Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014078.1 Kokia drynarioides strain JFW-HI SEQ_129109, 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: 33199
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:1080 original size:17 final size:18
Alignment explanation
Indices: 1055--1166 Score: 85
Period size: 17 Copynumber: 6.3 Consensus size: 18
1045 TAATTTAACA
*
1055 TTAAGTTTTAAATCAAA-
1 TTAAATTTTAAATCAAAT
*
1072 TTAAATTTT-AATTAAAT
1 TTAAATTTTAAATCAAAT
*
1089 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAATCAAAT
*
1106 TTAAA-TTTAAAACGATAAAT
1 TTAAATTTTAAATC---AAAT
1126 TTAAA-TTTAAGAT-AAAT
1 TTAAATTTTAA-ATCAAAT
*
1143 TTAAATTTAAAAAT-AAAT
1 TTAAATTT-TAAATCAAAT
1161 TTAAAT
1 TTAAAT
1167 CAATTTAAAC
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
16 9 0.11
17 40 0.50
18 14 0.17
19 2 0.03
20 14 0.17
21 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (18 bp):
TTAAATTTTAAATCAAAT
Found at i:1086 original size:11 final size:11
Alignment explanation
Indices: 1069--1175 Score: 56
Period size: 11 Copynumber: 9.3 Consensus size: 11
1059 GTTTTAAATC
1069 AAATTAAATTT
1 AAATTAAATTT
*
1080 TAATTAAATTT
1 AAATTAAATTT
**
1091 AAATTTAAA-GC
1 AAA-TTAAATTT
1102 AAATTTAAATTT
1 AAA-TTAAATTT
*
1114 AAAACGATAAATTT
1 -AAA--TTAAATTT
* **
1128 AAATTTAAGAT
1 AAATTAAATTT
1139 AAATTTAAATTT
1 AAA-TTAAATTT
*
1151 AAAAATAAATTT
1 -AAATTAAATTT
*
1163 AAA-TCAATTT
1 AAATTAAATTT
1173 AAA
1 AAA
1176 CCCAACTTAA
Statistics
Matches: 73, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
10 9 0.12
11 31 0.42
12 17 0.23
13 9 0.12
14 7 0.10
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:1092 original size:6 final size:6
Alignment explanation
Indices: 1072--1166 Score: 72
Period size: 6 Copynumber: 16.0 Consensus size: 6
1062 TTAAATCAAA
* ** *
1072 TTAAAT TTTAA- TTAAAT TTAAAT TTAAA- GCAAAT TTAAAT TTAAAACG
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAA-T
* * *
1120 ATAAAT TTAAAT TTAAGA- -TAAAT TTAAAT TTAAAA ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
1167 CAATTTAAAC
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
4 1 0.01
5 10 0.15
6 49 0.72
7 7 0.10
8 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:1132 original size:37 final size:35
Alignment explanation
Indices: 1068--1166 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 35
1058 AGTTTTAAAT
* * * *
1068 CAAA-TTAAATTT-TAATTAAATTTAAATTTAAAG-
1 CAAATTTAAATTTAAAAATAAATTT-AAATTTAAGA
1101 CAAATTTAAATTTAAAACGATAAATTTAAATTTAAGA
1 CAAATTTAAATTTAAAA--ATAAATTTAAATTTAAGA
*
1138 TAAATTTAAATTTAAAAATAAATTTAAAT
1 CAAATTTAAATTTAAAAATAAATTTAAAT
1167 CAATTTAAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
33 4 0.07
34 8 0.14
35 14 0.25
36 7 0.12
37 23 0.41
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (35 bp):
CAAATTTAAATTTAAAAATAAATTTAAATTTAAGA
Found at i:6785 original size:5 final size:5
Alignment explanation
Indices: 6775--6815 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
6765 AGTGCATAAC
*
6775 TAAAA TAAAA TAAGA TAAAA TAAAA TAAAA TTGAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA -T-AAAA TAAA
6816 TATACTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 26 0.81
6 2 0.06
7 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:10420 original size:69 final size:69
Alignment explanation
Indices: 10339--10476 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
10329 TTTATCTACT
10339 TTCACAAGCACATCTTCAAAAATTCCCCTAGGATATTTAACAGATCTGTCAGCTAATTGAATACT
1 TTCACAAGCACATCTTCAAAAATTCCCCTAGGATATTTAACAGATCTGTCAGCTAATTGAATACT
10404 CATC
66 CATC
10408 TTCACAAGCACATCTTCAAAAATTCCCCTAGGATATTTAACAGATCTGTCAGCTAATTGAATACT
1 TTCACAAGCACATCTTCAAAAATTCCCCTAGGATATTTAACAGATCTGTCAGCTAATTGAATACT
10473 CATC
66 CATC
10477 CTAGTGGGTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (69 bp):
TTCACAAGCACATCTTCAAAAATTCCCCTAGGATATTTAACAGATCTGTCAGCTAATTGAATACT
CATC
Found at i:12178 original size:14 final size:13
Alignment explanation
Indices: 12158--12189 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
12148 ATAAAAGAGA
12158 AAAAAATTAAATT
1 AAAAAATTAAATT
12171 AGAAAAATTAAATT
1 A-AAAAATTAAATT
12185 AAAAA
1 AAAAA
12190 TGCAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (13 bp):
AAAAAATTAAATT
Found at i:12223 original size:14 final size:14
Alignment explanation
Indices: 12193--12222 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
12183 TTAAAAATGC
12193 AAATAATAAAATAA
1 AAATAATAAAATAA
12207 AAATAA-AAAATAA
1 AAATAATAAAATAA
12220 AAA
1 AAA
12223 AATGGCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAATAAAATAA
Found at i:17475 original size:12 final size:12
Alignment explanation
Indices: 17460--17485 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17450 TTTGTTGTTC
17460 TTTTTTTCTTTA
1 TTTTTTTCTTTA
17472 TTTTTTTCTTTA
1 TTTTTTTCTTTA
17484 TT
1 TT
17486 CGAACTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTCTTTA
Found at i:18341 original size:15 final size:16
Alignment explanation
Indices: 18312--18341 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18302 TTTGAGTCTG
18312 AAATAAAAATATTAAT
1 AAATAAAAATATTAAT
18328 AAATAAAAAT-TTAA
1 AAATAAAAATATTAA
18342 AATACCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAATATTAAT
Found at i:18401 original size:17 final size:18
Alignment explanation
Indices: 18369--18402 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18359 AAGAGAAATA
18369 AAATAATATAAATAACAT
1 AAATAATATAAATAACAT
*
18387 AAATAA-ATTAATAACA
1 AAATAATATAAATAACA
18403 AAGTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATAATATAAATAACAT
Found at i:23062 original size:28 final size:28
Alignment explanation
Indices: 22996--23144 Score: 135
Period size: 29 Copynumber: 5.1 Consensus size: 28
22986 TAGAAGCTTG
22996 GGGGTAAAATGGGA-ATTTTTAGAGAA-TTT-
1 GGGGTAAAAT--GATATTTTT-GA-AAGTTTA
*
23025 GGGGTTAAAATGATATTTTTGGAAGTTTA
1 GGGG-TAAAATGATATTTTTGAAAGTTTA
*
23054 GGGGTAAAATGGTAATTTTTGAAAGTTTA
1 GGGGTAAAATGAT-ATTTTTGAAAGTTTA
* **
23083 GGGGTAAAAATGTGATTTTTTTGCTAGTTTA
1 GGGGT-AAAA--TGATATTTTTGAAAGTTTA
23114 GGGGTAAAATG-TAATTTTTGAAAGTTTA
1 GGGGTAAAATGAT-ATTTTTGAAAGTTTA
23142 GGG
1 GGG
23145 TCAAAAATGA
Statistics
Matches: 101, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
27 3 0.03
28 31 0.31
29 33 0.33
30 14 0.14
31 17 0.17
32 3 0.03
ACGTcount: A:0.32, C:0.01, G:0.29, T:0.39
Consensus pattern (28 bp):
GGGGTAAAATGATATTTTTGAAAGTTTA
Found at i:23103 original size:30 final size:29
Alignment explanation
Indices: 22996--23543 Score: 204
Period size: 30 Copynumber: 18.6 Consensus size: 29
22986 TAGAAGCTTG
* *
22996 GGGGTAAAATGGGAATTTTTAGAGAA-TTT-
1 GGGGTAAAAT-GTAATTTTTTGA-AAGTTTA
*
23025 GGGGTTAAAATG--ATATTTTTGGAAGTTTA
1 GGGG-TAAAATGTAAT-TTTTTGAAAGTTTA
23054 GGGGTAAAATGGTAA-TTTTTGAAAGTTTA
1 GGGGTAAAAT-GTAATTTTTTGAAAGTTTA
* **
23083 GGGGTAAAAATGTGATTTTTTTGCTAGTTTA
1 GGGGT-AAAATGT-AATTTTTTGAAAGTTTA
23114 GGGGTAAAATGTAA-TTTTTGAAAGTTTA
1 GGGGTAAAATGTAATTTTTTGAAAGTTTA
* * * *
23142 -GGGTCAAAAATG-AAATTTTAGACA-TCTA
1 GGGGT--AAAATGTAATTTTTTGAAAGTTTA
** *
23170 ATGGTAAAATGGTAATTTTTTGAAAG-TTC
1 GGGGTAAAAT-GTAATTTTTTGAAAGTTTA
* * *
23199 GAGGTCAAAAATGGAATTTTTGGAAA-TTTA
1 GGGGT--AAAATGTAATTTTTTGAAAGTTTA
* * * *
23229 GAGGTAAAATGGTAAATTTTGGAAA--TTC
1 GGGGTAAAAT-GTAATTTTTTGAAAGTTTA
* * *** *
23257 GAGAGCAAAATGATAATTTTCAAAAAG-TTC
1 G-GGGTAAAATG-TAATTTTTTGAAAGTTTA
* **
23287 GAGGTCAAGAATG--ATATTTTTGAAAGTTCG
1 GGGGT-AA-AATGTAAT-TTTTTGAAAGTTTA
* *
23317 GGGGTAAAATGGTAATTTTTTG-AATTTTT
1 GGGGTAAAAT-GTAATTTTTTGAAAGTTTA
* * * *
23346 GGGGCAAAAATGTGATTTTTTGGAAGTTCA
1 GGGG-TAAAATGTAATTTTTTGAAAGTTTA
* * *
23376 AGGGTAAAATGTAATTTGTGGAAAGTTTA
1 GGGGTAAAATGTAATTTTTTGAAAGTTTA
* * * *
23405 GGGGCAAAAATATAATTATTGTG-AAG-TTC
1 GGGG-TAAAATGTAATT-TTTTGAAAGTTTA
*
23434 GAGGGTAAAAATGTAATTTTTCT-AAAG-TTC
1 G-GGGT-AAAATGTAATTTTT-TGAAAGTTTA
* **
23464 GAGGGTCAAAATGTGATTTTTAAAAAGTTT-
1 G-GGGT-AAAATGTAATTTTTTGAAAGTTTA
* * * *
23494 GGGAGTCAAATTATAATTTTTGGAAAGTTTG
1 GGG-GT-AAAATGTAATTTTTTGAAAGTTTA
* *
23525 GGGGTCAAATCGTGATTTT
1 GGGGTAAAAT-GTAATTTT
23544 AAAAAATTTA
Statistics
Matches: 396, Mismatches: 79, Indels: 87
0.70 0.14 0.15
Matches are distributed among these distances:
27 13 0.03
28 46 0.12
29 148 0.37
30 153 0.39
31 36 0.09
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGGTAAAATGTAATTTTTTGAAAGTTTA
Found at i:23112 original size:31 final size:30
Alignment explanation
Indices: 22996--23144 Score: 125
Period size: 28 Copynumber: 5.1 Consensus size: 30
22986 TAGAAGCTTG
* * *
22996 GGGGTAAAATGGGAATTTTTAGAGAA-TTT-
1 GGGGTAAAATGTGATTTTTTTGA-AAGTTTA
* *
23025 GGGGTTAAAA--TGATATTTTTGGAAGTTTA
1 GGGG-TAAAATGTGATTTTTTTGAAAGTTTA
*
23054 GGGGTAAAATG-G-TAATTTTTGAAAGTTTA
1 GGGGTAAAATGTGAT-TTTTTTGAAAGTTTA
**
23083 GGGGTAAAAATGTGATTTTTTTGCTAGTTTA
1 GGGGT-AAAATGTGATTTTTTTGAAAGTTTA
*
23114 GGGGTAAAATGT-A-ATTTTTGAAAGTTTA
1 GGGGTAAAATGTGATTTTTTTGAAAGTTTA
23142 GGG
1 GGG
23145 TCAAAAATGA
Statistics
Matches: 99, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
27 2 0.02
28 31 0.31
29 29 0.29
30 18 0.18
31 18 0.18
32 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.29, T:0.39
Consensus pattern (30 bp):
GGGGTAAAATGTGATTTTTTTGAAAGTTTA
Found at i:23137 original size:59 final size:60
Alignment explanation
Indices: 22996--23249 Score: 219
Period size: 58 Copynumber: 4.3 Consensus size: 60
22986 TAGAAGCTTG
* * *
22996 GGGGTAAAATGGGAATTTTTAGAGAA-TTT-GGGGTTAAAA--TGATATTTTTGGAAGTTTA
1 GGGGTAAAATGGTAATTTTT-GA-AAGTTTAGGGGTAAAAATGTGATATTTTTGCAAGTTTA
* *
23054 GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGTAAAAATGTGATTTTTTTGCTAGTTTA
1 GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGTAAAAATGTGATATTTTTGCAAGTTTA
* * *
23114 GGGGTAAAAT-GTAATTTTTGAAAGTTTA-GGGTCAAAAA--TGAAATTTTAG-ACA-TCTA
1 GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGT-AAAAATGTGATATTTTTGCA-AGTTTA
** * * * *
23170 ATGGTAAAATGGTAATTTTTTGAAAG-TTCGAGGTCAAAAATG-GA-ATTTTTGGAAATTTA
1 GGGGTAAAATGGTAA-TTTTTGAAAGTTTAGGGGT-AAAAATGTGATATTTTTGCAAGTTTA
* *
23229 GAGGTAAAATGGTAAATTTTG
1 GGGGTAAAATGGTAATTTTTG
23250 GAAATTCGAG
Statistics
Matches: 164, Mismatches: 19, Indels: 26
0.78 0.09 0.12
Matches are distributed among these distances:
56 13 0.08
57 20 0.12
58 63 0.38
59 42 0.26
60 26 0.16
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (60 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGTAAAAATGTGATATTTTTGCAAGTTTA
Found at i:23205 original size:58 final size:57
Alignment explanation
Indices: 23116--23316 Score: 166
Period size: 58 Copynumber: 3.5 Consensus size: 57
23106 CTAGTTTAGG
* *
23116 GGTAAAAT-GTAATTTTTGAAAGTT-TAGGGTCAAAAATGAAATTTTAGACATCTA-A
1 GGTAAAATGGTAATTTTTGAAAGTTCGA-GGTCAAAAATGAAATTTTAGAAATCTAGA
* * *
23171 TGGTAAAATGGTAATTTTTTGAAAGTTCGAGGTCAAAAATGGAATTTTTGGAAATTTAGA
1 -GGTAAAATGGTAA-TTTTTGAAAGTTCGAGGTCAAAAAT-GAAATTTTAGAAATCTAGA
* * *
23231 GGTAAAATGGTAAATTTTGGAAA-TTCGAGAG-C-AAAATGATAATTTTCAAAAAGT-TCGA
1 GGTAAAATGGT-AATTTTTGAAAGTTCGAG-GTCAAAAATGA-AATTTT-AGAAA-TCTAGA
*
23289 GGTCAAGAATGAT-ATTTTTGAAAGTTCG
1 GGT-AA-AATGGTAATTTTTGAAAGTTCG
23317 GGGGTAAAAT
Statistics
Matches: 120, Mismatches: 12, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
56 10 0.08
57 14 0.12
58 47 0.39
59 41 0.34
60 8 0.07
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (57 bp):
GGTAAAATGGTAATTTTTGAAAGTTCGAGGTCAAAAATGAAATTTTAGAAATCTAGA
Found at i:25161 original size:18 final size:17
Alignment explanation
Indices: 25125--25167 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
25115 GTTTAAAACC
*
25125 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAAATAA
25143 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
25161 ATTTAAA
1 ATTTAAA
25168 ACCAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:25705 original size:39 final size:38
Alignment explanation
Indices: 25670--26506 Score: 413
Period size: 39 Copynumber: 21.5 Consensus size: 38
25660 TGATCTACCT
* *
25670 CAGGCTCGAGGTAAGAGATCGAATGACTGCAATCTACCC
1 CAGGCTCGGGGTAAGAGATCGAATGA-TGCAATCTGCCC
* * ** ** *
25709 CAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCT
1 CAGGCTCGGGGTAAGAGATCGAATGAT-GCAATCTGCCC
* * * * *
25748 CAGCCTTGAGGTAAGAGATTGAATGGTTGCAATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAAT-GATGCAATCTGCCC
* ** * *
25787 CAGGCTCGGGGTAAGAAATTTACTGAT-AATGATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGATGCA--ATCTGCCC
** *
25826 CAAACTCGGGGTAAGAGATCGAATGACTACAATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGA-TGCAATCTGCCC
* * ** ** *
25865 CAGGCTCGGGTTAAGAGATTGGTTGATGGTGATTTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGAT-GCAATCTGCCC
* * * * *
25904 CAAGCTCGGGGTAAAAGATCGAATGGTTACAATATGCCC
1 CAGGCTCGGGGTAAGAGATCGAAT-GATGCAATCTGCCC
* * * ** *
25943 TAGGCTAGGGGTAAGAGATTGGCTGATG-ATGATCTGTCC
1 CAGGCTCGGGGTAAGAGATCGAATGATGCA--ATCTGCCC
* * * * *
25982 CAGGCTCGGGGTAAGAGATCGAATGGCTGTATTCTACCT
1 CAGGCTCGGGGTAAGAGATCGAAT-GATGCAATCTGCCC
* * * * * *
26021 CAGGCTCGAGGTAAGAGATTGAATGGCTGTAATTTACCC
1 CAGGCTCGGGGTAAGAGATCGAAT-GATGCAATCTGCCC
* * * ** * *
26060 TAGGCTCGGGGTAAGAGATTTG-TTGATGGTTATCTACCG
1 CAGGCTCGGGGTAAGAGA-TCGAATGAT-GCAATCTGCCC
* * *
26099 TAGGCTTGGGGTAAGAGATCGAATGACTGTAATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGA-TGCAATCTGCCC
* *
26138 CAGACTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAAT-GATGCAATCTGCCC
* * * **
26177 CAAGCTCGGGGTAAGAGATTTGCTAATGATG--ATCTTCTT
1 CAGGCTCGGGGTAAGAGA--T-CGAATGATGCAATCTGCCC
* *
26216 CAGGTTCGGGGTAAGAGATTTGCTAATGATG--ATCTGCCC
1 CAGGCTCGGGGTAAGAGA--T-CGAATGATGCAATCTGCCC
* * * *
26255 CAAGCTCGGGGTAAGAGATCGGATGGCTGCAATCTACCC
1 CAGGCTCGGGGTAAGAGATCGAAT-GATGCAATCTGCCC
* *
26294 CAAGCTCGGGGTAAGAGATTTGCTG-ATGATG--ATCTTCCC
1 CAGGCTCGGGGTAAGAGA--T-C-GAATGATGCAATCTGCCC
* * * * * *
26333 TAGGCTC-GTGTAAAAGATCGGATGGCTACAATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAAT-GATGCAATCTGCCC
* * * **
26371 CCGGCTCGGGGTAAGAGATTTG-CTGATTTTAATCTGCCC
1 CAGGCTCGGGGTAAGAGA-TCGAATGA-TGCAATCTGCCC
* * * *
26410 TAAGCTCGGGGTAAGAGATCGAATGGCTGCAATCTACCC
1 CAGGCTCGGGGTAAGAGATCGAAT-GATGCAATCTGCCC
* * ** *
26449 CAAGCTCGGGGTAAGAGATTGGTTGATG-ATGATCTGCCG
1 CAGGCTCGGGGTAAGAGATCGAATGATGCA--ATCTGCCC
*
26488 CAAGCTCGGGGTAAGAGAT
1 CAGGCTCGGGGTAAGAGAT
26507 TGGGATCTTC
Statistics
Matches: 613, Mismatches: 147, Indels: 76
0.73 0.18 0.09
Matches are distributed among these distances:
34 1 0.00
35 3 0.00
36 6 0.01
37 7 0.01
38 36 0.06
39 526 0.86
40 16 0.03
41 10 0.02
42 7 0.01
43 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (38 bp):
CAGGCTCGGGGTAAGAGATCGAATGATGCAATCTGCCC
Found at i:25749 original size:78 final size:78
Alignment explanation
Indices: 25611--26312 Score: 506
Period size: 78 Copynumber: 9.0 Consensus size: 78
25601 CTTTATCGCT
* * * * * * * * *
25611 TCGAATGATTGCCATCTACCCCATGATC-GGGTGAGAGATTAGCTAATGATGATCTACCTCAGGC
1 TCGAATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
*
25675 TCGAGGTAAGAGA
66 TCGGGGTAAGAGA
* * * *
25688 TCGAATGACTGCAATCTACCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGCC
1 TCGAATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* *
25753 TTGAGGTAAGAGA
66 TCGGGGTAAGAGA
* ** * * ** * **
25766 TTGAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAAATTTACTGATAATGATCTGCCCCAAAC
1 TCGAATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
25831 TCGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * * * * *
25844 TCGAATGACTACAATCTGCCCCAGGCTCGGGTTAAGAGATTGGTTGATGGTGATTTGCCCCAAGC
1 TCGAATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
*
25909 TCGGGGTAAAAGA
66 TCGGGGTAAGAGA
** * * * * * *
25922 TCGAATGGTTACAATATGCCCTAGGCTAGGGGTAAGAGATTGGCTGATGATGATCTGTCCCAGGC
1 TCGAATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
25987 TCGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * * * ** * * * * *
26000 TCGAATGGCTGTATTCTACCTCAGGCTCGAGGTAAGAGATTGAATGGCTG-TAATTTACCCTAGG
1 TCGAATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCT-GATGATGATCTGCCCCAGG
26064 CTCGGGGTAAGAGA
65 CTCGGGGTAAGAGA
* * ** ** * * ** *
26078 TTTG-TTGA-TGGTTATCTACCGTAGGCTTGGGGTAAGAGATCGAATGACTG-TAATCTGCCCCA
1 -TCGAATGACT-GCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGATGATCTGCCCCA
*
26140 GACTCGGGGTAAGAGA
63 GGCTCGGGGTAAGAGA
* * * * * * ** *
26156 TCGAATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTAATGATGATCTTCTTCAGGT
1 TCGAATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
26221 TCGGGGTAAGAGA
66 TCGGGGTAAGAGA
* * * * * * *
26234 TTTGCTAATGA-TG--ATCTGCCCCAAGCTCGGGGTAAGAGATCGGATG--GCTGCAATCTACCC
1 --T-CGAATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG--ATCTGCCC
*
26294 CAAGCTCGGGGTAAGAGA
61 CAGGCTCGGGGTAAGAGA
26312 T
1 T
26313 TTGCTGATGA
Statistics
Matches: 493, Mismatches: 119, Indels: 27
0.77 0.19 0.04
Matches are distributed among these distances:
76 4 0.01
77 30 0.06
78 445 0.90
79 6 0.01
80 3 0.01
81 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (78 bp):
TCGAATGACTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
TCGGGGTAAGAGA
Found at i:25978 original size:117 final size:116
Alignment explanation
Indices: 25639--26506 Score: 541
Period size: 117 Copynumber: 7.4 Consensus size: 116
25629 CCCCATGATC
* * * * * * * *
25639 GGGTGAGAGATTAGCTAATGATGATCTACCTCAGGCTCGAGGTAAGAGATCGAATGACTGCAATC
1 GGGTAAGAGATT-GGTAATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGCTGCAATC
* * * * * * *
25704 TACCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGCCTTG
65 TACCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCG
* * * ** * * *
25756 AGGTAAGAGATT-G-AATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAAATTTACT-GAT-AAT
1 GGGTAAGAGATTGGTAATGG-TG--ATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGCTGCA-
* * * * **
25817 GATCTGCCCCAAACTCGGGGTAAGAGA-TCGAATGACT-ACAATCTGCCCCAGGCTCG
62 -ATCTACCCCAAGCTCGGGGTAAGAGATTTG-CTGA-TGATGATCTGCCCCAGGCTCG
* * * * * * *
25873 GGTTAAGAGATTGGTTGATGGTGATTTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTACAATA
1 GGGTAAGAGATTGG-TAATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGCTGCAATC
* * * * * *
25938 TGCCCTAGGCTAGGGGTAAGAGATTGGCTGATGATGATCTGTCCCAGGCTCG
65 TACCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCG
* * * * * * *
25990 GGGTAAGAGA-TCG-AATGGCTGTATTCTACCTCAGGCTCGAGGTAAGAGATTGAATGGCTGTAA
1 GGGTAAGAGATTGGTAATGG-TG-A-TCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGCTGCAA
* * * * * * * ** *
26053 TTTACCCTAGGCTCGGGGTAAGAGATTTGTTGATGGTTATCTACCGTAGGCTTG
63 TCTACCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCG
* *
26107 GGGTAAGAGA-TCG-AATGACTGTAATCTGCCCC-AGACTCGGGGTAAGAGATCGAATGGCTGCA
1 GGGTAAGAGATTGGTAATG---GTGATCTGCCCCAAG-CTCGGGGTAAGAGATCGAATGGCTGCA
* * * ** *
26169 ATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTAATGATGATCTTCTTCAGGTTCG
62 ATCTACCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCG
* * *
26224 GGGTAAGAGATTTGCTAATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGGCTGCAATC
1 GGGTAAGAGA-TTGGTAATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGCTGCAATC
* *
26289 TACCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTTCCCTAGGCTC-
65 TACCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCG
* * * * ** * * ** **
26340 GTGTAAAAGATCGG--ATGGCTACAATCTGCCCCCGGCTCGGGGTAAGAGATTTG-CTGATTTTA
1 GGGTAAGAGATTGGTAATGG-T--GATCTGCCCCAAGCTCGGGGTAAGAGA-TCGAATGGCTGCA
* * * * *
26402 ATCTGCCCTAAGCTCGGGGTAAGAGA--T-C-GAATGGCTGCAATCTACCCCAAGCTCG
62 ATCTACCCCAAGCTCGGGGTAAGAGATTTGCTG-AT-GATG--ATCTGCCCCAGGCTCG
* * *
26457 GGGTAAGAGATTGGTTGATGATGATCTGCCGCAAGCTCGGGGTAAGAGAT
1 GGGTAAGAGATTGG-TAATGGTGATCTGCCCCAAGCTCGGGGTAAGAGAT
26507 TGGGATCTTC
Statistics
Matches: 581, Mismatches: 133, Indels: 75
0.74 0.17 0.10
Matches are distributed among these distances:
112 1 0.00
113 6 0.01
114 13 0.02
115 7 0.01
116 81 0.14
117 446 0.77
118 9 0.02
119 6 0.01
120 12 0.02
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (116 bp):
GGGTAAGAGATTGGTAATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGCTGCAATCT
ACCCCAAGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCG
Done.