Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3169
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: 40808
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1221 original size:46 final size:46
Alignment explanation
Indices: 1171--1338 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
1161 TGGTTGAGCA
*
1171 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
1217 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GA-GTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
1263 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGC-AACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
1308 --C-AGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1339 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 31 0.30
43 3 0.03
44 1 0.01
45 3 0.03
46 58 0.56
47 3 0.03
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:4410 original size:13 final size:13
Alignment explanation
Indices: 4392--4417 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4382 GAATCAGATA
4392 AATCAGAGGCATT
1 AATCAGAGGCATT
4405 AATCAGAGGCATT
1 AATCAGAGGCATT
4418 GTCTAGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
AATCAGAGGCATT
Found at i:8747 original size:46 final size:46
Alignment explanation
Indices: 8694--8862 Score: 173
Period size: 46 Copynumber: 3.7 Consensus size: 46
8684 TGAGCATCCA
* *
8694 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAATGTCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGTCCG
* * * *
8740 AACTCGTTGAGTTGAGTCCGAGTT--CGT-GAGATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAA--A--CGTCCG
* * * * *
8787 AACTCGTTGAGTTGAGTTCGAGTTCATTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGTCCG
*
8833 AGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
8863 GGGGTAGGTT
Statistics
Matches: 98, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
43 7 0.07
44 2 0.02
45 1 0.01
46 55 0.56
47 26 0.27
48 1 0.01
49 1 0.01
50 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGTCCG
Found at i:8846 original size:93 final size:93
Alignment explanation
Indices: 8687--8857 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
8677 GGATGGTTGA
* * *
8687 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAATGTCTGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGCCCGAACTCGTTGAGT
8752 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * * * *
8780 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGCCCGAACTCGTTGAGT
8845 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
8858 ACTTAGGGGT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:13854 original size:20 final size:20
Alignment explanation
Indices: 13818--13864 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
13808 CTAGAAAATT
*
13818 TATATATATAACCACATGCA
1 TATATATATAACCACATCCA
*
13838 TATATATAT-ACATACATCCA
1 TATATATATAAC-CACATCCA
13858 TA-ATATA
1 TATATATA
13865 AACACCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (20 bp):
TATATATATAACCACATCCA
Found at i:22945 original size:20 final size:20
Alignment explanation
Indices: 22891--22953 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
22881 TTCTCAATCA
* *
22891 TATAAACAGTAATTCATTCG
1 TATAAACAGTACTTCATCCG
*
22911 -AT-AATAGTAAC-TCATCCG
1 TATAAACAGT-ACTTCATCCG
22929 TATAAACAGTACTTCATCCG
1 TATAAACAGTACTTCATCCG
22949 TATAA
1 TATAA
22954 CACATAGCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 11 0.31
19 7 0.20
20 17 0.49
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (20 bp):
TATAAACAGTACTTCATCCG
Found at i:23157 original size:24 final size:25
Alignment explanation
Indices: 23114--23218 Score: 92
Period size: 24 Copynumber: 4.2 Consensus size: 25
23104 AGCTCCTCCT
* *
23114 AAGCTGATGGACAGTAAGCTCTGACG
1 AAGCTGA-GAACAGTAAGCTCTTACG
*
23140 AA-CTGAGAATAGTAAGCTCTTAC-
1 AAGCTGAGAACAGTAAGCTCTTACG
*
23163 AAGCTGAGAACAGTAACCTCTTACG
1 AAGCTGAGAACAGTAAGCTCTTACG
* * *
23188 -AGATGATATATCAGTAAGCTCATACG
1 AAGCTGAGA-A-CAGTAAGCTCTTACG
23214 -AGCTG
1 AAGCTG
23219 CGGTGAGTCC
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.03
24 39 0.60
25 5 0.08
26 19 0.29
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (25 bp):
AAGCTGAGAACAGTAAGCTCTTACG
Found at i:24087 original size:85 final size:85
Alignment explanation
Indices: 23947--24127 Score: 330
Period size: 85 Copynumber: 2.1 Consensus size: 85
23937 TGAGAATCAA
23947 AATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAATCA
1 AATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAATCA
24012 GAATCAGAATTAGGTGACAG
66 GAATCAGAATTAGGTGACAG
24032 AATCAGAATCAG-AATCAGTAA-CAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
1 AATCAGAATCAGTAA-CAG-AATCAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
24095 CAGAATCAGAATTAGGTGACAG
64 CAGAATCAGAATTAGGTGACAG
24117 AATCAGAATCA
1 AATCAGAATCA
24128 AAATGTGAAT
Statistics
Matches: 94, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
84 2 0.02
85 90 0.96
86 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (85 bp):
AATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAATCA
GAATCAGAATTAGGTGACAG
Found at i:24126 original size:6 final size:6
Alignment explanation
Indices: 23939--24106 Score: 184
Period size: 6 Copynumber: 27.8 Consensus size: 6
23929 AACCAAAATG
*
23939 AGAATC AAAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
* * * *
23987 AGTATT AGTAA-C AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC
* *
24036 AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTATT AGTAA-C
1 AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC
24084 AGAATC AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAATC AGAAT
24107 TAGGTGACAG
Statistics
Matches: 137, Mismatches: 14, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
5 9 0.07
6 119 0.87
7 8 0.06
8 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:24297 original size:27 final size:26
Alignment explanation
Indices: 24249--24330 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 26
24239 AGCATGGCTG
* * * *
24249 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAAATATTGTGGCAGAGCCA
24275 CCAGATACAAATATTGTGGCAGAGCCA
1 CCAGA-ACAAATATTGTGGCAGAGCCA
* *
24302 CCAGAATCAAATAATGTGGCAAAGCCA
1 CCAGAA-CAAATATTGTGGCAGAGCCA
24329 CC
1 CC
24331 TAACAGAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.12
27 42 0.88
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (26 bp):
CCAGAACAAATATTGTGGCAGAGCCA
Found at i:24672 original size:27 final size:26
Alignment explanation
Indices: 24633--24715 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
24623 TCGATCAGTC
* *
24633 AACAGATATTGTGACAGAGTCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
*
24659 ATACAGATATTGTGGCAGAGCCACTAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
24686 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
24713 AAC
1 AAC
24716 GCTTCCTCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.16
27 42 0.84
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:24944 original size:27 final size:27
Alignment explanation
Indices: 24914--25109 Score: 239
Period size: 27 Copynumber: 7.3 Consensus size: 27
24904 GGGGTAAAAT
* * *
24914 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
24941 GGTAATTCTACCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
24968 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
24995 GATAATTCTACCCTACATGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
25022 GGTAATTCTATCCTATAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
25049 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
25076 GGAAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
25103 AGTAATT
1 GGTAATT
25110 TCACAATCAA
Statistics
Matches: 145, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 145 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:25144 original size:27 final size:27
Alignment explanation
Indices: 25114--25604 Score: 578
Period size: 27 Copynumber: 18.2 Consensus size: 27
25104 GTAATTTCAC
*
25114 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
25141 AATCGAGGGTAAAATGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
25168 AA-CTGAGGGTAAACCAGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* **
25195 AATCGAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
25222 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* **
25249 AATCGAAGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
25276 AA-CTGAGGGTAAAACGATAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
25303 AATCGAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
25330 AA-CTGAGGGTAAAACGATAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
25357 AATCGAGGGTAAAACGATAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
25384 AATTGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
**
25411 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
25438 AA-CTGAGGGTAAAATGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * *
25465 AATCGAGGGTAAAATGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
25492 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* **
25519 AATCGAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
***
25546 AATCGAGGGTAAAATAATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
25573 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
25600 AATCG
1 AATCG
25605 GGAGTACTTT
Statistics
Matches: 397, Mismatches: 57, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.01
27 387 0.97
28 5 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:25621 original size:54 final size:54
Alignment explanation
Indices: 25119--25601 Score: 664
Period size: 54 Copynumber: 8.9 Consensus size: 54
25109 TTCACAATCA
* *
25119 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGATAATTTTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACTG
* * * * *
25173 AGGGTAAACCAGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTACAAA-TCG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACT-G
* * * * *
25227 AGGGTAAAACAGTAATTCTGTAAATCGAAGGTAAAATAGTAATTCTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACTG
* * *
25281 AGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACTG
* * * * *
25335 AGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGATAATTTTACAAATTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACTG
* * *
25389 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACTG
*
25443 AGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACTG
* *
25497 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTA-AAAATCG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACT-G
*** *
25551 AGGGTAAAATAATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAA
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAA
25602 TCGGGAGTAC
Statistics
Matches: 380, Mismatches: 45, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
53 5 0.01
54 371 0.98
55 4 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (54 bp):
AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTATAAACTG
Found at i:27638 original size:6 final size:6
Alignment explanation
Indices: 27604--27790 Score: 134
Period size: 6 Copynumber: 30.8 Consensus size: 6
27594 AACCAAAATG
* * * *
27604 AGAATC AAAATT AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
* * *
27652 AGTAA-C AGAATC AGAATA AGAATC AGAATT AG-GTGAC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * * *
27701 AGAATC AGTAA-C AAAATC AGAATC AAAATC AGTATT AGTAA-C AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC
* * *
27749 AGAATC AAAATC AGAATT AG-GTGAC AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAAT
27791 GTGAATGCAA
Statistics
Matches: 139, Mismatches: 28, Indels: 28
0.71 0.14 0.14
Matches are distributed among these distances:
5 10 0.07
6 117 0.84
7 10 0.07
8 2 0.01
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:27638 original size:30 final size:30
Alignment explanation
Indices: 27604--27786 Score: 209
Period size: 30 Copynumber: 6.2 Consensus size: 30
27594 AACCAAAATG
* *
27604 AGAATCAAAATTAGAATCAGTAACAGAATC
1 AGAATCAAAATCAGAATTAGTAACAGAATC
* *
27634 AGAATCAGAATCAGTATTAGTAACAGAATC
1 AGAATCAAAATCAGAATTAGTAACAGAATC
27664 AGAAT-AAGAATCAGAATTAGGT----G-A-C
1 AGAATCAA-AATCAGAATTA-GTAACAGAATC
* * *
27689 AGAATCAGAATCAGAATCAGTAACAAAATC
1 AGAATCAAAATCAGAATTAGTAACAGAATC
*
27719 AGAATCAAAATCAGTATTAGTAACAGAATC
1 AGAATCAAAATCAGAATTAGTAACAGAATC
*
27749 AGAATCAAAATCAGAATTAGGTGACAGAATC
1 AGAATCAAAATCAGAATTA-GTAACAGAATC
27780 AGAATCA
1 AGAATCA
27787 GAATGTGAAT
Statistics
Matches: 128, Mismatches: 15, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
24 2 0.02
25 16 0.12
26 2 0.02
27 1 0.01
29 2 0.02
30 86 0.67
31 19 0.15
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.20
Consensus pattern (30 bp):
AGAATCAAAATCAGAATTAGTAACAGAATC
Found at i:27706 original size:85 final size:85
Alignment explanation
Indices: 27604--27790 Score: 322
Period size: 85 Copynumber: 2.2 Consensus size: 85
27594 AACCAAAATG
* * * *
27604 AGAATCAAAATTAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAAAATCAGAATCAAAATCAGTATTAGTAACAGAATCAGAAT
27669 -AAGAATCAGAATTAGGTGAC
66 CAA-AATCAGAATTAGGTGAC
27689 AGAATCAGAATCAGAATCAGTAACAAAATCAGAATCAAAATCAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAAAATCAGAATCAAAATCAGTATTAGTAACAGAATCAGAAT
27754 CAAAATCAGAATTAGGTGAC
66 CAAAATCAGAATTAGGTGAC
27774 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
27791 GTGAATGCAA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 95 0.98
86 2 0.02
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (85 bp):
AGAATCAGAATCAGAATCAGTAACAAAATCAGAATCAAAATCAGTATTAGTAACAGAATCAGAAT
CAAAATCAGAATTAGGTGAC
Found at i:27957 original size:27 final size:27
Alignment explanation
Indices: 27922--27973 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
27912 GTATCGTGAT
* *
27922 AGAGTCACCAG-ATACAGATATTGTGGC
1 AGAGCCACCAGAAT-CAGATAATGTGGC
27949 AGAGCCACCAGAATCAGATAATGTG
1 AGAGCCACCAGAATCAGATAATGTG
27974 TTAAAGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (27 bp):
AGAGCCACCAGAATCAGATAATGTGGC
Found at i:28189 original size:22 final size:22
Alignment explanation
Indices: 28141--28199 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
28131 GTAAATACGT
*
28141 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
28163 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
28185 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
28200 TAATAACGAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:28365 original size:27 final size:26
Alignment explanation
Indices: 28286--28368 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
28276 TCGATCGGTC
* * *
28286 AACAGATATTGTGACAGAGTCACCAAA
1 AACAGATATTGTGGCAGAGCCACC-AG
28313 AACAGATATTGTGGCAGAGCCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
*
28339 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
28366 AAC
1 AAC
28369 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.18
27 42 0.82
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:28665 original size:26 final size:27
Alignment explanation
Indices: 28566--28748 Score: 198
Period size: 27 Copynumber: 6.9 Consensus size: 27
28556 GGCAAAATGG
* * * *
28566 TAATTTTACCCCACAAGGGTATCTT-GG
1 TAATTCTACCCTACAGGGGTAT-TTCGA
*
28593 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
28620 TATTTCTACCCTACAAGGGTATTTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
28647 TAATTCTA-CCTACAGGGGTATTTTGG
1 TAATTCTACCCTACAGGGGTATTTCGA
* * *
28673 TAATTCTATCCTATAAGGGTATTTC-A
1 TAATTCTACCCTACAGGGGTATTTCGA
28699 GTAATTCTACCCTA-A-GGGTATTTCGA
1 -TAATTCTACCCTACAGGGGTATTTCGA
28725 -AATTCTACCCTACAGGGGTATTTC
1 TAATTCTACCCTACAGGGGTATTTC
28749 AGTAATTTCA
Statistics
Matches: 135, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
24 12 0.09
25 10 0.07
26 36 0.27
27 77 0.57
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCGA
Found at i:28680 original size:80 final size:78
Alignment explanation
Indices: 28567--28747 Score: 247
Period size: 80 Copynumber: 2.3 Consensus size: 78
28557 GCAAAATGGT
* * * * * * *
28567 AATTTTACCCCACAAGGGTATCTTGGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCT
1 AATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCT
28632 ACAAGGGTATTTCGA
66 --AAGGGTATTTCGA
* *
28647 TAATTCTA-CCTACAGGGGTATTTTGGTAATTCTATCCTATAAGGGTATTTCAGTAATTCTACCC
1 -AATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
28711 TAAGGGTATTTCGA
65 TAAGGGTATTTCGA
28725 AATTCTACCCTACAGGGGTATTT
1 AATTCTACCCTACAGGGGTATTT
28748 CAGTAATTTC
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
77 7 0.08
78 28 0.31
80 49 0.54
81 6 0.07
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (78 bp):
AATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCT
AAGGGTATTTCGA
Found at i:28691 original size:53 final size:54
Alignment explanation
Indices: 28563--28748 Score: 222
Period size: 53 Copynumber: 3.5 Consensus size: 54
28553 AGGGGCAAAA
* * *
28563 TGGTAATTTTACCCCACAAGGGTATCTT-GGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTAT-TTCGATAATTCTACCCTACAGGGGTATTT
* *
28617 CGGTATTTCTACCCTACAAGGGTATTTCGATAATTCTA-CCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* *
28670 TGGTAATTCTATCCTATAAGGGTATTTC-AGTAATTCTACCCTA-A-GGGTA-TT
1 TGGTAATTCTACCCTACAAGGGTATTTCGA-TAATTCTACCCTACAGGGGTATTT
* * *
28721 TCGAAATTCTACCCTACAGGGGTATTTC
1 TGGTAATTCTACCCTACAAGGGTATTTC
28749 AGTAATTTCA
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
51 25 0.22
52 6 0.05
53 50 0.43
54 34 0.30
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (54 bp):
TGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
Found at i:28790 original size:27 final size:27
Alignment explanation
Indices: 28760--28962 Score: 275
Period size: 27 Copynumber: 7.5 Consensus size: 27
28750 GTAATTTCAC
*
28760 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
28787 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
28814 AA-CTGAGGGTAAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
28841 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
28868 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
28895 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
28922 AA-CTGAGGGTAAAACGATAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
28949 AATCGAGGGTAAAA
1 AATCGAGGGTAAAA
28963 TGATATTCGT
Statistics
Matches: 152, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
26 2 0.01
27 148 0.97
28 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.26
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:28853 original size:81 final size:81
Alignment explanation
Indices: 28760--28967 Score: 303
Period size: 81 Copynumber: 2.6 Consensus size: 81
28750 GTAATTTCAC
*
28760 AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTTTGTAAA-CTGAGGGT
1 AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATC-GAGGGT
*
28824 AAACCAGTAATTCTGTA
65 AAAACAGTAATTCTGTA
* ** *
28841 AATCAAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
1 AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTA
28906 AAACAGTAATTCTGTA
66 AAACAGTAATTCTGTA
* * *
28922 AA-CTGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGATA
1 AATC-AAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATA
28968 TTCGTACACT
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.01
81 110 0.98
82 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.26
Consensus pattern (81 bp):
AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTA
AAACAGTAATTCTGTA
Found at i:36127 original size:29 final size:27
Alignment explanation
Indices: 36095--36243 Score: 95
Period size: 28 Copynumber: 5.1 Consensus size: 27
36085 ACGTCCTGAT
36095 TTACAGAATTTACCATGTTTACCCATCGA
1 TTACAGAA-TTACCAT-TTTACCCATCGA
**
36124 TTACAGAATTATTATTTTACCCACTCGA
1 TTACAGAATTACCATTTTACCCA-TCGA
** *
36152 TTTTAAAATTACCATTTTACCC-TCGA
1 TTACAGAATTACCATTTTACCCATCGA
*
36178 TTTAACAGAAGATGTATCCATTTGTACCCGTCGA
1 -TT-ACAG-A-AT-TA-CCATTT-TACCCATCGA
* *
36212 TTTACAGAGTATACGATTCTTACCC-TCGA
1 -TTACAGAAT-TACCATT-TTACCCATCGA
36241 TTA
1 TTA
36244 TTATAGAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
26 4 0.04
27 10 0.10
28 30 0.31
29 13 0.13
30 11 0.11
31 6 0.06
32 7 0.07
33 9 0.09
34 7 0.07
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (27 bp):
TTACAGAATTACCATTTTACCCATCGA
Found at i:37900 original size:19 final size:19
Alignment explanation
Indices: 37850--37901 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
37840 AATTACTTGA
*
37850 ATTCT-ATTCTGATTTTTG
1 ATTCTGATTCTGATTTCTG
37868 ATCTCTG-TTACTGATTTCTG
1 AT-TCTGATT-CTGATTTCTG
37888 ATTCTGATTCTGAT
1 ATTCTGATTCTGAT
37902 CACCTAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.07
19 14 0.48
20 13 0.45
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.54
Consensus pattern (19 bp):
ATTCTGATTCTGATTTCTG
Done.