Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009669.1 Kokia drynarioides strain JFW-HI SEQ_124387, 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: 40552
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:691 original size:22 final size:22
Alignment explanation
Indices: 663--715 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
653 TTTTGTCAAC
663 TACCCCAAAATTGAGTACAATT
1 TACCCCAAAATTGAGTACAATT
**
685 TACCCCAAAATTGAGTGTAATT
1 TACCCCAAAATTGAGTACAATT
707 TACCCCAAA
1 TACCCCAAA
716 TATAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (22 bp):
TACCCCAAAATTGAGTACAATT
Found at i:1176 original size:22 final size:22
Alignment explanation
Indices: 1151--1257 Score: 135
Period size: 22 Copynumber: 4.8 Consensus size: 22
1141 AGTATATTGT
1151 TGTTTTGGTGCTGTTTTTTTAC
1 TGTTTTGGTGCTGTTTTTTTAC
* *
1173 TGTTTTGATTGCT-ATTTTTTAC
1 TGTTTTG-GTGCTGTTTTTTTAC
* *
1195 TGTTTTGGTGTTGTGTTTTTAC
1 TGTTTTGGTGCTGTTTTTTTAC
*
1217 TGTTTTGGTGCTATTTTTTTTAC
1 TGTTTTGGTGCT-GTTTTTTTAC
*
1240 TATTTTGGTGCTGTTTTT
1 TGTTTTGGTGCTGTTTTT
1258 ATTATTATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
21 3 0.04
22 45 0.63
23 23 0.32
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.64
Consensus pattern (22 bp):
TGTTTTGGTGCTGTTTTTTTAC
Found at i:1190 original size:23 final size:22
Alignment explanation
Indices: 1151--1282 Score: 131
Period size: 22 Copynumber: 5.9 Consensus size: 22
1141 AGTATATTGT
*
1151 TGTTTTGGTGCTGTTTTTTTAC
1 TGTTTTGGTGCTATTTTTTTAC
*
1173 TGTTTTGATTGCTA-TTTTTTAC
1 TGTTTTG-GTGCTATTTTTTTAC
* * *
1195 TGTTTTGGTGTTGTGTTTTTAC
1 TGTTTTGGTGCTATTTTTTTAC
1217 TGTTTTGGTGCTATTTTTTTTAC
1 TGTTTTGGTGCTA-TTTTTTTAC
* * *
1240 TATTTTGGTGCTGTTTTTATTAT
1 TGTTTTGGTGCTATTTTT-TTAC
* *
1263 TATTTTTGTTGCTATTTTTT
1 T-GTTTTGGTGCTATTTTTT
1283 ATATTATTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
21 3 0.03
22 45 0.50
23 28 0.31
24 14 0.16
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.66
Consensus pattern (22 bp):
TGTTTTGGTGCTATTTTTTTAC
Found at i:1214 original size:44 final size:43
Alignment explanation
Indices: 1151--1283 Score: 167
Period size: 45 Copynumber: 3.0 Consensus size: 43
1141 AGTATATTGT
1151 TGTTTTGGTGCTGTTTTTTTACTGTTTTGATTGCTATTTTTTAC
1 TGTTTTGGTGCTGTTTTTTTACTGTTTTG-TTGCTATTTTTTAC
* * *
1195 TGTTTTGGTGTTGTGTTTTTACTGTTTTGGTGCTATTTTTTTTAC
1 TGTTTTGGTGCTGTTTTTTTACTGTTTTGTTGCTA--TTTTTTAC
* * *
1240 TATTTTGGTGCTGTTTTTATTATTATTTTTGTTGCTATTTTTTA
1 TGTTTTGGTGCTGTTTTT-TTACT-GTTTTGTTGCTATTTTTTA
1284 TATTATTTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
43 5 0.07
44 27 0.36
45 30 0.39
46 4 0.05
47 10 0.13
ACGTcount: A:0.10, C:0.07, G:0.18, T:0.65
Consensus pattern (43 bp):
TGTTTTGGTGCTGTTTTTTTACTGTTTTGTTGCTATTTTTTAC
Found at i:1269 original size:24 final size:24
Alignment explanation
Indices: 1219--1316 Score: 101
Period size: 24 Copynumber: 4.1 Consensus size: 24
1209 GTTTTTACTG
* *
1219 TTTTGGTGCTATTTTTTTTACTA-
1 TTTTGGTGCTATTTTTATTATTAT
*
1242 TTTTGGTGCTGTTTTTATTATTAT
1 TTTTGGTGCTATTTTTATTATTAT
*
1266 TTTTGTTGCTATTTTT-TATATTAT
1 TTTTGGTGCTATTTTTAT-TATTAT
* * * *
1290 TTTTGCTGCTGTTTTGATTGTTAT
1 TTTTGGTGCTATTTTTATTATTAT
1314 TTT
1 TTT
1317 GATTATTTGG
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
23 21 0.33
24 41 0.65
25 1 0.02
ACGTcount: A:0.12, C:0.06, G:0.14, T:0.67
Consensus pattern (24 bp):
TTTTGGTGCTATTTTTATTATTAT
Found at i:1292 original size:23 final size:23
Alignment explanation
Indices: 1219--1292 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
1209 GTTTTTACTG
* *
1219 TTTTGGTGCTATTTTTTTTACTA
1 TTTTGGTGCTATTTTTTATATTA
*
1242 TTTTGGTGCT-GTTTTTATTATTA
1 TTTTGGTGCTATTTTTTA-TATTA
*
1265 TTTTTGTTGCTATTTTTTATATTA
1 -TTTTGGTGCTATTTTTTATATTA
1289 TTTT
1 TTTT
1293 TGCTGCTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.12
23 18 0.42
24 14 0.33
25 6 0.14
ACGTcount: A:0.14, C:0.05, G:0.12, T:0.69
Consensus pattern (23 bp):
TTTTGGTGCTATTTTTTATATTA
Found at i:7178 original size:49 final size:46
Alignment explanation
Indices: 7070--7178 Score: 112
Period size: 49 Copynumber: 2.3 Consensus size: 46
7060 AATAATATAA
* * * **
7070 TAGTTTTACCTTTTAACTTAATAAGTAAATATTTATCTGAACGACG
1 TAGTTTTGCTTTTTAACTTAAAAAGTAAATATTTATCAAAACGACG
* *
7116 T-GATTTTGATTTTTAACTTTAAAAAAGATAAATATTTATCAAAACGATG
1 TAG-TTTTGCTTTTTAAC-TT-AAAAAG-TAAATATTTATCAAAACGACG
7165 TAGTTTTGCTTTTT
1 TAGTTTTGCTTTTT
7179 CTTATTCGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
45 1 0.02
46 12 0.24
47 2 0.04
48 5 0.10
49 29 0.58
50 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (46 bp):
TAGTTTTGCTTTTTAACTTAAAAAGTAAATATTTATCAAAACGACG
Found at i:8751 original size:19 final size:18
Alignment explanation
Indices: 8716--8751 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8706 TGAATTTTCA
*
8716 TCAAATCAACTCTAAAAT
1 TCAAATCAACACTAAAAT
8734 TCAAATCAAACACTAAAA
1 TCAAATC-AACACTAAAA
8752 AGTTAACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (18 bp):
TCAAATCAACACTAAAAT
Found at i:12256 original size:6 final size:6
Alignment explanation
Indices: 12245--12311 Score: 75
Period size: 6 Copynumber: 11.3 Consensus size: 6
12235 CAAATGTATT
* **
12245 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTATCT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
*
12293 TTT-AA TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
12312 GATTTAAAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
5 8 0.16
6 38 0.76
7 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:12257 original size:18 final size:18
Alignment explanation
Indices: 12231--12316 Score: 104
Period size: 17 Copynumber: 4.8 Consensus size: 18
12221 GTTTTAAATT
* *
12231 AATTCAAATGTATTTTTA
1 AATTTAAATTTATTTTTA
12249 AATTTAAATTTA-TTTTA
1 AATTTAAATTTATTTTTA
12266 AATTTAAATTTATCTTTTA
1 AATTTAAATTTAT-TTTTA
* *
12285 AATTTAAATTTA-ATTAA
1 AATTTAAATTTATTTTTA
*
12302 AATTTAAATTGATTT
1 AATTTAAATTTATTT
12317 AAAACTTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
17 31 0.53
18 11 0.19
19 17 0.29
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
AATTTAAATTTATTTTTA
Found at i:12288 original size:36 final size:35
Alignment explanation
Indices: 12231--12316 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 35
12221 GTTTTAAATT
* * * *
12231 AATTCAAATGTATTTTTAAATTTAAATTTATTTTA
1 AATTTAAATTTATTTTTAAATTTAAATTTAATTAA
12266 AATTTAAATTTATCTTTTAAATTTAAATTTAATTAA
1 AATTTAAATTTAT-TTTTAAATTTAAATTTAATTAA
*
12302 AATTTAAATTGATTT
1 AATTTAAATTTATTT
12317 AAAACTTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
35 13 0.29
36 32 0.71
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (35 bp):
AATTTAAATTTATTTTTAAATTTAAATTTAATTAA
Found at i:12318 original size:17 final size:17
Alignment explanation
Indices: 12248--12325 Score: 93
Period size: 17 Copynumber: 4.5 Consensus size: 17
12238 ATGTATTTTT
*
12248 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTA
*
12265 AAATTTAAATTTATCTTTT
1 AAATTTAAATTTA--TTTA
*
12284 AAATTTAAATTTAATTA
1 AAATTTAAATTTATTTA
*
12301 AAATTTAAATTGATTTA
1 AAATTTAAATTTATTTA
*
12318 AAACTTAA
1 AAATTTAA
12326 TTAAATTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
17 37 0.69
19 17 0.31
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (17 bp):
AAATTTAAATTTATTTA
Found at i:12334 original size:16 final size:17
Alignment explanation
Indices: 12288--12336 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
12278 TCTTTTAAAT
* *
12288 TTAAATTTAATTAAAAT
1 TTAAATTAAATTAAAAC
* *
12305 TTAAATTGATTTAAAAC
1 TTAAATTAAATTAAAAC
12322 TT-AATTAAATTAAAA
1 TTAAATTAAATTAAAA
12337 ATCCAAAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAATTAAATTAAAAC
Found at i:12764 original size:30 final size:29
Alignment explanation
Indices: 12678--12808 Score: 131
Period size: 29 Copynumber: 4.5 Consensus size: 29
12668 TCGAATTTCT
* * *
12678 AAAAATTCCATTTTGACCCCAAAACTTCT
1 AAAAATTCCATTTTTAACCCAAAACTTCC
* *
12707 AAGAAA-TCCATTTTTATCCCTAAACTTCC
1 AA-AAATTCCATTTTTAACCCAAAACTTCC
*
12736 AAAAATTCCATTTTTAACCAAAAAACTTCC
1 AAAAATTCCATTTTTAACC-CAAAACTTCC
* * *
12766 AAAAATTCCATTTTTGACCTAAGA-TGTCC
1 AAAAATTCCATTTTTAACCCAAAACT-TCC
*
12795 AAAAACTCCATTTT
1 AAAAATTCCATTTT
12809 CGACCTTGAA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.05
29 54 0.62
30 29 0.33
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATTCCATTTTTAACCCAAAACTTCC
Found at i:12796 original size:59 final size:58
Alignment explanation
Indices: 12678--12808 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 58
12668 TCGAATTTCT
* ** *
12678 AAAAATTCCA-TTTTGACCCCAAAACTTCTAAGAAATCCATTTTTATCCCTAAACTTCC
1 AAAAATTCCATTTTTAACCAAAAAACTTCCAAGAAATCCATTTTTA-CCCTAAACTTCC
12736 AAAAATTCCATTTTTAACCAAAAAACTTCCAA-AAATTCCATTTTTGA-CCTAAGA-TGTCC
1 AAAAATTCCATTTTTAACCAAAAAACTTCCAAGAAA-TCCATTTTT-ACCCTAA-ACT-TCC
*
12795 AAAAACTCCATTTT
1 AAAAATTCCATTTT
12809 CGACCTTGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
58 19 0.30
59 43 0.68
60 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAAATTCCATTTTTAACCAAAAAACTTCCAAGAAATCCATTTTTACCCTAAACTTCC
Found at i:12867 original size:29 final size:28
Alignment explanation
Indices: 12649--12868 Score: 101
Period size: 29 Copynumber: 7.6 Consensus size: 28
12639 TTAAACTCCC
** * *
12649 AAAAATTCCATGATTACCCTCGAATTTCT
1 AAAAATTCCATTTTTACCCT-TAAATTCT
* **
12678 AAAAATTCCATTTTGACCCCAAAACTTCT
1 AAAAATTCCATTTTTACCCTTAAA-TTCT
*
12707 AAGAAA-TCCATTTTTATCCC-TAAACTTCC
1 AA-AAATTCCATTTTTA-CCCTTAAA-TTCT
*** *
12736 AAAAATTCCATTTTTAACCAAAAAACTTCC
1 AAAAATTCCATTTTT-ACCCTTAAA-TTCT
*
12766 AAAAATTCCATTTTTGA-CC-TAAGATGTCC
1 AAAAATTCCATTTTT-ACCCTTAA-AT-TCT
* * *
12795 AAAAACTCCATTTTCGA-CCTTGAAACTCT
1 AAAAATTCCATTTT-TACCCTT-AAATTCT
* * *
12824 CAAAATTACC-CTTTTACCCTTGAATGTCT
1 AAAAATT-CCATTTTTACCCTTAAAT-TCT
12853 AAAAATTCCATTTTTA
1 AAAAATTCCATTTTTA
12869 ACTTCGAACT
Statistics
Matches: 150, Mismatches: 26, Indels: 30
0.73 0.13 0.15
Matches are distributed among these distances:
28 13 0.09
29 100 0.67
30 35 0.23
31 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCCTTAAATTCT
Found at i:24431 original size:205 final size:204
Alignment explanation
Indices: 24024--24643 Score: 778
Period size: 205 Copynumber: 3.0 Consensus size: 204
24014 CGAATCCTAG
* * * *
24024 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTAAGGCAGTCATCTTCCTGATGAGATAT
1 CTTCCTGATGAGATACAGAGAAGC-GATTGAAATAAGCAATGCAGTCATCTTCCTGATAAGATAT
* * * * *
24089 -AG-AGAAG---AATACCAACTCAGGGCTCAATGCGAACAAATCTTCGAACCCCAACTTCTTGAT
65 GAGAAGAAGACAAATACAAACCCA-CGCTCAATGTGAACAAATCTTCGAACCCCAACTTCCTGAT
*
24149 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAAAAGTGA
129 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGA
24214 ACCAAATTCGT
194 ACCAAATTCGT
* * *
24225 CTTCCTGATGAGATATAGAGAAGCAGATTGAAATAAGCAATGCAGTCACCTTCCCGATAAGATAC
1 CTTCCTGATGAGATACAGAGAAGC-GATTGAAATAAGCAATGCAGTCATCTTCCTGATAAGATA-
**
24290 TGAGAAGAAGACCAAATA-AAACCCACGCTCAATGTGAACAAATCTTCGAACCTTAACTTCCTGA
64 TGAGAAGAAGA-CAAATACAAACCCACGCTCAATGTGAACAAATCTTCGAACCCCAACTTCCTGA
* *
24354 TGAGATACTGAGAAGTAGGT-GAAGCAATAAAATGATTAGCTTCCTGATGAGATA-TCGAGAAGT
128 TGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACT-GAGAAGT
*
24417 GGACCAAATTCGT
192 GAACCAAATTCGT
* * * * *
24430 CTTCCTGATGAGATACAGAGAAGCGAATTGAAGTAAGCGATACGGTCATCTTCTTGATGAA-ATA
1 CTTCCTGATGAGATACAGAGAAGCG-ATTGAAATAAGCAATGCAGTCATCTTCCTGAT-AAGATA
* * * * * *
24494 TTGAGAAGAAGATCAAA-ACAAACCCACGCTCGACGTGAGCAAATCTTCGAACCCCAGCTTTCTA
64 -TGAGAAGAAGA-CAAATACAAACCCACGCTCAATGTGAACAAATCTTCGAACCCCAACTTCCTG
* *
24558 ATGAGATACTGAGAAGCAGGTCGAAGCAAT-AAATGGTTAGCTTCCTGTTGAAATACTGAGAAGT
127 ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGT
24622 GAACCAAA-TCTGT
192 GAACCAAATTC-GT
24635 CTTCCTGAT
1 CTTCCTGAT
24644 AAAACACAGA
Statistics
Matches: 363, Mismatches: 42, Indels: 24
0.85 0.10 0.06
Matches are distributed among these distances:
201 56 0.15
202 1 0.00
203 2 0.01
204 10 0.03
205 221 0.61
206 64 0.18
207 5 0.01
208 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (204 bp):
CTTCCTGATGAGATACAGAGAAGCGATTGAAATAAGCAATGCAGTCATCTTCCTGATAAGATATG
AGAAGAAGACAAATACAAACCCACGCTCAATGTGAACAAATCTTCGAACCCCAACTTCCTGATGA
GATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAAC
CAAATTCGT
Found at i:25110 original size:6 final size:6
Alignment explanation
Indices: 25099--25165 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
25089 CAAATGTATT
** * **
25099 TTTAAA TTTAAA TTTATCT TTTCAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
25147 TTT-AA TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
25166 GATTTAAAAC
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
5 7 0.15
6 36 0.78
7 3 0.07
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:25125 original size:19 final size:19
Alignment explanation
Indices: 25098--25150 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
25088 TCAAATGTAT
*
25098 TTTTAAATTTAAATTTATC
1 TTTTAAATTTAAATTTAGC
*
25117 TTTTCAATTTAAATTT-GC
1 TTTTAAATTTAAATTTAGC
25135 -TTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
25151 ATTAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTAAATTTAAATTTAGC
Found at i:25144 original size:17 final size:17
Alignment explanation
Indices: 25099--25165 Score: 80
Period size: 17 Copynumber: 3.8 Consensus size: 17
25089 CAAATGTATT
25099 TTTAAATTTAAATTTATC
1 TTTAAATTTAAATTTA-C
* *
25117 TTTTCAATTTAAATTTGC
1 -TTTAAATTTAAATTTAC
*
25135 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAC
*
25152 TTAAAATTTAAATT
1 TTTAAATTTAAATT
25166 GATTTAAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
17 27 0.64
18 1 0.02
19 14 0.33
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAC
Found at i:25172 original size:17 final size:17
Alignment explanation
Indices: 25122--25179 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
25112 TTATCTTTTC
*
25122 AATTTAAATTTGCTTT-A
1 AATTTAAA-TTGATTTAA
* *
25139 AATTTAAATTTAATTAA
1 AATTTAAATTGATTTAA
25156 AATTTAAATTGATTTAA
1 AATTTAAATTGATTTAA
*
25173 AACTTAA
1 AATTTAA
25180 TTAAATTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 4 0.12
17 30 0.88
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
AATTTAAATTGATTTAA
Found at i:25187 original size:33 final size:34
Alignment explanation
Indices: 25122--25190 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
25112 TTATCTTTTC
* * *
25122 AATTTAAATTTGCTTTAAATTTAAATTTAATTAA
1 AATTTAAATTTGATTTAAACTTAAATTAAATTAA
25156 AATTTAAA-TTGATTTAAAACTT-AATTAAATTAA
1 AATTTAAATTTGATTT-AAACTTAAATTAAATTAA
25189 AA
1 AA
25191 GTCCAAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (34 bp):
AATTTAAATTTGATTTAAACTTAAATTAAATTAA
Found at i:25188 original size:16 final size:17
Alignment explanation
Indices: 25142--25190 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
25132 TGCTTTAAAT
* *
25142 TTAAATTTAATTAAAAT
1 TTAAATTAAATTAAAAC
* *
25159 TTAAATTGATTTAAAAC
1 TTAAATTAAATTAAAAC
25176 TT-AATTAAATTAAAA
1 TTAAATTAAATTAAAA
25191 GTCCAAAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAATTAAATTAAAAC
Found at i:25560 original size:29 final size:28
Alignment explanation
Indices: 25527--25776 Score: 245
Period size: 30 Copynumber: 8.6 Consensus size: 28
25517 CCTAAACTCT
* *
25527 CAAAAATTCCATGTTTACCCCTAACTTC
1 CAAAAATTCCATTTTTACCCCAAACTTC
* *
25555 CAAAAATTTCATTTTTGACCCCAAAACTTT
1 CAAAAATTCCATTTTT-ACCCC-AAACTTC
25585 CAAAAATTCCATTTTTACCCCCAAACTTC
1 CAAAAATTCCATTTTTA-CCCCAAACTTC
25614 CAAAAATTCCA-TTTTACCCCCAAACTTC
1 CAAAAATTCCATTTTTA-CCCCAAACTTC
***
25642 CAAAAATTCCATTTTTGATCGTAAAACTTC
1 CAAAAATTCCATTTTT-A-CCCCAAACTTC
* *
25672 CAAAAATTCCATTTTTACCCTCGAACTTT
1 CAAAAATTCCATTTTTACCC-CAAACTTC
*
25701 CAAAAATTCCATTTTTGACCCTAAAACTTC
1 CAAAAATTCCATTTTT-ACCC-CAAACTTC
* **
25731 TAAAAATTACCATTTTGCCCCCAAA-TGTC
1 CAAAAATT-CCATTTTTACCCCAAACT-TC
*
25760 TAAAAACTT-CATTTTTA
1 CAAAAA-TTCCATTTTTA
25777 ACCTCAAAAC
Statistics
Matches: 188, Mismatches: 24, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
28 50 0.27
29 60 0.32
30 71 0.38
31 7 0.04
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (28 bp):
CAAAAATTCCATTTTTACCCCAAACTTC
Found at i:25635 original size:58 final size:58
Alignment explanation
Indices: 25520--25839 Score: 296
Period size: 59 Copynumber: 5.5 Consensus size: 58
25510 GGAGATCCCT
* * * * *
25520 AAACTCTCAAAAATTCCATGTTT-ACCCC-TAACTTCCAAAAATTTCATTTTTGACCCCA
1 AAACTTTCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCA-TTTT-ACCCCC
*
25578 AAACTTTCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTACCCCC
1 AAACTTTCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTACCCCC
* * ** *
25635 AAACTTCCAAAAATTCCATTTTTGATCGTAAAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTTCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCA-TTTTACCCCC
* * * *
25694 GAACTTTCAAAAATTCCATTTTTGACCCTAAAACTTCTAAAAATTACCATTTTGCCCCC
1 AAACTTTCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATT-CCATTTTACCCCC
* * * * *
25753 AAA-TGTCTAAAAACTT-CATTTTTAACCTCAAAAC-TCTC-AAAATTACCCTTTTACCCCT
1 AAACTTTC-AAAAA-TTCCATTTTTGACCCCAAAACTTC-CAAAAATT-CCATTTTACCCCC
* * *
25811 GAA-TGTTTAAAAATTCCATTTTTAACCCC
1 AAACT-TTCAAAAATTCCATTTTTGACCCC
25840 GAGCTTTCTA
Statistics
Matches: 222, Mismatches: 31, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
57 29 0.13
58 92 0.41
59 96 0.43
60 5 0.02
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTTCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTACCCCC
Found at i:25668 original size:87 final size:87
Alignment explanation
Indices: 25527--25755 Score: 291
Period size: 87 Copynumber: 2.6 Consensus size: 87
25517 CCTAAACTCT
* * *
25527 CAAAAATTCCATGTTTA-CCCCTAACTTCCAAAAATTTCATTTTTGACCCCAAAACTTTCAAAAA
1 CAAAAATTCCAT-TTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAA
25591 TTCCATTTTTACCCCCAAACTTC
65 TTCCATTTTTACCCCCAAACTTC
* **
25614 CAAAAATTCCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGATCGTAAAACTTCCAAAAAT
1 CAAAAATTCCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAT
* * *
25679 TCCATTTTTACCCTCGAACTTT
66 TCCATTTTTACCCCCAAACTTC
** * *
25701 CAAAAATTCCATTTTTGACCCTAAAACTTCTAAAAATTACCA-TTTTGCCCCCAAA
1 CAAAAATTCCA-TTTT-ACCCCCAAACTTCCAAAAATT-CCATTTTTGACCCCAAA
25756 TGTCTAAAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
86 4 0.03
87 84 0.69
88 4 0.03
89 27 0.22
90 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (87 bp):
CAAAAATTCCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAT
TCCATTTTTACCCCCAAACTTC
Found at i:25709 original size:59 final size:58
Alignment explanation
Indices: 25520--25838 Score: 275
Period size: 58 Copynumber: 5.5 Consensus size: 58
25510 GGAGATCCCT
* * *
25520 AAACTCTCAAAAATTCCATGTTT-ACCCCT--AACTTCCAAAAATTTCATTTTTGACCCC
1 AAACTTTCAAAAATTCCATTTTTGA-CCCTAAAACTTCCAAAAATTCCATTTTT-ACCCC
**
25577 AAAACTTTCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCA-TTTTACCCCC
1 -AAACTTTCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTA-CCCC
* * *
25635 AAACTTCCAAAAATTCCATTTTTGATCGTAAAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTTCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCC-C
* * **
25694 GAACTTTCAAAAATTCCATTTTTGACCCTAAAACTTCTAAAAATTACCATTTTGCCCCC
1 AAACTTTCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATT-CCATTTTTACCCC
* * *
25753 AAA-TGTCTAAAAACTT-CATTTTT-AACCTCAAAAC-TCTC-AAAATTACC-CTTTTACCCC
1 AAACTTTC-AAAAA-TTCCATTTTTGACCCT-AAAACTTC-CAAAAATT-CCATTTTTACCCC
* * *
25810 TGAA-TGTTTAAAAATTCCATTTTTAACCC
1 -AAACT-TTCAAAAATTCCATTTTTGACCC
25839 CGAGCTTTCT
Statistics
Matches: 219, Mismatches: 27, Indels: 29
0.80 0.10 0.11
Matches are distributed among these distances:
57 35 0.16
58 86 0.39
59 86 0.39
60 12 0.05
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTTCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCC
Found at i:25833 original size:29 final size:28
Alignment explanation
Indices: 25528--25834 Score: 144
Period size: 29 Copynumber: 10.6 Consensus size: 28
25518 CTAAACTCTC
* *
25528 AAAAATTCCATGTTTACCCCT-AA-CTTCC
1 AAAAATTCCATTTTTA-CCCTAAATCTT-T
* * *
25556 AAAAATTTCATTTTTGACCCCAAAACTTT
1 AAAAATTCCATTTTT-ACCCTAAATCTTT
* *
25585 CAAAAATTCCATTTTTACCCCCAAA-CTTCC
1 -AAAAATTCCATTTTTA-CCCTAAATCTT-T
* *
25615 AAAAATTCCA-TTTTACCCCCAAA-CTTCC
1 AAAAATTCCATTTTTA-CCCTAAATCTT-T
* * * *
25643 AAAAATTCCATTTTTGATCGTAAAACTTCC
1 AAAAATTCCATTTTT-ACCCTAAATCTT-T
*
25673 AAAAATTCCATTTTTACCCTCGAA-CTTT
1 AAAAATTCCATTTTTACCCT-AAATCTTT
*
25701 CAAAAATTCCATTTTTGACCCTAAAACTTCT
1 -AAAAATTCCATTTTT-ACCCTAAATCTT-T
** * * *
25732 AAAAATTACCATTTTGCCCCCAAATGTCT
1 AAAAATT-CCATTTTTACCCTAAATCTTT
* * *
25761 AAAAACTT-CATTTTTAACCTCAAAACTCT
1 AAAAA-TTCCATTTTTACCCT-AAATCTTT
* * * *
25790 CAAAATTACC-CTTTTACCCCTGAATGTTT
1 AAAAATT-CCATTTTTA-CCCTAAATCTTT
25819 AAAAATTCCATTTTTA
1 AAAAATTCCATTTTTA
25835 ACCCCGAGCT
Statistics
Matches: 223, Mismatches: 35, Indels: 41
0.75 0.12 0.14
Matches are distributed among these distances:
28 56 0.25
29 84 0.38
30 75 0.34
31 8 0.04
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCCTAAATCTTT
Found at i:28694 original size:36 final size:36
Alignment explanation
Indices: 28646--28715 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
28636 GGGNGGAGGG
* * *
28646 AACATGGGAATGACCCACGAACCAAAGCATAATGGA
1 AACATGGCAATGACCCACAAACCAAAACATAATGGA
*
28682 AACATGGCAATGACTCACAAACCAAAACATAATG
1 AACATGGCAATGACCCACAAACCAAAACATAATG
28716 TACGTTGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (36 bp):
AACATGGCAATGACCCACAAACCAAAACATAATGGA
Found at i:30965 original size:14 final size:15
Alignment explanation
Indices: 30940--30974 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
30930 TAATGTGTTC
30940 TAAAAT-ACATAATA
1 TAAAATAACATAATA
30954 -AAAATAACATAATA
1 TAAAATAACATAATA
30968 TAAAATA
1 TAAAATA
30975 TTATACACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 8 0.42
15 6 0.32
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAATAACATAATA
Found at i:31641 original size:436 final size:437
Alignment explanation
Indices: 30801--31668 Score: 958
Period size: 436 Copynumber: 2.0 Consensus size: 437
30791 TTTTTAATTT
30801 TTTAAAAATTAATTATTTTATTTTATTTTAATATTTAATAATTTTATACATTTTTTATATAATCA
1 TTTAAAAATTAATTATTTTATTTTATTTTAATATTTAATAATTTTATACATTTTTTATATAATCA
* **
30866 TCTTAACATTATTTTAATGTTTATATTAAACTAACATTATATATTTAATATAACTTTAATTTTTT
66 TCTTAAAATTATTTTAATGTTTATATTAAACTAACATTATATATTTAATATAAAATTAATTTTTT
* * * * **
30931 AATGTGTTCTAAAATACATAATAAAAATAACATAATATAAAATATTATACACTTAAAACAGCTTT
131 AATATCTTCTAAAATACATAATAAAAATAACATAATATAAAATATTATAAAATTAAAACAGAATT
*
30996 GGTCAGGTCAGGCTCGAGCCTTGAATGTTCAAACCCAAACCCGACTCATATTTTAAACGAACCTA
196 GG--AGGTCA-G--CGAGCCTTGAATGTCCAAACCCAAACCCGACTCATATTTTAAACGAACCTA
* * **
31061 ATTTTTTTTTGCCGAAGCCTATTTTTCGAGCTTAATATTTTTGCCCAAACTCTCTTAAATTTCAA
256 ATTTTTTTTGGCCAAAGCCTATTTTTAAAGCTTAATATTTTTGCCCAAACTCTCTTAAATTTCAA
* * * *
31126 ACGGACCTTCGAACCTGAGCAGGTAGCCCGTCCCATGAATAGGTCTACACATTACCAAAACATAG
321 ACGGACCTTCGAACCTGAGCAGATAACCCGACCCATGAATAGGTCTACAAATTACCAAAACATAG
* * **
31191 ATAAATATAAATATTATTT-TTAAAAAAATTAAATGTATGAAGTAATATTCA
386 ATAAAGAGAAATATTATTTAAAAAAAAAATTAAATGTATGAAGTAATATTCA
* * * *
31242 TTTAGAAATTAATTATTTTATTTTATTTTAATATTTAATAGTTTTATACATTTTTTATGTAGTCA
1 TTTAAAAATTAATTATTTTATTTTATTTTAATATTTAATAATTTTATACATTTTTTATATAATCA
** * *
31307 TCTTAAAATTATTTTAATGTTTATATTAGAA-TAGTATTATATATTTAGTATAAAATTATTATTT
66 TCTTAAAATTATTTTAATGTTTATATTA-AACTAACATTATATATTTAATATAAAATTAAT-TTT
* * * * *
31371 TTAGTATACTT-TAAATTATATAGTACATGAAAAATAATATAATATAGAGTATTATAAAATTAAA
129 TTAATAT-CTTCTAAA--ATACA-TA-AT-AAAAATAACATAATATAAAATATTATAAAATTAAA
* * * *** * **
31435 A-TGAATT-G-GGTC-G-GA-CCTTGAATGTCCAAGA-TCGAATTTGACTCATATTTTAAATGGG
188 ACAGAATTGGAGGTCAGCGAGCCTTGAATGTCCAA-ACCCAAACCCGACTCATATTTTAAACGAA
* ** * *
31493 CTTAATTTTTTTTGGTTAAAGTCC-ATTTTTAAAGCTTAATATTTTTGGCTAAA-TC-CTGTCAA
252 CCTAATTTTTTTTGGCCAAAG-CCTATTTTTAAAGCTTAATATTTTTGCCCAAACTCTCT-T-AA
* * * *
31555 ATTTCAAAC-GAGCCTTC-AAGCTTGAGC-GAATAATCCGACCCATGGATAGGTTTACAAATTAC
314 ATTTCAAACGGA-CCTTCGAA-CCTGAGCAG-ATAACCCGACCCATGAATAGGTCTACAAATTAC
*
31617 CAAAACATATATAAAGAGAAATATTATTTAAAAAAAAAATTAAATGTATGAA
376 CAAAACATAGATAAAGAGAAATATTATTTAAAAAAAAAATTAAATGTATGAA
31669 CCAATATTTG
Statistics
Matches: 357, Mismatches: 54, Indels: 36
0.80 0.12 0.08
Matches are distributed among these distances:
434 2 0.01
435 8 0.02
436 147 0.41
437 25 0.07
440 1 0.00
441 111 0.31
442 18 0.05
443 2 0.01
444 4 0.01
445 3 0.01
446 5 0.01
447 31 0.09
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (437 bp):
TTTAAAAATTAATTATTTTATTTTATTTTAATATTTAATAATTTTATACATTTTTTATATAATCA
TCTTAAAATTATTTTAATGTTTATATTAAACTAACATTATATATTTAATATAAAATTAATTTTTT
AATATCTTCTAAAATACATAATAAAAATAACATAATATAAAATATTATAAAATTAAAACAGAATT
GGAGGTCAGCGAGCCTTGAATGTCCAAACCCAAACCCGACTCATATTTTAAACGAACCTAATTTT
TTTTGGCCAAAGCCTATTTTTAAAGCTTAATATTTTTGCCCAAACTCTCTTAAATTTCAAACGGA
CCTTCGAACCTGAGCAGATAACCCGACCCATGAATAGGTCTACAAATTACCAAAACATAGATAAA
GAGAAATATTATTTAAAAAAAAAATTAAATGTATGAAGTAATATTCA
Done.