Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold417
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: 17156
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:2152 original size:47 final size:47
Alignment explanation
Indices: 2058--2504 Score: 703
Period size: 47 Copynumber: 9.6 Consensus size: 47
2048 CATAAGCTAT
2058 TGAATGTGAAAGTGATTATATATGTGAT-AGGCCTAATGGCCGATGTGA
1 TGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGA
*
2106 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
2153 TGAATGTGAAA--GTATATATGTGATAAGGCCTAATGGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
2198 TGAATGT--AAGTGTA-ATATGTGATAAGGCCTAATGGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
*
2242 TGAATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
2289 TGAATGTGAAAGTG-ATATATGTGATAAGGCCTAATGGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
*
2335 TGAATGTGAAAGTGTATATATAAT-ATAAGGCCTAATGGCCGATGTGA
1 TGAATGTGAAAGTGTATATAT-GTGATAAGGCCTAATGGCCGATGTGA
2382 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
* * * * * *
2429 TGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGA
1 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
* * *
2476 TGGATGTGAAAGTGCATAAATGTGATAAG
1 TGAATGTGAAAGTGTATATATGTGATAAG
2505 TCCCGAGGGC
Statistics
Matches: 373, Mismatches: 17, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
43 2 0.01
44 37 0.10
45 43 0.12
46 65 0.17
47 211 0.57
48 15 0.04
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
Found at i:2198 original size:22 final size:22
Alignment explanation
Indices: 2170--2242 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
2160 GAAAGTATAT
2170 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* ****
2192 ATGTGATGAATG--TAAGTGTAAT
1 ATGTGAT-AAGGCCTAA-TGGCCG
2214 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
2236 ATGTGAT
1 ATGTGAT
2243 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 6 0.16
22 25 0.68
23 6 0.16
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:2289 original size:22 final size:22
Alignment explanation
Indices: 2261--2335 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
2251 AAGTATATAT
2261 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* *** ****
2283 ATGTGATGAATGTGAAAGTGATAT
1 ATGTGAT-AAGGCCTAA-TGGCCG
2307 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
2329 ATGTGAT
1 ATGTGAT
2336 GAATGTGAAA
Statistics
Matches: 35, Mismatches: 16, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
22 16 0.46
23 10 0.29
24 9 0.26
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.28
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:2404 original size:140 final size:140
Alignment explanation
Indices: 2058--2489 Score: 671
Period size: 140 Copynumber: 3.1 Consensus size: 140
2048 CATAAGCTAT
*
2058 TGAATGTGAAAGTG-AT-TATATATGTGATAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 TGAATGTGAAAGTGTATATATA-ATAT-A-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
2121 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT-ATATATGTGATAAGGCCTA
63 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATGTGATAAGGCCTA
2185 ATGGCCGATGTGA
128 ATGGCCGATGTGA
* *
2198 TGAATGT--AAGTGTA-ATAT-GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATAT
1 TGAATGTGAAAGTGTATATATAAT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
2259 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATGTGATAAGGCCTAAT
65 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATGTGATAAGGCCTAAT
2324 GGCCGATGTGA
130 GGCCGATGTGA
2335 TGAATGTGAAAGTGTATATATAATATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TGAATGTGAAAGTGTATATATAATATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * * *
2400 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGT
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATGTGATAAGGCCTAAT
* *
2465 GGCCAACGTGA
130 GGCCGATGTGA
*
2476 TGGATGTGAAAGTG
1 TGAATGTGAAAGTG
2490 CATAAATGTG
Statistics
Matches: 270, Mismatches: 13, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
136 78 0.29
137 41 0.15
138 6 0.02
139 11 0.04
140 94 0.35
141 40 0.15
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (140 bp):
TGAATGTGAAAGTGTATATATAATATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATGTGATAAGGCCTAATG
GCCGATGTGA
Found at i:2678 original size:37 final size:36
Alignment explanation
Indices: 2622--2699 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 36
2612 CCGAGCTCTA
* * *
2622 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATG-CCGGGT
*
2659 AAGACCCGATAACTTCGTGTGGAGATTATGCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGCCGGGT
2695 AAGAC
1 AAGAC
2700 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 11 0.30
37 26 0.70
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (36 bp):
AAGACCCGATAACTACGTGTGGAGATTATGCCGGGT
Found at i:4482 original size:43 final size:43
Alignment explanation
Indices: 4434--4536 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
4424 TTGGTTTTCA
4434 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
4477 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
4520 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
4537 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:4553 original size:29 final size:29
Alignment explanation
Indices: 4518--4591 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
4508 GTTGTGAGAT
* *
4518 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
4547 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
4576 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
4592 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:5039 original size:39 final size:37
Alignment explanation
Indices: 4901--5077 Score: 135
Period size: 38 Copynumber: 4.6 Consensus size: 37
4891 TCGAATGATG
* * * *
4901 TCCGGGCTAAGTCCCGAAGGCTTTG-GCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTGTGCGAA-T-ACTAAA
* *
4940 TCCGGACTAAGATCCGAAGGC-TTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTGTGCGA-ATACTAAA
* *
4978 TCCGGGCTAAGCCCGAAGGCATTGGTGCGATTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATT-GTGCGAATACTAAA
* * * **
5016 TCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTA-TGTA
1 TCCGGGCTAAGTCCGAAG-GCATT-GTGCGAATACTAAA
5054 TCCGGGCTAAGTCCGAAGAGCATT
1 TCCGGGCTAAGTCCGAAG-GCATT
5078 CATGCTAGTG
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
37 8 0.07
38 67 0.58
39 39 0.34
40 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (37 bp):
TCCGGGCTAAGTCCGAAGGCATTGTGCGAATACTAAA
Found at i:5057 original size:38 final size:38
Alignment explanation
Indices: 5015--5161 Score: 192
Period size: 38 Copynumber: 3.8 Consensus size: 38
5005 CGATTACTAA
5015 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTATGT
1 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTATGT
5053 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGT-ATGT
* * *
5092 ATCCGGGCTAAAGTTCCGAAGAGCATTCGTGCTGGTGT-T
1 ATCCGGGCT-AAG-TCCGAAGAGCATTCATGCTAGTATGT
*
5131 ATTCCGGGCT-A-TCCCGAAGAGCAATCATGCT
1 A-TCCGGGCTAAGT-CCGAAGAGCATTCATGCT
5162 GGTGACGTGT
Statistics
Matches: 99, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
36 1 0.01
37 16 0.16
38 35 0.35
39 15 0.15
40 12 0.12
41 20 0.20
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (38 bp):
ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTATGT
Found at i:5137 original size:79 final size:76
Alignment explanation
Indices: 5015--5166 Score: 200
Period size: 79 Copynumber: 2.0 Consensus size: 76
5005 CGATTACTAA
*
5015 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTATGTATCCGGGCTAAGT-CCGAAGAGCATTC
1 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTATGTATCCGGGCT-A-TCCCGAAGAGCAATC
5079 ATGCTAGTGATGT
64 ATGCTAGTGATGT
* * *
5092 ATCCGGGCTAAAGTTCCGAAGAGCATTCGTGCTGGTGT-TATTCCGGGCTATCCCGAAGAGCAAT
1 ATCCGGGCT-AAG-TCCGAAGAGCATTCATGCTAGTATGTA-TCCGGGCTATCCCGAAGAGCAAT
*
5156 CATGCTGGTGA
63 CATGCTAGTGA
5167 CGTGTATTCG
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
77 10 0.15
78 27 0.41
79 29 0.44
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (76 bp):
ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTATGTATCCGGGCTATCCCGAAGAGCAATCAT
GCTAGTGATGT
Found at i:8580 original size:46 final size:47
Alignment explanation
Indices: 8409--8796 Score: 616
Period size: 46 Copynumber: 8.4 Consensus size: 47
8399 GCTATTGATT
8409 AAAGTG-ATATTATGTGAT-A-GCCTAATGG-CGATGTGATGAATGTG
1 AAAGTGTATA-TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
8453 AAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
8500 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
8547 AAAGTGTATATA-GTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
8593 AAAGTG--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
8638 AAAGTGTATATATGTGAT-AGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
8684 AAAGTGTATATATGTGAT-AGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
* * * * * * *
8730 AAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
8777 AAAGTG-ATAAATGTGATAAG
1 AAAGTGTATATATGTGATAAG
8797 TCCCGAAGGG
Statistics
Matches: 324, Mismatches: 12, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
44 17 0.05
45 44 0.14
46 151 0.47
47 112 0.35
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
Found at i:8643 original size:91 final size:93
Alignment explanation
Indices: 8409--8796 Score: 619
Period size: 91 Copynumber: 4.2 Consensus size: 93
8399 GCTATTGATT
*
8409 AAAGTGATATTATGTGAT-A-GCCTAATGG-CGATGTGATGAATGTGAAAGTATATATATGTGAT
1 AAAGTGATA-TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
8471 AAGGCCTAATGGCCGATGTGATGAATGTG
65 AAGGCCTAATGGCCGATGTGATGAATGTG
8500 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA-GTGAT
1 AAAGTG-ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
8564 AAGGCCTAATGGCCGATGTGATGAATGTG
65 AAGGCCTAATGGCCGATGTGATGAATGTG
8593 AAAGTG-TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT-
1 AAAGTGATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATA
8656 AGGCCTAATGGCCGATGTGATGAATGTG
66 AGGCCTAATGGCCGATGTGATGAATGTG
*
8684 AAAGTGTATATATGTGAT-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAC
1 AAAGTG-ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
* * * * * *
8748 AGGGCCGAGTGGCCAACGTGATGGATGTG
65 AAGGCCTAATGGCCGATGTGATGAATGTG
*
8777 AAAGTGATAAATGTGATAAG
1 AAAGTGATATATGTGATAAG
8797 TCCCGAAGGG
Statistics
Matches: 279, Mismatches: 9, Indels: 16
0.92 0.03 0.05
Matches are distributed among these distances:
91 99 0.35
92 64 0.23
93 89 0.32
94 27 0.10
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (93 bp):
AAAGTGATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATA
AGGCCTAATGGCCGATGTGATGAATGTG
Found at i:8970 original size:36 final size:36
Alignment explanation
Indices: 8915--8992 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
8905 CCGAGCTCTA
* * *
8915 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGA-CCGATAACTACGTGTGGAGATTATGTCCGGGT
*
8952 AAGACCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCGATAACTACGTGTGGAGATTATGTCCGGGT
8988 AAGAC
1 AAGAC
8993 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 33 0.89
37 4 0.11
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (36 bp):
AAGACCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:12135 original size:37 final size:37
Alignment explanation
Indices: 12062--12140 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
12052 TTATTACGAA
* * *
12062 GTCTTACCCGGACTAATCTCCACCACGAAGTTATCGG
1 GTCTTACCCGGACAAATCCCCACCACGAAGTCATCGG
*
12099 GTCTTACCCGGACAAAATCCCCA-CACGTAGTCATCGG
1 GTCTTACCCGGAC-AAATCCCCACCACGAAGTCATCGG
12136 GTCTT
1 GTCTT
12141 TAGAGCTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 30 0.81
38 7 0.19
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAATCCCCACCACGAAGTCATCGG
Found at i:12409 original size:47 final size:47
Alignment explanation
Indices: 12262--12664 Score: 451
Period size: 47 Copynumber: 8.6 Consensus size: 47
12252 TTCGGGACTT
* * * * * *
12262 TATCAC-ATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC
1 TATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* *
12308 --TCA--ATATATATACTTTCACATTTCATCACATC-GCCATTAGCCC
1 TATCACTATATATACACTTTCACA-TTCATCACATCGGCCATTAGGCC
12351 TATCACATATATATACACTTTCAC-TTCATCACATCGGCCATTAGGCC
1 TATCAC-TATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
12398 TATCACTTATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TATCAC-TATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* *
12446 TTATCAC-GTATATACACTTTCACATTCATCACATCGGCCATTAGGCT
1 -TATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
*
12493 TATCACT-TATATAGTAC-TT-ACATTCATCACAT-GTCGCCATTAGGCC
1 TATCACTATATATA-CACTTTCACATTCATCACATCG--GCCATTAGGCC
12539 TATCAC-AT-TAT-CACTTTCACATTCATCACATCGGCCATTAGTGCC
1 TATCACTATATATACACTTTCACATTCATCACATCGGCCATTAG-GCC
*
12584 TTATCAC-ATATATATACTTTCACATTCATCACATCGGCCCATTAGGCCTC
1 -TATCACTATATATACACTTTCACATTCATCACATCGG-CCATTAGG-C-C
12634 TATCACATATATATACACTTTTCAACATTCA
1 TATCAC-TATATATACAC-TTTC-ACATTCA
12665 ATAGCTATGA
Statistics
Matches: 311, Mismatches: 18, Indels: 49
0.82 0.05 0.13
Matches are distributed among these distances:
43 25 0.08
44 22 0.07
45 35 0.11
46 51 0.16
47 76 0.24
48 61 0.20
49 20 0.06
50 1 0.00
51 9 0.03
52 4 0.01
53 7 0.02
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
TATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
Found at i:12439 original size:95 final size:95
Alignment explanation
Indices: 12262--12664 Score: 471
Period size: 95 Copynumber: 4.3 Consensus size: 95
12252 TTCGGGACTT
* * * * * *
12262 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC--TCA---ATATATATACT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACTTATATATATACT
12322 TTCACATTTCATCACATC-GCCATTA-GCCC
66 TTCACA-TTCATCACATCGGCCATTAGGCCC
*
12351 TATCACATATATATACACTTTCAC-TTCATCACATCGGCCATTAGGCCTATCACTTATATATACA
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACTTATATATATA
*
12415 CTTTCACATTCATCACATCGGCCATTAGGCCT
64 CTTTCACATTCATCACATCGGCCATTAGGCCC
* * *
12447 TATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCTTATCACTTATATA-GTAC-
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACTTATATATATACT
12510 TT-ACATTCATCACAT-GTCGCCATTAGG-CC
66 TTCACATTCATCACATCG--GCCATTAGGCCC
12539 TATCACAT-TAT-CACTTTCACATTCATCACATCGGCCATTAGTGCCTTATCAC--ATATATATA
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAG-GCC-TATCACTTATATATATA
12600 CTTTCACATTCATCACATCGGCCCATTAGGCCTC
64 CTTTCACATTCATCACATCGG-CCATTAGGCC-C
12634 TATCACATATATATACACTTTTCAACATTCA
1 TATCAC--ATATATACAC-TTTC-ACATTCA
12665 ATAGCTATGA
Statistics
Matches: 271, Mismatches: 16, Indels: 42
0.82 0.05 0.13
Matches are distributed among these distances:
89 6 0.02
90 53 0.20
91 24 0.09
92 33 0.12
93 32 0.12
94 30 0.11
95 65 0.24
96 9 0.03
97 2 0.01
98 3 0.01
99 3 0.01
100 4 0.01
101 7 0.03
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (95 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACTTATATATATACT
TTCACATTCATCACATCGGCCATTAGGCCC
Found at i:12573 original size:185 final size:185
Alignment explanation
Indices: 12261--12664 Score: 511
Period size: 185 Copynumber: 2.2 Consensus size: 185
12251 CTTCGGGACT
* * * * * *
12261 TTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCTCAATATATATACTTTCA
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCATCAATATATATACTTTCA
12326 CATTTCATCACATCGCCATTAGCCCTATCACATATATATACACTTTCACTTCATCACATCGGCCA
66 CATTTCATCACATCGCCATTAGCCCTATCACA-ATATATACACTTTCACTTCATCACATCGGCCA
12391 TTAG-GCC-TATCACTTATATATACACTTTCACATTCATCACATCGG-CCATTAGGCC
130 TTAGTGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCCATTAGGCC
* * *
12446 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCTTATCACTTATATAGTAC-
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC--ATCA-ATATATA-TACT
*
12510 TT-ACA-TTCATCACATGTCGCCATTAGGCCTATCAC-AT-TAT-CACTTTCACATTCATCACAT
62 TTCACATTTCATCACA--TCGCCATTAGCCCTATCACAATATATACACTTTCAC-TTCATCACAT
*
12570 CGGCCATTAGTGCCTTATCACATATATATACTTTCACATTCATCACATCGGCCCATTAGGCC
124 CGGCCATTAGTGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCCATTAGGCC
12632 TCTATCACATATATATACACTTTTCAACATTCA
1 T-TATCAC--ATATATACAC-TTTC-ACATTCA
12665 ATAGCTATGA
Statistics
Matches: 192, Mismatches: 12, Indels: 24
0.84 0.05 0.11
Matches are distributed among these distances:
184 9 0.05
185 91 0.47
186 25 0.13
187 18 0.09
188 26 0.14
189 12 0.06
190 4 0.02
191 7 0.04
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (185 bp):
TTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCATCAATATATATACTTTCA
CATTTCATCACATCGCCATTAGCCCTATCACAATATATACACTTTCACTTCATCACATCGGCCAT
TAGTGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCCATTAGGCC
Found at i:12613 original size:138 final size:137
Alignment explanation
Indices: 12262--12653 Score: 485
Period size: 138 Copynumber: 2.8 Consensus size: 137
12252 TTCGGGACTT
* * * * *
12262 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC---TCA-ATATATATACTT
1 TATCACA-TTATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACTT
* * *
12323 TCACATTTCATCACATC-GCCATTAGCCCTATCACATATATATACACTTTCACTTCATCACATCG
65 TCACA-TTCATCACATCGGCCATTAGGCTTATCAC-T-TATATACACTTACACTTCATCACATCG
12387 GCCATTAGGCC
127 GCCATTAGGCC
* *
12398 TATCACTTATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACAC
1 TATCAC--AT-TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
12463 TTTCACATTCATCACATCGGCCATTAGGCTTATCACTTATATAGTACTTACA-TTCATCACAT-G
63 TTTCACATTCATCACATCGGCCATTAGGCTTATCACTTATATA-CACTTACACTTCATCACATCG
12526 TCGCCATTAGGCC
127 --GCCATTAGGCC
12539 TATCACATTAT-CACTTTCACATTCATCACATCGGCCATTAGTGCCTTATCACATATATATACTT
1 TATCACATTATACACTTTCACATTCATCACATCGGCCATTAG-GCCTTATCACATATATATACTT
12603 TCACATTCATCACATCGGCCCATTAGGCCTCTATCACATATATATACACTT
65 TCACATTCATCACATCGG-CCATTAGG-CT-TATCAC-T-TATATACACTT
12654 TTCAACATTC
Statistics
Matches: 225, Mismatches: 14, Indels: 28
0.84 0.05 0.10
Matches are distributed among these distances:
136 6 0.03
137 31 0.14
138 74 0.33
139 11 0.05
140 18 0.08
141 44 0.20
142 35 0.16
143 6 0.03
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (137 bp):
TATCACATTATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACTTT
CACATTCATCACATCGGCCATTAGGCTTATCACTTATATACACTTACACTTCATCACATCGGCCA
TTAGGCC
Found at i:15712 original size:23 final size:24
Alignment explanation
Indices: 15685--15732 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
15675 AAGGAATTCG
15685 CACACACACAGTGCTC-AATCATT
1 CACACACACAGTGCTCTAATCATT
* *
15708 CACACACATAGTGCTCTTATCATT
1 CACACACACAGTGCTCTAATCATT
15732 C
1 C
15733 GTTATTACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.27
Consensus pattern (24 bp):
CACACACACAGTGCTCTAATCATT
Found at i:15995 original size:78 final size:80
Alignment explanation
Indices: 15896--16051 Score: 208
Period size: 78 Copynumber: 2.0 Consensus size: 80
15886 CGAATACACG
* *
15896 TCACCAGCATGATTGCTCTTCGGGAC-AGCCCGGACATAACACCAGCACGAAT-GCTCTTCGGAA
1 TCACCAGCATGAATGCTCTTCGGGACTAGCCCGGACACAACACCAGCACGAATGGCTCTTCGGAA
15959 CTTAGCCCGGATACA
66 CTTAGCCCGGATACA
* * * * * * *
15974 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGGCTCTTTGGG
1 TCACCAGCATGAATGCTCTTCGGGAC-TAGCCCGGACACAACACCAGCACGAATGGCTCTTCGGA
16039 ACTTAGCCCGGAT
65 ACTTAGCCCGGAT
16052 TTAGTAACTC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
78 24 0.36
80 21 0.32
81 21 0.32
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (80 bp):
TCACCAGCATGAATGCTCTTCGGGACTAGCCCGGACACAACACCAGCACGAATGGCTCTTCGGAA
CTTAGCCCGGATACA
Found at i:16045 original size:41 final size:40
Alignment explanation
Indices: 15896--16051 Score: 208
Period size: 40 Copynumber: 3.9 Consensus size: 40
15886 CGAATACACG
* * *
15896 TCACCAGCATGATTGCTCTTCGGGAC--AGCCCGGACATA
1 TCACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * *
15934 ACACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
15974 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
16014 TCACTAGCATGAATGGCTCTTTGGGACTTAGCCCGGAT
1 TCACCAGCATGAAT-GCTCTTCGGGACTTAGCCCGGAT
16052 TTAGTAACTC
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
38 22 0.21
40 60 0.58
41 22 0.21
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
TCACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:16516 original size:29 final size:29
Alignment explanation
Indices: 16482--16548 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
16472 TCAACCACGT
* *
16482 ACACTTAGTGCCATGT-ATTTTAAACTCGC
1 ACACTTAGTGCCAT-TCATTTCAAACCCGC
*
16511 ACACTTAGTGCCATTCATTTCAAGCCCGC
1 ACACTTAGTGCCATTCATTTCAAACCCGC
16540 ACACTTAGT
1 ACACTTAGT
16549 CCAATCTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 1 0.03
29 33 0.97
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.31
Consensus pattern (29 bp):
ACACTTAGTGCCATTCATTTCAAACCCGC
Found at i:16617 original size:43 final size:42
Alignment explanation
Indices: 16534--16634 Score: 170
Period size: 43 Copynumber: 2.4 Consensus size: 42
16524 TTCATTTCAA
16534 GCCCGCACACTTAGT-CCAATCTCACAACGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACGTGAACACTTATT
16575 GCCCGCACACTTAGTGCCAATCTCAACAACCGT-AACACTTATT
1 GCCCGCACACTTAGTGCCAATCTC-ACAA-CGTGAACACTTATT
16618 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
16635 TGAAACCAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
41 15 0.26
42 8 0.14
43 31 0.54
44 3 0.05
ACGTcount: A:0.28, C:0.36, G:0.14, T:0.23
Consensus pattern (42 bp):
GCCCGCACACTTAGTGCCAATCTCACAACGTGAACACTTATT
Done.