Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013714.1 Kokia drynarioides strain JFW-HI SEQ_128742, 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: 54357
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:1415 original size:32 final size:31
Alignment explanation
Indices: 1363--1424 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
1353 TGAAATTCAA
1363 AAATTGATATAAACTTTAAACT-TCAAATTTG
1 AAATTGATATAAACTTTAAACTCT-AAATTTG
*
1394 AAATTCGATTTAAA-TTCTAAACTCTAAATTT
1 AAATT-GATATAAACTT-TAAACTCTAAATTT
1425 TTAGACTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 7 0.26
32 19 0.70
33 1 0.04
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (31 bp):
AAATTGATATAAACTTTAAACTCTAAATTTG
Found at i:3128 original size:17 final size:17
Alignment explanation
Indices: 3106--3153 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
3096 TAAGATTGAG
3106 TTAAGAAAATT-ATTTAA
1 TTAAG-AAATTAATTTAA
*
3123 TTAAGAAATTAATTTAG
1 TTAAGAAATTAATTTAA
**
3140 TTAATTAATTAATT
1 TTAAGAAATTAATT
3154 ATATTTTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TTAAGAAATTAATTTAA
Found at i:3153 original size:21 final size:22
Alignment explanation
Indices: 3119--3159 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3109 AGAAAATTAT
3119 TTAATTAAGAAATTA-ATTTAG
1 TTAATTAAGAAATTATATTTAG
**
3140 TTAATTAATTAATTATATTT
1 TTAATTAAGAAATTATATTT
3160 TGGATAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTAATTAAGAAATTATATTTAG
Found at i:3194 original size:16 final size:18
Alignment explanation
Indices: 3173--3211 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3163 ATAAGAGAAA
3173 ATAAAT-AT-AGGGTTGG
1 ATAAATCATAAGGGTTGG
*
3189 ATAAATCATAAGTGTTGG
1 ATAAATCATAAGGGTTGG
3207 ATAAA
1 ATAAA
3212 AACCAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.31
Consensus pattern (18 bp):
ATAAATCATAAGGGTTGG
Found at i:4645 original size:21 final size:21
Alignment explanation
Indices: 4613--4661 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4603 CAGTAACAGT
* *
4613 CTTCTA-TCGATACTAGTGATA
1 CTTCTACT-GATACAAGTGACA
*
4634 GTTCTACTGATACAAGTGACA
1 CTTCTACTGATACAAGTGACA
4655 CTTCTAC
1 CTTCTAC
4662 CGAAATAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (21 bp):
CTTCTACTGATACAAGTGACA
Found at i:8105 original size:26 final size:23
Alignment explanation
Indices: 8076--8136 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 23
8066 AGCACGAATT
8076 GTGCTCTCCGATTATTAGCA-TGTAAA
1 GTGCTCTCCG--T-TTAGCACT-TAAA
*
8102 GTGCTCTCCGTTTAGCACTTATA
1 GTGCTCTCCGTTTAGCACTTAAA
8125 GTGCTCTCCGTT
1 GTGCTCTCCGTT
8137 CATTTATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 21 0.64
24 2 0.06
26 10 0.30
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.38
Consensus pattern (23 bp):
GTGCTCTCCGTTTAGCACTTAAA
Found at i:14515 original size:23 final size:23
Alignment explanation
Indices: 14451--14543 Score: 80
Period size: 23 Copynumber: 4.0 Consensus size: 23
14441 TCTCCGTTAT
* *
14451 TTTAGCACGAATTGTGCTCTCCGA
1 TTTAGCACGTATAGTGCTCTCC-A
* *
14475 TTATTGGCACGTAAAGTGCTCTCCA
1 -T-TTAGCACGTATAGTGCTCTCCA
*
14500 TTTAGCACGTATAGTGCTCTCCG
1 TTTAGCACGTATAGTGCTCTCCA
* * *
14523 TTTAACACCT-TTGTGCTCTCC
1 TTTAGCACGTATAGTGCTCTCC
14544 GTTTCTTAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
22 10 0.18
23 27 0.47
24 1 0.02
25 2 0.04
26 17 0.30
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.35
Consensus pattern (23 bp):
TTTAGCACGTATAGTGCTCTCCA
Found at i:30392 original size:23 final size:23
Alignment explanation
Indices: 30361--30533 Score: 165
Period size: 23 Copynumber: 7.4 Consensus size: 23
30351 ATCACGTCTC
*
30361 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTTTGT
30386 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
30409 GTGCTCTCTGATTAACACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
30432 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * * * *
30455 GTACTCTCTGTTTTGCACTGTAT
1 GTGCTCTCTGATTAGCACTTTGT
*
30478 GTGCTCTCTG-TTGCCCAGCAC-TTAT
1 GTGCTCTCTGATT----AGCACTTTGT
*
30503 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
30524 GTACTCTCTG
1 GTGCTCTCTG
30534 TTTGTTCCGT
Statistics
Matches: 127, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
21 13 0.10
22 4 0.03
23 81 0.64
25 25 0.20
26 4 0.03
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:30481 original size:69 final size:68
Alignment explanation
Indices: 30361--30536 Score: 187
Period size: 69 Copynumber: 2.5 Consensus size: 68
30351 ATCACGTCTC
* * * * * *
30361 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATT-AAC
1 GTGCTCTCTG--ATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTATGTGCTCTCTG-TTCAAC
*
30425 ACTTTGT
63 AC-TTAT
* *
30432 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTTGCACTGTATGTGCTCTCTGTTGCCCAGC
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTATGTGCTCTCTGTT---CAAC
30497 ACTTAT
63 ACTTAT
30503 GTGCTCTCTG-TTAGTACTTTG-GTACTCTCTGTTT
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTT
30537 GTTCCGTATA
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
68 2 0.02
69 52 0.57
70 11 0.12
71 23 0.25
72 4 0.04
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (68 bp):
GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTATGTGCTCTCTGTTCAACACT
TAT
Found at i:32237 original size:16 final size:16
Alignment explanation
Indices: 32216--32246 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32206 CTATTTCTTA
*
32216 ATAAATGTTTTGTTTT
1 ATAAATGTTATGTTTT
32232 ATAAATGTTATGTTT
1 ATAAATGTTATGTTT
32247 ACTTATTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (16 bp):
ATAAATGTTATGTTTT
Found at i:34142 original size:3 final size:3
Alignment explanation
Indices: 34134--34162 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34124 ATGGCAGCAA
34134 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
34163 ATTAATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:38152 original size:31 final size:29
Alignment explanation
Indices: 37926--38164 Score: 139
Period size: 29 Copynumber: 8.1 Consensus size: 29
37916 CCGAGGGTAG
* * *
37926 AATGGTAATTTTGGGAAATTTTAGGGTTAAA
1 AATGG-AATTTTTGGAAGTTTTGGGGTT-AA
* * *
37957 AATGGAATTTTTAG-A-TATTCGGGGGTAA
1 AATGGAATTTTTGGAAGT-TTTGGGGTTAA
* ** * *
37985 AAGGGAAAATTT-GAGAGTTTTGAGGTCGAA
1 AATGGAATTTTTGGA-AGTTTTGGGGT-TAA
* *
38015 AATGGAGA-TTTTGGAAG-TTCGAGGGTAAA
1 AATGGA-ATTTTTGGAAGTTTTG-GGGTTAA
*** *
38044 AATGGAATTTTTGGAAGTTTCAAGGTCAA
1 AATGGAATTTTTGGAAGTTTTGGGGTTAA
* *
38073 AATGGCATTTTTGGAA-ATTTGGGGTTTAA
1 AATGGAATTTTTGGAAGTTTTGGGG-TTAA
38102 AATGGAATTTTTGGAAGTTTTGGGGTTAA
1 AATGGAATTTTTGGAAGTTTTGGGGTTAA
* * * *
38131 TAATGGGATTTTTTGAGAGTTTGGGGGTAAA
1 -AATGGAATTTTTGGA-AGTTTTGGGGTTAA
38162 AAT
1 AAT
38165 ATTTCGGGGT
Statistics
Matches: 162, Mismatches: 32, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.01
28 17 0.10
29 75 0.46
30 49 0.30
31 20 0.12
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.36
Consensus pattern (29 bp):
AATGGAATTTTTGGAAGTTTTGGGGTTAA
Found at i:38237 original size:30 final size:30
Alignment explanation
Indices: 38166--38339 Score: 194
Period size: 30 Copynumber: 5.9 Consensus size: 30
38156 GGTAAAAATA
*
38166 TTTCGGGGTTAAAAATGAGATTTTTGGAAG
1 TTTCGGGGGTAAAAATGAGATTTTTGGAAG
*
38196 -TTCGAGGGTAAAAATGAGATTTTTGGAAG
1 TTTCGGGGGTAAAAATGAGATTTTTGGAAG
* * *
38225 TTTGGGGGGTAAAATTGGGATTTTTGGAAG
1 TTTCGGGGGTAAAAATGAGATTTTTGGAAG
* * *
38255 TTTTGGGGTTAAAAATGGGATTTTTGGAA-
1 TTTCGGGGGTAAAAATGAGATTTTTGGAAG
** *
38284 TTTTTGGGGTCAAAAATGGGATTTTTGGAAG
1 TTTCGGGGGT-AAAAATGAGATTTTTGGAAG
*
38315 -TTCGAGGGTAAAAAT-AGAATTTTTG
1 TTTCGGGGGTAAAAATGAG-ATTTTTG
38340 AAAAGTTTAG
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
28 1 0.01
29 48 0.38
30 76 0.61
ACGTcount: A:0.29, C:0.02, G:0.32, T:0.37
Consensus pattern (30 bp):
TTTCGGGGGTAAAAATGAGATTTTTGGAAG
Found at i:38278 original size:60 final size:59
Alignment explanation
Indices: 38165--38339 Score: 214
Period size: 59 Copynumber: 3.0 Consensus size: 59
38155 GGGTAAAAAT
* * *
38165 ATTTCGGGGTTAAAAATGAGATTTTTGGAAG-TTCGAGGGTAAAAATGAGATTTTTGGA
1 ATTTGGGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGGTAAAAATGAGATTTTTGGA
* * *
38223 AGTTTGGGGGGTAAAATTGGGATTTTTGGAAGTTTTG-GGGTTAAAAATGGGATTTTTGGA
1 A-TTTGGGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGG-TAAAAATGAGATTTTTGGA
**
38283 ATTTTTGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGGTAAAAAT-AGAATTTTTG
1 ATTTGGGGGGT-AAAAATGGGATTTTTGGAAGTTTCGAGGGTAAAAATGAG-ATTTTTG
38340 AAAAGTTTAG
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
58 2 0.02
59 54 0.54
60 44 0.44
ACGTcount: A:0.30, C:0.02, G:0.31, T:0.37
Consensus pattern (59 bp):
ATTTGGGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGGTAAAAATGAGATTTTTGGA
Found at i:38293 original size:135 final size:136
Alignment explanation
Indices: 38032--38300 Score: 361
Period size: 135 Copynumber: 2.0 Consensus size: 136
38022 ATTTTGGAAG
*
38032 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCAAAATGGCATTTTTGGAAATTTGGGG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTAAAAATGGCATTTTTGGAAATTTGGGG
** * *
38097 TTTAAAATGGAATTTTTGGAAGTTTTGGGGTTAATAATGGGATTTTTTGAGAGTTTGGGGGT-AA
66 GGTAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAGAGTTTGGGGGTCAA
38161 AAATAT
131 AAATAT
* *
38167 TTCG-GGGTTAAAAAT-GAGATTTTTGGAAG-TTCGAGGGTAAAAATGAG-ATTTTTGGAAGTTT
1 TTCGAGGG-TAAAAATGGA-ATTTTTGGAAGTTTC-AAGGTAAAAATG-GCATTTTTGGAAATTT
* * *
38228 GGGGGGTAAAATTGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGA-ATTTTTGGG
62 GGGGGGTAAAA-TGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAGAGTTTGGGG
38292 GTCAAAAAT
126 GTCAAAAAT
38301 GGGATTTTTG
Statistics
Matches: 118, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
134 8 0.07
135 63 0.53
136 47 0.40
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37
Consensus pattern (136 bp):
TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTAAAAATGGCATTTTTGGAAATTTGGGG
GGTAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAGAGTTTGGGGGTCAA
AAATAT
Found at i:39366 original size:9 final size:9
Alignment explanation
Indices: 39347--39406 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
39337 CTTTTTTATT
39347 TATTAATTAA
1 TATT-ATTAA
39357 TATTATTAA
1 TATTATTAA
39366 TATTATTAA
1 TATTATTAA
* **
39375 T-GTAAAAA
1 TATTATTAA
* *
39383 CAGTTATTAT
1 TA-TTATTAA
39393 TATTATTAA
1 TATTATTAA
39402 TATTA
1 TATTA
39407 ATTATGGTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
8 4 0.11
9 26 0.68
10 8 0.21
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (9 bp):
TATTATTAA
Found at i:40126 original size:17 final size:17
Alignment explanation
Indices: 40111--40206 Score: 84
Period size: 17 Copynumber: 5.5 Consensus size: 17
40101 TTAAAATTTT
40111 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
40129 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** **
40146 ACTCCAAATAAGCTTAA
1 ATTTAAAATAAATTTAA
* *
40163 ATTTACAATAAATTTGA
1 ATTTAAAATAAATTTAA
* * *
40180 ACTTAAAATGAATTAAAA
1 ATTTAAAATAAATT-TAA
40198 ATTTAAAAT
1 ATTTAAAAT
40207 CTAAAATTGG
Statistics
Matches: 59, Mismatches: 18, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
17 46 0.78
18 13 0.22
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.35
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:40155 original size:34 final size:34
Alignment explanation
Indices: 40114--40206 Score: 105
Period size: 34 Copynumber: 2.7 Consensus size: 34
40104 AAATTTTATT
40114 TCAAAATAAATTTAAATTTAAAATAAATTTAAAC
1 TCAAAATAAATTTAAATTTAAAATAAATTTAAAC
* ** * *
40148 TCCAAATAAGCTTAAATTTACAATAAATTTGAAC
1 TCAAAATAAATTTAAATTTAAAATAAATTTAAAC
* * *
40182 TTAAAATGAATTAAAAATTTAAAAT
1 TCAAAATAAATT-TAAATTTAAAAT
40207 CTAAAATTGG
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
34 36 0.78
35 10 0.22
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (34 bp):
TCAAAATAAATTTAAATTTAAAATAAATTTAAAC
Found at i:40877 original size:59 final size:59
Alignment explanation
Indices: 40785--40904 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
40775 GTTTGTTTCA
40785 ATTCGCTTCTCTGTACATCGTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATC
1 ATTCGCTTCTCTGTACATCGTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATC
40844 ATTCGCTTCTCTGTACATCGTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATC
1 ATTCGCTTCTCTGTACATCGTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATC
40903 AT
1 AT
40905 GAAGCTAACC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (59 bp):
ATTCGCTTCTCTGTACATCGTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATC
Found at i:41094 original size:253 final size:256
Alignment explanation
Indices: 40589--41097 Score: 677
Period size: 253 Copynumber: 2.0 Consensus size: 256
40579 GTTCAATCCA
* * *
40589 CTTCTCTGTACCTCCTCAAGAAGACAAATTTGGTCTACTTCTCAGTATTTCATCAGGAAGCTAAC
1 CTTCTCTGTACATCCTCAAGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
*
40654 CATTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCA
66 CATTTTATTGCTTCAACCTACTTCTCAATATCTCATCAGGAAGCTGGGATTCGAAGATTTGCT--
* * ** **
40719 CATCGGGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAAGTAGATAACCGTCCTGTTTGTTTC
129 -ATC-GGCACTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATAACCACCCCATTTGTTTC
* * *
40784 AATTCGCTTCTCTGTACATCGTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCATTCG
192 AATCCGCTTCTCTGTACATCATCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCATTCG
* * * * *
40849 CTTCTCTGTACATCGTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCATGAAGCTAAC
1 CTTCTCTGTACATCCTCAAGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
* * * * *
40914 CTTTTTATTGGTTC-GCCTTACTTCTCAGTATCTCATTAGGAAGCTAGGG-TTCGAAGATTTG-T
66 CATTTTATTGCTTCAACC-TACTTCTCAATATCTCATCAGGAAGCT-GGGATTCGAAGATTTGCT
* * * *
40976 -TC-GCATTGAGTTGGTATACTTCTTTGTATCTCATCAGGAAGATAATCACCCCATTTGTTTCAA
129 ATCGGCACTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATAACCACCCCATTTGTTTCAA
*
41039 TCCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCA
194 TCCGCTTCTCTGTACATCATCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCA
41098 AGAAGCTACC
Statistics
Matches: 219, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
253 106 0.48
255 2 0.01
259 3 0.01
260 105 0.48
261 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.35
Consensus pattern (256 bp):
CTTCTCTGTACATCCTCAAGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
CATTTTATTGCTTCAACCTACTTCTCAATATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTAT
CGGCACTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATAACCACCCCATTTGTTTCAATC
CGCTTCTCTGTACATCATCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCATTCG
Found at i:42013 original size:42 final size:43
Alignment explanation
Indices: 41918--42024 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 43
41908 GAACCTGAGC
* * *
41918 CGCCCTTTACGAGTTTTCAACCTAAAGTTTCCTTGATTTCAGGA
1 CGCCCTTTGCGAGTTTTCATCCTAAACTTT-CTTGATTTCAGGA
* ** *
41962 CGCCCTTTGCGAGTTTTCATCCTGAACTTT-TTTTTTTCGGGA
1 CGCCCTTTGCGAGTTTTCATCCTAAACTTTCTTGATTTCAGGA
*
42004 CGCCCTTTGCGGGTTTTCATC
1 CGCCCTTTGCGAGTTTTCATC
42025 TCAATTCCCC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 29 0.53
44 26 0.47
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (43 bp):
CGCCCTTTGCGAGTTTTCATCCTAAACTTTCTTGATTTCAGGA
Found at i:52485 original size:96 final size:96
Alignment explanation
Indices: 52301--52492 Score: 241
Period size: 96 Copynumber: 2.0 Consensus size: 96
52291 TTTTTGTGAA
** *
52301 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAAGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAATATTTCA
*
52366 GAATCGAAGATAAGGAATCATTGCCTCGATT
66 GAATCGAAGATAAAGAATCATTGCCTCGATT
* * *
52397 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTT-AAGACACAA-ATTTT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAG-CACAATA-TTT
52460 C-GAAACTCGAA-ATAAAAGAAT-ATTGCCTCGATT
64 CAG-AA-TCGAAGAT-AAAGAATCATTGCCTCGATT
52493 TTAAAGCTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
95 5 0.06
96 68 0.81
97 11 0.13
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAATATTTCA
GAATCGAAGATAAAGAATCATTGCCTCGATT
Found at i:52879 original size:30 final size:29
Alignment explanation
Indices: 52759--52927 Score: 134
Period size: 29 Copynumber: 5.8 Consensus size: 29
52749 TTTGGGGTTC
*
52759 AAAAATGGAATTTTTTGACA--TTCGAGTGT
1 AAAAATGGAATTTTTGGA-AGTTTCGAGT-T
* * *
52788 -AAAAGGGAAATTAT-GAGAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGA-AGTTTCGA-GTT
* **
52817 GAAAATGGAGATTTTT-GAAG-TTCGAGGGC
1 AAAAATGGA-ATTTTTGGAAGTTTCGA-GTT
52846 AAAAATGGAATTTTTGGAAGTTTCGAGTT
1 AAAAATGGAATTTTTGGAAGTTTCGAGTT
* * * *
52875 CAAAAATGGCATTTTTGGAAGTTTAGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGAGTT
52905 AAAAATGGAATTTTTGGAAGTTT
1 AAAAATGGAATTTTTGGAAGTTT
52928 TGGGGTTAAT
Statistics
Matches: 115, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
27 3 0.03
28 17 0.15
29 48 0.42
30 41 0.36
31 6 0.05
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGTT
Found at i:52881 original size:59 final size:58
Alignment explanation
Indices: 52730--53321 Score: 413
Period size: 59 Copynumber: 10.2 Consensus size: 58
52720 CCGGGGGTAG
* * * * * *
52730 AATGGTAATTTTGGGAAAATTTGGGGTTCAAAAATGGAATTTTTTGACA-TTCGAGTGT-AA
1 AATGG-AATTTTTGG-AAGTTTCGGGTT-AAAAATGGGATTTTTGGA-AGTTCGAGGGTAAA
* * * * *
52790 AAGGGAAATTAT-GAGAGTTTCGAGGTTGAAAATGGAGATTTTT-GAAGTTCGAGGGCAAA
1 AATGGAATTTTTGGA-AGTTTCG-GGTTAAAAATGG-GATTTTTGGAAGTTCGAGGGTAAA
* * *
52849 AATGGAATTTTTGGAAGTTTCGAGTTCAAAAATGGCATTTTTGGAAGTT-TAGGGGTAAA
1 AATGGAATTTTTGGAAGTTTCGGGTT-AAAAATGGGATTTTTGGAAGTTCGA-GGGTAAA
* * * * *
52908 AATGGAATTTTTGGAAGTTTTGGGGTTAATAATGGGATTTTATAG-AGTTTGATGGTAAA
1 AATGGAATTTTTGGAAG-TTTCGGGTTAAAAATGGGATTTT-TGGAAGTTCGAGGGTAAA
*
52967 AA---CA-TTTT----G----GGGTTAAAAATGGGATTTTTGGAAGTTC-AGGGGTAAA
1 AATGGAATTTTTGGAAGTTTCGGGTTAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAA
* * * * * *
53013 AATAGAATTTTTCGAAGTTTCGAGGCTAAAAATAGGATTTTTGGAAGTTCAGGGGGTAGA
1 AATGGAATTTTTGGAAGTTTCG-GGTTAAAAATGGGATTTTTGGAAGTTC-GAGGGTAAA
* * * *
53073 AATAGG-ATTTTTAGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTATG-GGGTCAAA
1 AAT-GGAATTTTTGGAAGTTTCG-GGTTAAAAATGGGATTTTTGGAAGTT-CGAGGGT-AAA
* * **
53132 AATGGAATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTTAAA
1 AATGGAATTTTTGGAAGTTTCG-GGTTAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAA
* * *** *
53191 AATGGGA-TTTTGGAAGTTATGGGGTTAAAAATGGGATTTTTGGAAGTTTTTGGGTTTAA
1 AATGGAATTTTTGGAAGTT-TCGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAA
* * *
53250 AATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTAGAAGTTCGAGGGTTAA
1 AATGGAATTTTTGGAAGTTTCG-GGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAA
*
53309 AACGGAATTTTTG
1 AATGGAATTTTTG
53322 AAAGGTTTAG
Statistics
Matches: 436, Mismatches: 57, Indels: 79
0.76 0.10 0.14
Matches are distributed among these distances:
45 3 0.01
46 30 0.07
49 1 0.00
50 4 0.01
51 1 0.00
54 1 0.00
55 4 0.01
56 1 0.00
57 2 0.00
58 49 0.11
59 262 0.60
60 77 0.18
61 1 0.00
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (58 bp):
AATGGAATTTTTGGAAGTTTCGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAA
Found at i:52927 original size:29 final size:29
Alignment explanation
Indices: 52818--52948 Score: 140
Period size: 30 Copynumber: 4.4 Consensus size: 29
52808 TTCGAGGTTG
*
52818 AAAATGGAGATTTTT-GAAG-TTCGAGGGCA
1 AAAATGGA-ATTTTTGGAAGTTTCG-GGGTA
* *
52847 AAAATGGAATTTTTGGAAGTTTCGAGTTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
* *
52877 AAAATGGCATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
*
52906 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
* *
52936 ATAATGGGATTTT
1 AAAATGGAATTTT
52949 ATAGAGTTTG
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.07
29 39 0.45
30 42 0.48
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:52948 original size:30 final size:30
Alignment explanation
Indices: 52813--52948 Score: 129
Period size: 29 Copynumber: 4.6 Consensus size: 30
52803 AGAGTTTCGA
* *
52813 GGTTGAAAATGGAGATTTTT-GAAG-TTCGAG
1 GGTTAAAAATGGA-ATTTTTGGAAGTTTTG-G
* *
52843 GG-CAAAAATGGAATTTTTGGAAG-TTTCG
1 GGTTAAAAATGGAATTTTTGGAAGTTTTGG
* * *
52871 AGTTCAAAAATGGCATTTTTGGAAGTTTAGG
1 GGTT-AAAAATGGAATTTTTGGAAGTTTTGG
52902 GG-TAAAAATGGAATTTTTGGAAGTTTTGG
1 GGTTAAAAATGGAATTTTTGGAAGTTTTGG
* *
52931 GGTTAATAATGGGATTTT
1 GGTTAAAAATGGAATTTT
52949 ATAGAGTTTG
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
28 8 0.09
29 40 0.46
30 35 0.40
31 4 0.05
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (30 bp):
GGTTAAAAATGGAATTTTTGGAAGTTTTGG
Found at i:53045 original size:30 final size:30
Alignment explanation
Indices: 52980--53321 Score: 332
Period size: 30 Copynumber: 11.6 Consensus size: 30
52970 ATTTTGGGGT
52980 TAAAAATGGGATTTTTGGAAG-TTC-AGGGG
1 TAAAAATGGGATTTTTGGAAGTTTCGA-GGG
* * * *
53009 TAAAAATAGAATTTTTCGAAGTTTCGAGGC
1 TAAAAATGGGATTTTTGGAAGTTTCGAGGG
* *
53039 TAAAAATAGGATTTTTGGAAG-TTCAGGGGG
1 TAAAAATGGGATTTTTGGAAGTTTC-GAGGG
* * *
53069 TAGAAATAGGATTTTTAGAAG-TTCGAGGG
1 TAAAAATGGGATTTTTGGAAGTTTCGAGGG
*
53098 TAAAAATGGAATTTTTGGAAGTTAT-G-GGG
1 TAAAAATGGGATTTTTGGAAGTT-TCGAGGG
*
53127 TCAAAAATGGAATTTTTGGAAG-TTCGAGGG
1 T-AAAAATGGGATTTTTGGAAGTTTCGAGGG
* *
53157 TAAAAATGGAATTTTTGGAAGTTT-TAGGG
1 TAAAAATGGGATTTTTGGAAGTTTCGAGGG
53186 TTAAAAATGGGA-TTTTGGAAGTTAT-G-GGG
1 -TAAAAATGGGATTTTTGGAAGTT-TCGAGGG
* *
53215 TTAAAAATGGGATTTTTGGAAGTTTTTG-GGT
1 -TAAAAATGGGATTTTTGGAAG-TTTCGAGGG
* *
53246 TTAAAATGGGATTTTTGGAAGTTTCGAGGT
1 TAAAAATGGGATTTTTGGAAGTTTCGAGGG
*
53276 TAAAAATGGGATTTTTAGAAG-TTCGAGGG
1 TAAAAATGGGATTTTTGGAAGTTTCGAGGG
* * *
53305 TTAAAACGGAATTTTTG
1 TAAAAATGGGATTTTTG
53322 AAAGGTTTAG
Statistics
Matches: 270, Mismatches: 28, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.00
29 122 0.45
30 140 0.52
31 7 0.03
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (30 bp):
TAAAAATGGGATTTTTGGAAGTTTCGAGGG
Found at i:53142 original size:89 final size:86
Alignment explanation
Indices: 52982--53298 Score: 336
Period size: 89 Copynumber: 3.6 Consensus size: 86
52972 TTTGGGGTTA
* * *
52982 AAAATGGGATTTTTGGAAGTTC-AGGGGTAAAAATAGAATTTTTCGAAGTT-TCGAGG-CTAAAA
1 AAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTGGAAGTTAT-GGGGTC-AAAA
53044 ATAGGATTTTTGGAAGTTCAGGGGGT
63 AT-GGATTTTTGGAAGTTC-GGGGGT
* *
53070 AGAAATAGGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTATGGGGTCAAAAAT
1 A-AAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTATGGGGTCAAAAAT
*
53135 GGAATTTTTGGAAGTTCGAGGGT
65 GG-ATTTTTGGAAGTTCGGGGGT
* ** * *
53158 AAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAAATGGGA-TTTTGGAAGTTATGGGGTTAAAAA
1 -AAAATGGGATTTTTGGAAGTTCGAGGG-TAAAAATGGAATTTTTGGAAGTTATGGGGTCAAAAA
* **
53222 TGGGATTTTTGGAAGTTTTTGGGTTT
64 T-GGATTTTTGGAAG--TTCGGGGGT
* * *
53248 AAAATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTAGAAGTT
1 AAAATGGGATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTT
53299 CGAGGGTTAA
Statistics
Matches: 195, Mismatches: 22, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
88 64 0.33
89 108 0.55
90 23 0.12
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (86 bp):
AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTATGGGGTCAAAAATG
GATTTTTGGAAGTTCGGGGGT
Done.