAATTATAG
* * * *
2835 TTTTC---AAAAATCAACTCATATTGCGAG-GAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTA
1 TTTTCAAAAAAAATCAACTCATATTGCGAGAG-GTGAGTTGAGCCTCGGGTCACATGCTGAGGTA
2896 TTTTCAATTTCTGTTTT
65 TTTTCAATTTCTGTTTT
2913 TAATGTCTGT
Statistics
Matches: 145, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
87 1 0.01
88 63 0.43
89 5 0.03
92 40 0.28
93 5 0.03
94 11 0.08
96 20 0.14
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (92 bp):
TTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTAT
TTTCAATTTCTGTTTTGCAAATTATAG
Found at i:2942 original size:88 final size:87
Alignment explanation
Indices: 2752--2962 Score: 230
Period size: 88 Copynumber: 2.4 Consensus size: 87
2742 TTTTCAAAAA
* * * *
2752 AAAAATCAACTCATATTGAGA-GAGGTGAGTTGAGGCTCGGGTCACATGCTGAGGTATTTTCAAA
1 AAAAATCAACTCATATTGCGAGGA-GTGAGTTGAGCCTCGGCTCACATGCTGAGCTATTTTCAAA
2816 ATCTGTTTTGCAAATTCTGTTTTC
65 ATCTGTTTT-CAAATTCTGTTTTC
* * **
2840 AAAAATCAACTCATATTGCGAGGAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGGAGTGAGTTGAGCCTCGGCTCACATGCTGAGCTATTTTCAAAA
*
2905 TCTGTTTT-TAATGTCTGTATTT-
66 TCTGTTTTCAAAT-TCTGT-TTTC
* * * * *
2927 AAAGAGTTAATTCATATTGCGAGAAATGAGTTGAGC
1 AAA-AATCAACTCATATTGCGAGGAGTGAGTTGAGC
2963 TCAAGATCAC
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
86 3 0.03
87 8 0.08
88 92 0.88
89 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGGAGTGAGTTGAGCCTCGGCTCACATGCTGAGCTATTTTCAAAA
TCTGTTTTCAAATTCTGTTTTC
Found at i:4586 original size:18 final size:18
Alignment explanation
Indices: 4563--4597 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4553 CTGTTTTTTA
*
4563 TTATTTATTATTATTATG
1 TTATTTACTATTATTATG
*
4581 TTATTTACTGTTATTAT
1 TTATTTACTATTATTAT
4598 TATATTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (18 bp):
TTATTTACTATTATTATG
Found at i:4720 original size:18 final size:18
Alignment explanation
Indices: 4697--4735 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4687 GTTTCAATTA
*
4697 ATACTTACGTATATATAT
1 ATACTTACATATATATAT
* *
4715 ATACTTTCATATATATTT
1 ATACTTACATATATATAT
4733 ATA
1 ATA
4736 GTTTTTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (18 bp):
ATACTTACATATATATAT
Found at i:4932 original size:19 final size:19
Alignment explanation
Indices: 4905--4942 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4895 TACTATTTTA
*
4905 TGTACATTTCTAATATCAT
1 TGTACATTTCTAACATCAT
*
4924 TGTATATTTCTAACATCAT
1 TGTACATTTCTAACATCAT
4943 CATTATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (19 bp):
TGTACATTTCTAACATCAT
Found at i:21239 original size:42 final size:42
Alignment explanation
Indices: 21115--21314 Score: 232
Period size: 42 Copynumber: 4.8 Consensus size: 42
21105 TACCATACCA
* * ** *
21115 ATGCCATATCCAAGATATGGTCTTACATGCGATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
* * *
21157 ATGCCACTAGCCCA-ACTA----ATTACACG-AAGTCTCATGTCG
1 ATGCCA-TATCCCAGA-TATGGTCTTACACGTAA-TCTCATATCG
*
21196 ATGCCATATCCCAGATATGGTCTTACCCGTAATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
21238 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
* *
21280 ATGCCATATCCCAGATATGGTCTTCCACTTAATCT
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCT
21315 TAATAACCCT
Statistics
Matches: 135, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
38 9 0.07
39 21 0.16
42 96 0.71
43 9 0.07
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCG
Found at i:22625 original size:53 final size:53
Alignment explanation
Indices: 22544--22689 Score: 213
Period size: 53 Copynumber: 2.7 Consensus size: 53
22534 CTTACACGGT
* *
22544 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
22599 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
**
22652 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTA
22690 AACGAGCACA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
52 1 0.01
53 77 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:25586 original size:93 final size:93
Alignment explanation
Indices: 25473--25644 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
25463 CGCCCATAAG
***
25473 CGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
25538 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
25566 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
25631 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
25645 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:25641 original size:46 final size:46
Alignment explanation
Indices: 25466--25641 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
25456 TGTAACCCGC
* ***
25466 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
25512 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
25562 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
25605 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
25642 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:29807 original size:49 final size:52
Alignment explanation
Indices: 29725--29832 Score: 141
Period size: 49 Copynumber: 2.1 Consensus size: 52
29715 ATATCTTCAA
* ** *
29725 TCATTTTGAGAAATTCCATGTTCATTTCTAAATGAATTGA-TTTCT-CATTT
1 TCATTTTGAGAAATACCACATTCATTTCCAAATGAATTGATTTTCTCCATTT
* *
29775 TCATTTTGAGAAA-ACCACATTCATTTCCAAATGATTTTATTTTCTCCATTT
1 TCATTTTGAGAAATACCACATTCATTTCCAAATGAATTGATTTTCTCCATTT
29826 TCATTTT
1 TCATTTT
29833 CATTTTGGAG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
49 20 0.40
50 18 0.36
51 12 0.24
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (52 bp):
TCATTTTGAGAAATACCACATTCATTTCCAAATGAATTGATTTTCTCCATTT
Found at i:32193 original size:27 final size:27
Alignment explanation
Indices: 32162--32337 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
32152 TAAATTGTAC
32162 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
32189 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
32215 ATGCAC-AAGTGTGCGAATTGACCATGG
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
32242 CGGACTAAGTGTGCGAGTTTGACTATG-
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
32269 AGCACTAAGTGTGCGATTGGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
32296 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
32323 AGCACTGAGTTTGCG
1 AGCACTAAGTGTGCG
32338 GACTCAATAT
Statistics
Matches: 121, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
26 27 0.22
27 86 0.71
28 8 0.07
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40128 original size:27 final size:27
Alignment explanation
Indices: 40097--40274 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40087 TAAATTGTAC
40097 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40124 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40150 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40178 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40206 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40233 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40260 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40275 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40211 original size:82 final size:81
Alignment explanation
Indices: 40098--40253 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40088 AAATTGTACA
* *
40098 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40162 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40179 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40244 TGCGAGTTGA
65 TGCGAATTGA
40254 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40265 original size:82 final size:81
Alignment explanation
Indices: 40094--40274 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
40084 GATTAAATTG
* *
40094 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40159 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40175 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40239 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40257 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40275 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.