Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011854.1 Kokia drynarioides strain JFW-HI SEQ_126850, 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: 18487
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Found at i:998 original size:28 final size:29
Alignment explanation
Indices: 945--1008 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 29
935 TCAAACACTG
*
945 TAATTTTTGGATGTTCGGGGGTAAAATGA
1 TAATTTTTGGATGTTCGGGGGCAAAATGA
*
974 TAATTTTTGGATGTTC-GGGGCAAAATTA
1 TAATTTTTGGATGTTCGGGGGCAAAATGA
1002 TAATTTT
1 TAATTTT
1009 GGAGAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (29 bp):
TAATTTTTGGATGTTCGGGGGCAAAATGA
Found at i:1038 original size:30 final size:30
Alignment explanation
Indices: 1002--1185 Score: 196
Period size: 30 Copynumber: 6.2 Consensus size: 30
992 GGCAAAATTA
*
1002 TAATTTTGGAGAAGTTTGAGGGTCAAAATG
1 TAATTTTGGAAAAGTTTGAGGGTCAAAATG
*
1032 TAATTTTGGAAAAGTTT-AGGGGTTAAAATG
1 TAATTTTGGAAAAGTTTGA-GGGTCAAAATG
*
1062 TAATTTTGGAAAAGTTTAAGGGTCAAAATG
1 TAATTTTGGAAAAGTTTGAGGGTCAAAATG
* * *
1092 TAATTTTGGATAAGTTTG-GGGCCAAAATT
1 TAATTTTGGAAAAGTTTGAGGGTCAAAATG
* * *
1121 TAATTTTGGAGAA-TTTTAGGAT-AAAATG
1 TAATTTTGGAAAAGTTTGAGGGTCAAAATG
* * ** *
1149 TAATTTTAGAAAAATTCAAGGGTTAAAATG
1 TAATTTTGGAAAAGTTTGAGGGTCAAAATG
*
1179 TGATTTT
1 TAATTTT
1186 TAAAGAAAAG
Statistics
Matches: 131, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
28 19 0.15
29 30 0.23
30 81 0.62
31 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTGAGGGTCAAAATG
Found at i:1068 original size:60 final size:60
Alignment explanation
Indices: 1002--1185 Score: 230
Period size: 60 Copynumber: 3.1 Consensus size: 60
992 GGCAAAATTA
*
1002 TAATTTTGGAGAAGTTTGAGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATG
1 TAATTTTGGAGAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATG
* * ** *
1062 TAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGATAAGTTT-GGGGCCAAAATT
1 TAATTTTGGAGAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATG
* * * * * *
1121 TAATTTTGGAGAA-TTTTAGGAT-AAAATGTAATTTTAGAAAAATTCAAGGGTTAAAATG
1 TAATTTTGGAGAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATG
*
1179 TGATTTT
1 TAATTTT
1186 TAAAGAAAAG
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
57 19 0.18
58 21 0.20
59 21 0.20
60 44 0.42
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (60 bp):
TAATTTTGGAGAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATG
Found at i:2261 original size:17 final size:17
Alignment explanation
Indices: 2239--2284 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
2229 TTGGAAATTG
* *
2239 AATTTAAGTTTATTTTA
1 AATTTAAATTTATTATA
2256 AATTTAAATTTATTATA
1 AATTTAAATTTATTATA
*
2273 AAATTAAATTTA
1 AATTTAAATTTA
2285 GAAAAGTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:2337 original size:22 final size:22
Alignment explanation
Indices: 2312--2356 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2302 AAAAATCCAA
*
2312 AACAAA-AGTCCAAATTACAAAT
1 AACAAATAGCCCAAA-TACAAAT
2334 AACAAATAGCCCAAATACAAAT
1 AACAAATAGCCCAAATACAAAT
2356 A
1 A
2357 GTCCAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.60, C:0.20, G:0.04, T:0.16
Consensus pattern (22 bp):
AACAAATAGCCCAAATACAAAT
Found at i:2355 original size:15 final size:16
Alignment explanation
Indices: 2329--2362 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2319 GTCCAAATTA
2329 CAAATAACAAATAGCC
1 CAAATAACAAATAGCC
*
2345 CAAAT-ACAAATAGTC
1 CAAATAACAAATAGCC
2360 CAA
1 CAA
2363 TTATAAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.56, C:0.24, G:0.06, T:0.15
Consensus pattern (16 bp):
CAAATAACAAATAGCC
Found at i:4177 original size:30 final size:30
Alignment explanation
Indices: 4143--4471 Score: 153
Period size: 29 Copynumber: 11.2 Consensus size: 30
4133 GGAGGTCCTT
*
4143 GAACTTTTTAAAAATTACCATTTTACCCCC
1 GAACTTTCTAAAAATTACCATTTTACCCCC
* *
4173 GAAC-TTCCAAAAA-T-CTCATTTTTGA-CCTC
1 GAACTTTCTAAAAATTAC-CA-TTTT-ACCCCC
4202 GAACTTTCTAAAAATTACCATTTTACCCCC
1 GAACTTTCTAAAAATTACCATTTTACCCCC
* *
4232 GAAC-TTCCAAAAA-T-CTCATTTTTGA-CCCT
1 GAACTTTCTAAAAATTAC-CA-TTTT-ACCCCC
*
4261 GAACCTTCT-AAAATTACCATTTTACCCCC
1 GAACTTTCTAAAAATTACCATTTTACCCCC
* * *
4290 AAAC-TTCCAAAAA-T-CTCATTTTTGA-CCCT
1 GAACTTTCTAAAAATTAC-CA-TTTT-ACCCCC
* * *
4319 AAACCTTCT-AAAATTACCATTTTACCCTC
1 GAACTTTCTAAAAATTACCATTTTACCCCC
*
4348 GAAC-TTCCAAAAA-T-CTCATTTTTGA-CCCC
1 GAACTTTCTAAAAATTAC-CA-TTTT-ACCCCC
* ** *
4377 GAACCTTCTTGAAATTACAATTTTACCCCC
1 GAACTTTCTAAAAATTACCATTTTACCCCC
* ***
4407 GAAC-TTCCAAAAA-T-CTCATTTTTGA-CATT
1 GAACTTTCTAAAAATTAC-CA-TTTT-ACCCCC
* * *
4436 AAACTTTCCAAAAATTACCATTTTACCCTC
1 GAACTTTCTAAAAATTACCATTTTACCCCC
4466 GAACTT
1 GAACTT
4472 CCAAAATCCT
Statistics
Matches: 229, Mismatches: 33, Indels: 74
0.68 0.10 0.22
Matches are distributed among these distances:
27 5 0.02
28 22 0.10
29 111 0.48
30 78 0.34
31 10 0.04
32 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.34
Consensus pattern (30 bp):
GAACTTTCTAAAAATTACCATTTTACCCCC
Found at i:4297 original size:117 final size:118
Alignment explanation
Indices: 4153--4489 Score: 531
Period size: 117 Copynumber: 2.9 Consensus size: 118
4143 GAACTTTTTA
*
4153 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACTTTCTAAAAATT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCAAACTTTCTAAAAATT
* *
4218 ACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTGAACCTTC-T
66 ACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTT
* *
4270 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACC-CTAAACCTTCT-AAAAT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTC-AAACTTTCTAAAAAT
4333 TACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTT
65 TACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTT
* * * * *
4387 GAAATTACAATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACATTAAACTTTCCAAAAATT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCAAACTTTCTAAAAATT
4452 ACCATTTTACCCTCGAACTTCC-AAAATC-CTATTTTTGA
66 ACCATTTTACCCTCGAACTTCCAAAAATCTC-ATTTTTGA
4490 TTCCGAACGT
Statistics
Matches: 203, Mismatches: 12, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
116 57 0.28
117 118 0.58
118 28 0.14
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (118 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCAAACTTTCTAAAAATT
ACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTT
Found at i:4302 original size:58 final size:58
Alignment explanation
Indices: 4153--4489 Score: 491
Period size: 59 Copynumber: 5.8 Consensus size: 58
4143 GAACTTTTTA
*
4153 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGA-CCTCGAACTTTCT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCT-GAACCTTCT
4211 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTGAACCTTCT
1 -AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTGAACCTTCT
* *
4270 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCTAAACCTTCT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTGAACCTTCT
* *
4328 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTGAACCTTC-T
* * ** * * *
4387 GAAATTACAATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACATTAAACTTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTGAACCTT-CT
*
4446 AAAATTACCATTTTACCCTCGAACTTCC-AAAATC-CTATTTTTGA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTC-ATTTTTGA
4490 TTCCGAACGT
Statistics
Matches: 255, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
57 1 0.00
58 123 0.48
59 127 0.50
60 4 0.02
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTGAACCTTCT
Found at i:4506 original size:58 final size:58
Alignment explanation
Indices: 4152--4506 Score: 457
Period size: 58 Copynumber: 6.1 Consensus size: 58
4142 TGAACTTTTT
* *
4152 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACTTTCT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACC-CGAACCTTCC
4211 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCTGAACCTT-C
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCC-GAACCTTCC
* * *
4269 TAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCTAAACCTT-C
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCC-GAACCTTCC
* * *
4327 TAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGA-CCCGAACCTTCC
** * *** *
4386 TGAAATTACAATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACATTAAACTTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGAC-CCGAACCTTCC
* * *
4445 AAAAATTACCATTTTACCCTCGAACTTCC-AAAATC-CTATTTTTGATTCCGAACGTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTC-ATTTTTGA-CCCGAACCTTCC
4503 AAAA
1 AAAA
4507 CTATCGTTTT
Statistics
Matches: 264, Mismatches: 26, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
57 1 0.00
58 132 0.50
59 131 0.50
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCGAACCTTCC
Found at i:4882 original size:96 final size:96
Alignment explanation
Indices: 4754--4927 Score: 237
Period size: 96 Copynumber: 1.8 Consensus size: 96
4744 AAACTTTAAT
* **
4754 ATCGAGGCAATATTCTTTTATTTCGGGTTCCGAAGAT-TTGCGCCTTAACTCACTAGGTGCAATT
1 ATCGAGGCAATATTCTTTTATTTCGGATTCCGAA-ATATTGCGCCTTAACTCACTAGGTGCAACC
4818 TTTCTTCAAATCGAAGTAGTCGAATACCCTTA
65 TTTCTTCAAATCGAAGTAGTCGAATACCCTTA
* * *
4850 ATCGAGGCAATGTT-TTCTTATCTTC-GATTCCGAAATATTGCGCCTTAACTTACTAGGTGCGAC
1 ATCGAGGCAATATTCTT-TTAT-TTCGGATTCCGAAATATTGCGCCTTAACTCACTAGGTGCAAC
*
4913 CTTTCTTTAAATCGA
64 CTTTCTTCAAATCGA
4928 GATAATCAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 4 0.06
96 61 0.90
97 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (96 bp):
ATCGAGGCAATATTCTTTTATTTCGGATTCCGAAATATTGCGCCTTAACTCACTAGGTGCAACCT
TTCTTCAAATCGAAGTAGTCGAATACCCTTA
Found at i:6869 original size:50 final size:50
Alignment explanation
Indices: 6723--7257 Score: 263
Period size: 50 Copynumber: 10.8 Consensus size: 50
6713 CTCGTCACTT
* ** *
6723 TTCTAAGGTGA-CAGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTTATATC
1 TTCTAAGGT-ATCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCTTCATATC
* * * * * * *
6773 TAC-ATGGTATCAGATTCGCCGTTGC-GACCACAATCC-TTCTCATCATATC
1 TTCTAAGGTATCGGGTTCGCCGTTGCAG-CCTCAA-CCTTTCCCTTCATATC
*
6822 TTCTAAGGTATCGGGTTCACCGTTGCAGCCTCAACCTTTCCCTTCATATC
1 TTCTAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCTTCATATC
* ** * * * *
6872 TCCGT--GGTATCGGGTTTACCATTGGA-CCTCAACCTTTCCCCTCACATC
1 TTC-TAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCTTCATATC
* * * *** * * *
6920 TTTTTAGGTA-CTGGGTTCGTCGTTATGGCCTCAATCTTTCCCTCCGTATC
1 TTCTAAGGTATC-GGGTTCGCCGTTGCAGCCTCAACCTTTCCCTTCATATC
* * * *
6970 TTC-ATGATACCGGGTTCGCCGTTGCAGCCTCAACCTTT-CCTATCACATC
1 TTCTAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCT-TCATATC
* ** * * *
7019 TTCTTAGGTATCAAGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATC
1 TTCTAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCTTCATATC
* * * * * * ** ** * * *
7069 TTTTAAGGTATCAGATTTGTCATTGTGGTTTCGATCC-TTCCTTTCAAATC
1 TTCTAAGGTATCGGGTTCGCCGTTGCAGCCTC-AACCTTTCCCTTCATATC
* * * * * * *
7119 TTC-ATGATACCGGGTTCGCCATTACGGCCTCAACCTTTCCCATCACT-TC
1 TTCTAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCTTCA-TATC
* * * ** * *
7168 TTCTTAGGTA-CTGAGCTCGTTGTTGCGGCCTCAACCTTTCCCTTCGTATC
1 TTCTAAGGTATC-GGGTTCGCCGTTGCAGCCTCAACCTTTCCCTTCATATC
* * **
7218 TTC-ATGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCC
1 TTCTAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTCC
7258 AATCACATCT
Statistics
Matches: 359, Mismatches: 104, Indels: 45
0.71 0.20 0.09
Matches are distributed among these distances:
47 1 0.00
48 30 0.08
49 157 0.44
50 164 0.46
51 7 0.02
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.35
Consensus pattern (50 bp):
TTCTAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCTTCATATC
Found at i:6908 original size:48 final size:49
Alignment explanation
Indices: 6828--6920 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 49
6818 TATCTTCTAA
* * *
6828 GGTATCGGGTTCACCGTTGCAGCCTCAACCTTTCCCTTCATATCTCCGT
1 GGTATCGGGTTCACCATTGCAGCCTCAACCTTTCCCCTCACATCTCCGT
* *
6877 GGTATCGGGTTTACCATTGGA-CCTCAACCTTTCCCCTCACATCT
1 GGTATCGGGTTCACCATTGCAGCCTCAACCTTTCCCCTCACATCT
6921 TTTTAGGTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 21 0.54
49 18 0.46
ACGTcount: A:0.16, C:0.34, G:0.17, T:0.32
Consensus pattern (49 bp):
GGTATCGGGTTCACCATTGCAGCCTCAACCTTTCCCCTCACATCTCCGT
Found at i:7070 original size:99 final size:99
Alignment explanation
Indices: 6736--7268 Score: 312
Period size: 99 Copynumber: 5.4 Consensus size: 99
6726 TAAGGTGACA
* * * * * *
6736 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTTATATCTACATGGTATCAGATTCGCCGTTGC-GA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCATGGTATCGGGTTCGCCGTTGCAG-
* * *
6800 CCACAATCC-TT-CTCATCATATCTTCTAAGGTATCG
65 CCTCAA-CCTTTCCT-ATCACATCTTCTTAGGTATCG
* * * * * ** * *
6835 GGTTCACCGTTGCAGCCTCAACCTTTCCCTTCATATCTCCGTGGTATCGGGTTTACCATTGGA-C
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCATGGTATCGGGTTCGCCGTTGCAGC
** *
6899 CTCAACCTTTCCCCTCACATCTTTTTAGGTA-CTG
66 CTCAACCTTTCCTATCACATCTTCTTAGGTATC-G
* ** * * ** * *
6933 GGTTCGTCGTTATGGCCTCAATCTTTCCCTCCGTATCTTCATGATACCGGGTTCGCCGTTGCAGC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCATGGTATCGGGTTCGCCGTTGCAGC
*
6998 CTCAACCTTTCCTATCACATCTTCTTAGGTATCA
66 CTCAACCTTTCCTATCACATCTTCTTAGGTATCG
* * * * * * * * * **
7032 AGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGATTTGTCATTGTGG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATC-TTCATGGTATCGGGTTCGCCGTTGCAG
** * * * * * *
7097 TTTCGATCC-TTCCTTTCAAATCTTCAT-GATACCG
65 CCTC-AACCTTTCCTATCACATCTTCTTAGGTATCG
* * * * * * * ** *
7131 GGTTCGCCATTACGGCCTCAACCTTTCCCATCACTTCTTCTTAGGTA-CTGAGCTCGTTGTTGCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCAT-GGTATC-GGGTTCGCCGTTGCA
** * *
7195 GCCTCAACCTTTCCCT-TCGTATCTTCAT-GGTACCG
64 GCCTCAACCTTT-CCTATCACATCTTCTTAGGTATCG
* **
7230 GGTTCGCCGTTGTGGCCTCAACCTTTCCAATCACATCTT
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTT
7269 TTAAGATACC
Statistics
Matches: 329, Mismatches: 93, Indels: 24
0.74 0.21 0.05
Matches are distributed among these distances:
97 3 0.01
98 75 0.23
99 211 0.64
100 37 0.11
101 3 0.01
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (99 bp):
GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCATGGTATCGGGTTCGCCGTTGCAGC
CTCAACCTTTCCTATCACATCTTCTTAGGTATCG
Found at i:7078 original size:149 final size:149
Alignment explanation
Indices: 6833--7257 Score: 412
Period size: 149 Copynumber: 2.9 Consensus size: 149
6823 TCTAAGGTAT
* * * * * ** *
6833 CGGGTTCACCGTTGCAGCCTCAACCTTTCCCT-TCATATCTCCGT-GGTATCGGGTTTACCATTG
1 CGGGTTCGCCGTTGCAGCCTCAACCTTT-CCTATCACATCTTCTTAGGTATCGAGTTCGCCGTTG
* * * *
6896 -GACCTCAACCTTTCCCCTCACATCTTTTTAGGTACTGGGTTCGTCGTTATGGCCTCAATCTTTC
65 CGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACTGGGTTCGTCGTTGTGGCCTCAATCTTTC
**
6960 CCTCCGTATCTTCATGATAC
130 CCTCCAAATCTTCATGATAC
*
6980 CGGGTTCGCCGTTGCAGCCTCAACCTTTCCTATCACATCTTCTTAGGTATCAAGTTCGCCGTTGC
1 CGGGTTCGCCGTTGCAGCCTCAACCTTTCCTATCACATCTTCTTAGGTATCGAGTTCGCCGTTGC
* * * * ** * *
7045 GGCCTCAACCTTTCCCATCACATCTTTTAAGGTA-TCAGATTTGTCATTGTGGTTTCGATCCTTC
66 GGCCTCAACCTTTCCCATCACATCTTTTAAGGTACT-GGGTTCGTCGTTGTGGCCTCAATCTTTC
* *
7109 CTTTCAAATCTTCATGATAC
130 CCTCCAAATCTTCATGATAC
* * * * * * **
7129 CGGGTTCGCCATTACGGCCTCAACCTTTCCCATCACTTCTTCTTAGGTA-CTGAGCTCGTTGTTG
1 CGGGTTCGCCGTTGCAGCCTCAACCTTTCCTATCACATCTTCTTAGGTATC-GAGTTCGCCGTTG
* ** * * * * *
7193 CGGCCTCAACCTTTCCCTTCGTATC-TTCATGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTC
65 CGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACTGGGTTCGTCGTTGTGGCCTCAATCTTTC
7257 C
130 C
7258 AATCACATCT
Statistics
Matches: 222, Mismatches: 50, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
146 3 0.01
147 36 0.16
148 42 0.19
149 141 0.64
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.35
Consensus pattern (149 bp):
CGGGTTCGCCGTTGCAGCCTCAACCTTTCCTATCACATCTTCTTAGGTATCGAGTTCGCCGTTGC
GGCCTCAACCTTTCCCATCACATCTTTTAAGGTACTGGGTTCGTCGTTGTGGCCTCAATCTTTCC
CTCCAAATCTTCATGATAC
Found at i:7308 original size:99 final size:98
Alignment explanation
Indices: 7033--7375 Score: 366
Period size: 99 Copynumber: 3.5 Consensus size: 98
7023 TAGGTATCAA
* *
7033 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGATTTGTCATTGTGGT
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTA-CAGATTCGTCATTGTGGC
* * *
7098 TTCGATCCTTCCTTTCAAATCTTCATGATACCGG
65 TTCAATCCTTCCCTTCAAATCTTCATGGTACCGG
* * * * * ** *
7132 GTTCGCCATTACGGCCTCAACCTTTCCCATCACTTCTTCTT-AGGTACTGAGCTCGTTGTTGCGG
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTAAGGTACAGA-TTCGTCATTGTGG
* **
7196 CCTCAA-CCTTTCCCTTCGTATCTTCATGGTACCGG
64 CTTCAATCC-TTCCCTTCAAATCTTCATGGTACCGG
* * * **
7231 GTTCGCCGTTGTGGCCTCAACCTTTCCAATCACATCTTTTAAGATACCAGATTCACCATTGTGGC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTA-CAGATTCGTCATTGTGGC
7296 TTCAATCCTTCCCTTCAAATCTTCATGGTACCGG
65 TTCAATCCTTCCCTTCAAATCTTCATGGTACCGG
*** * * * * *
7330 GTTTATCATTGCGGCCTCAGCTTTTCCCATCACGTCTTCTAAGGTA
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTA
7376 TCGGGTTTGT
Statistics
Matches: 195, Mismatches: 43, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
98 7 0.04
99 181 0.93
100 7 0.04
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (98 bp):
GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACAGATTCGTCATTGTGGCT
TCAATCCTTCCCTTCAAATCTTCATGGTACCGG
Found at i:7401 original size:198 final size:198
Alignment explanation
Indices: 7033--7405 Score: 514
Period size: 198 Copynumber: 1.9 Consensus size: 198
7023 TAGGTATCAA
* * * *** *
7033 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGATTTGTCATTGTGGT
1 GTTCGCCGTTGCGGCCTCAACCTTTCCAATCACATCTTTTAAGATACCAGATTCACCATTGTGGC
* * *
7098 TTCGATCCTTCCTTTCAAATCTTCATGATACCGGGTTCGCCATTACGGCCTCAACCTTTCCCATC
66 TTCAATCCTTCCCTTCAAATCTTCATGATACCGGGTTCACCATTACGGCCTCAACCTTTCCCATC
* * *
7163 ACTTCTTCTTAGGTACTGAGCTCGTTGTTGCGGCCTCAACCTTTCCCTTCGTATCTTCATGGTAC
131 ACGTCTTCTAAGGTACTGAGCTCGTTGTTACGGCCTCAACCTTTCCCTTCGTATCTTCATGGTAC
7228 CGG
196 CGG
*
7231 GTTCGCCGTTGTGGCCTCAACCTTTCCAATCACATCTTTTAAGATACCAGATTCACCATTGTGGC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCAATCACATCTTTTAAGATACCAGATTCACCATTGTGGC
* * * * * *
7296 TTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTTATCATTGCGGCCTCAGCTTTTCCCATC
66 TTCAATCCTTCCCTTCAAATCTTCATGATACCGGGTTCACCATTACGGCCTCAACCTTTCCCATC
* * * *
7361 ACGTCTTCTAAGGTA-TCGGGTTTGTTGTTACGGTCTCAACCTTTC
131 ACGTCTTCTAAGGTACT-GAGCTCGTTGTTACGGCCTCAACCTTTC
7406 TCATCGCATC
Statistics
Matches: 150, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
197 1 0.01
198 149 0.99
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.36
Consensus pattern (198 bp):
GTTCGCCGTTGCGGCCTCAACCTTTCCAATCACATCTTTTAAGATACCAGATTCACCATTGTGGC
TTCAATCCTTCCCTTCAAATCTTCATGATACCGGGTTCACCATTACGGCCTCAACCTTTCCCATC
ACGTCTTCTAAGGTACTGAGCTCGTTGTTACGGCCTCAACCTTTCCCTTCGTATCTTCATGGTAC
CGG
Found at i:8241 original size:41 final size:41
Alignment explanation
Indices: 8126--8242 Score: 110
Period size: 41 Copynumber: 2.8 Consensus size: 41
8116 TTGAGTCGCG
* *
8126 CTTTGCGGGTTTTCAACTCAAAATTCTTTTGATTTCAAGATGCC
1 CTTTGCGGGTTTTCATCTCAAACTTC-TTT--TTTCAAGATGCC
* * ** *
8170 CTTTGCGAGTTTTCATCTTGACCCTT-TTTTTTCGAGATGCC
1 CTTTGCGGGTTTTCATC-TCAAACTTCTTTTTTCAAGATGCC
* *
8211 CTTTACGGGTTTTCATCTCAATCTTCTTTTTT
1 CTTTGCGGGTTTTCATCTCAAACTTCTTTTTT
8243 TAGGCGAAGT
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
40 5 0.08
41 32 0.54
43 3 0.05
44 15 0.25
45 4 0.07
ACGTcount: A:0.16, C:0.22, G:0.15, T:0.47
Consensus pattern (41 bp):
CTTTGCGGGTTTTCATCTCAAACTTCTTTTTTCAAGATGCC
Done.