Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010654.1 Kokia drynarioides strain JFW-HI SEQ_125597, 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: 102545
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 164 characters in sequence are not A, C, G, or T
Found at i:411 original size:4 final size:4
Alignment explanation
Indices: 402--445 Score: 63
Period size: 4 Copynumber: 11.0 Consensus size: 4
392 ACACATTACT
*
402 TTTC TTTC TTT- ATTC TTTC TTTC TTTC TTTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC
446 CCGTTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 2 0.06
4 30 0.83
5 4 0.11
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:1582 original size:28 final size:28
Alignment explanation
Indices: 1467--2046 Score: 162
Period size: 30 Copynumber: 19.8 Consensus size: 28
1457 AAGGTCCTTG
*
1467 AACTTTTCAAAAATCATATTTTGAATCCC-A
1 AACTTTTCAAAAATCACATTTT---TCCCTA
* * * *
1497 AAATTTTCCAAAATTACATTTTAACCTCTA
1 AACTTTTCAAAAATCACATTTT-TCC-CTA
* * *
1527 AACTTTTCCAAAATTACATTTTGCCCCTA
1 AACTTTTCAAAAATCACATTTT-TCCCTA
*
1556 AACTTTT-AAAAATCACATTCTTTCCCTCG
1 AACTTTTCAAAAATCACATT-TTTCCCT-A
* *
1585 AAC-TTCCCAAAATCAC-TTTTTCCCCTA
1 AACTTTTCAAAAATCACATTTTT-CCCTA
* * *
1612 AACTTTTCAATAATCATATTTTAACCCCT-
1 AACTTTTCAAAAATCACATTTT--TCCCTA
* ** *
1641 AACATTTTCCAAAATTGCATTTTAACCCCTA
1 AAC-TTTTCAAAAATCACATTTT--TCCCTA
* * * * * *
1672 AATTTTTCTAAAATTACATTTTGACCTTCG
1 AACTTTTCAAAAATCACATTTT-TCCCT-A
* * * * * *
1702 AACTTTACAAAATTTATAGTTTTACCCTTG
1 AACTTTTCAAAAATCACA-TTTTTCCC-TA
* * * * *
1732 GACTTCTCAAAATTTACATTTTTGCCCCCA
1 AACTTTTCAAAAATCACATTTTT--CCCTA
*
1762 AAC-TTTCAAAAATCACATTTTTACCCTCG
1 AACTTTTCAAAAATCACATTTTT-CCCT-A
* * * *
1791 AA-TTTCCTAAAATCACATTTTTACTCTCG
1 AACTTTTCAAAAATCACATTTTT-CCCT-A
* *
1820 AACTTCTCAAAAATTACATTTTTACCCCTA
1 AACTTTTCAAAAATCACATTTTT--CCCTA
* * * * *
1850 AAC-TTCCAAAAATTATATTATTACCCTCG
1 AACTTTTCAAAAATCACATT-TTTCCCT-A
* *
1879 AACTTTT-GAAAATCACATTTTTACCCCCA
1 AACTTTTCAAAAATCACATTTTT--CCCTA
* *
1908 AACTTTTCCAAAAATTACATTTTTTCCCTCG
1 AACTTTT-CAAAAATCACA-TTTTTCCCT-A
*
1939 AAC-TTCCAAAAATCACATTTTTGCCCTTA
1 AACTTTTCAAAAATCACATTTTT-CCC-TA
* * * * **
1968 AAC-ATCCAAAAATTACCATTTTACCCCCG
1 AACTTTTCAAAAATCA-CATTTT-TCCCTA
* *
1997 AAC-ATTC-AAAATTACCATTTTTGCCCTTA
1 AACTTTTCAAAAATCA-CATTTTT-CCC-TA
2026 AA-TTTTCAAAAATCACATTTT
1 AACTTTTCAAAAATCACATTTT
2047 CAACCTCAAA
Statistics
Matches: 420, Mismatches: 92, Indels: 77
0.71 0.16 0.13
Matches are distributed among these distances:
27 6 0.01
28 65 0.15
29 156 0.37
30 164 0.39
31 24 0.06
32 5 0.01
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (28 bp):
AACTTTTCAAAAATCACATTTTTCCCTA
Found at i:1771 original size:29 final size:29
Alignment explanation
Indices: 1501--2067 Score: 301
Period size: 29 Copynumber: 19.3 Consensus size: 29
1491 ATCCCAAAAT
* *
1501 TTTCCAAAATTACA-TTTTAACCTCTAAAC
1 TTTCAAAAATTACATTTTTACCCTC-AAAC
* **
1530 TTTTCCAAAATTACATTTTGCCCCT-AAAC
1 -TTTCAAAAATTACATTTTTACCCTCAAAC
* * *
1559 TTTTAAAAATCACATTCTTT-CCCTCGAAC
1 TTTCAAAAATTACATT-TTTACCCTCAAAC
* * * *
1588 TTCCCAAAATCAC-TTTTTCCCCT-AAAC
1 TTTCAAAAATTACATTTTTACCCTCAAAC
* * * * *
1615 TTTTCAATAATCATATTTTAACCC-CTAACAT
1 -TTTCAAAAATTACATTTTTACCCTC-AA-AC
* * * *
1646 TTTCCAAAATTGCATTTTAACCC-CTAAATT
1 TTTCAAAAATTACATTTTTACCCTC-AAA-C
* * * *
1676 TTTCTAAAATTACATTTTGACCTTCGAAC
1 TTTCAAAAATTACATTTTTACCCTCAAAC
* * * ***
1705 TTTACAAAATTTATAGTTTTACCCTTGGAC
1 TTT-CAAAAATTACATTTTTACCCTCAAAC
* * *
1735 TTCTCAAAATTTACATTTTTGCCCCCAAAC
1 TT-TCAAAAATTACATTTTTACCCTCAAAC
* *
1765 TTTCAAAAATCACATTTTTACCCTCGAA-
1 TTTCAAAAATTACATTTTTACCCTCAAAC
* * * *
1793 TTTCCTAAAATCACATTTTTACTCTCGAAC
1 TTT-CAAAAATTACATTTTTACCCTCAAAC
1823 TTCTCAAAAATTACATTTTTACCC-CTAAAC
1 TT-TCAAAAATTACATTTTTACCCTC-AAAC
* * * *
1853 TTCCAAAAATTATATTATTACCCTCGAAC
1 TTTCAAAAATTACATTTTTACCCTCAAAC
** * *
1882 TTTTGAAAATCACATTTTTACCCCCAAAC
1 TTTCAAAAATTACATTTTTACCCTCAAAC
* *
1911 TTTTCCAAAAATTACATTTTTTCCCTCGAAC
1 -TTT-CAAAAATTACATTTTTACCCTCAAAC
* * * *
1942 TTCCAAAAATCACATTTTTGCCCTTAAAC
1 TTTCAAAAATTACATTTTTACCCTCAAAC
* * * *
1971 ATCCAAAAATTACCA-TTTTACCCCCGAAC
1 TTTCAAAAATTA-CATTTTTACCCTCAAAC
* * * *
2000 ATTC-AAAATTACCATTTTTGCCCTTAAAT
1 TTTCAAAAATTA-CATTTTTACCCTCAAAC
* * * *
2029 TTTCAAAAATCACATTTTCAACCTCAAAT
1 TTTCAAAAATTACATTTTTACCCTCAAAC
2058 TTTCCAAAAA
1 TTT-CAAAAA
2068 GTTCAACTTT
Statistics
Matches: 416, Mismatches: 97, Indels: 48
0.74 0.17 0.09
Matches are distributed among these distances:
27 6 0.01
28 45 0.11
29 190 0.46
30 145 0.35
31 30 0.07
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTCAAAAATTACATTTTTACCCTCAAAC
Found at i:2007 original size:58 final size:58
Alignment explanation
Indices: 1502--2046 Score: 334
Period size: 58 Copynumber: 9.3 Consensus size: 58
1492 TCCCAAAATT
* * * * * *
1502 TTCC-AAAATTACA-TTTTAACCTCTAAACTTTTCCAAAATTACA-TTTTGCCCCTAAAC
1 TTCCAAAAATTACATTTTTACCCTC-GAAC-TTTCAAAAATCACATTTTTACCCTTAAAC
** * * * *
1559 TTTTAAAAATCACATTCTTT-CCCTCGAACTTCCCAAAATCAC-TTTTT-CCCCTAAAC
1 TTCCAAAAATTACATT-TTTACCCTCGAACTTTCAAAAATCACATTTTTACCCTTAAAC
* * * * * * * ** * * *
1615 TTTTCAATAATCATATTTTAACCC-CTAACATTTTCCAAAATTGCATTTTAACCCCTAAATT
1 -TTCCAAAAATTACATTTTTACCCTCGAAC--TTTCAAAAATCACATTTTTACCCTTAAA-C
* * * * * * * * **
1676 TTTCTAAAATTACATTTTGACCTTCGAACTTTACAAAATTTATAGTTTTACCCTTGGAC
1 TTCCAAAAATTACATTTTTACCCTCGAACTTT-CAAAAATCACATTTTTACCCTTAAAC
* * * * ** *
1735 TTCTCAAAATTTACATTTTTGCCCCCAAACTTTCAAAAATCACATTTTTACCCTCGAAT
1 TTC-CAAAAATTACATTTTTACCCTCGAACTTTCAAAAATCACATTTTTACCCTTAAAC
* * * * *
1794 TTCCTAAAATCACATTTTTACTCTCGAACTTCTCAAAAATTACATTTTTACCCCTAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAACTT-TCAAAAATCACATTTTTACCCTTAAAC
* * ** **
1853 TTCCAAAAATTATATTATTACCCTCGAACTTTTGAAAATCACATTTTTACCCCCAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAACTTTCAAAAATCACATTTTTACCCTTAAAC
* * *
1911 TTTTCCAAAAATTACATTTTTTCCCTCGAACTTCCAAAAATCACATTTTTGCCCTTAAAC
1 --TTCCAAAAATTACATTTTTACCCTCGAACTTTCAAAAATCACATTTTTACCCTTAAAC
* * * * * *
1971 ATCCAAAAATTACCA-TTTTACCCCCGAACATTC-AAAATTACCATTTTTGCCCTTAAAT
1 TTCCAAAAATTA-CATTTTTACCCTCGAACTTTCAAAAATCA-CATTTTTACCCTTAAAC
* *
2029 TTTCAAAAATCACATTTT
1 TTCCAAAAATTACATTTT
2047 CAACCTCAAA
Statistics
Matches: 379, Mismatches: 89, Indels: 39
0.75 0.18 0.08
Matches are distributed among these distances:
56 15 0.04
57 41 0.11
58 118 0.31
59 86 0.23
60 115 0.30
61 4 0.01
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (58 bp):
TTCCAAAAATTACATTTTTACCCTCGAACTTTCAAAAATCACATTTTTACCCTTAAAC
Found at i:2066 original size:30 final size:28
Alignment explanation
Indices: 2025--2098 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 28
2015 TTTTGCCCTT
*
2025 AAATTTT-CAAAAATCACATTTTCAA-CCTC
1 AAATTTTCCAAAAATCA-ACTTT-AATCC-C
2054 AAATTTTCCAAAAAGTTCAACTTTAATCCC
1 AAATTTTCCAAAAA--TCAACTTTAATCCC
2084 AAATTTTCCAAAAAT
1 AAATTTTCCAAAAAT
2099 TTAAAATTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 1 0.03
29 7 0.17
30 23 0.57
31 6 0.15
32 3 0.08
ACGTcount: A:0.43, C:0.22, G:0.01, T:0.34
Consensus pattern (28 bp):
AAATTTTCCAAAAATCAACTTTAATCCC
Found at i:2113 original size:30 final size:30
Alignment explanation
Indices: 2053--2128 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
2043 TTTTCAACCT
* *
2053 CAAATTTTCCAAAAAGTTCAACTTTAATCC
1 CAAATTTTCCAAAAAGTTAAAATTTAATCC
* *
2083 CAAATTTTCCAAAAATTTAAAATTTGATCC
1 CAAATTTTCCAAAAAGTTAAAATTTAATCC
*
2113 CTAAATTCTTCGAAAA
1 C-AAATT-TTCCAAAA
2129 TCATGTTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 27 0.69
31 5 0.13
32 7 0.18
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (30 bp):
CAAATTTTCCAAAAAGTTAAAATTTAATCC
Found at i:6367 original size:6 final size:6
Alignment explanation
Indices: 6358--6410 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
6348 ATAAGAGAAG
*
6358 TGAGAC TGAGAC CGAGAC TGAGAC TGAGAC TGAGAC TGAGAC TGAGAC
1 TGAGAC TGAGAC TGAGAC TGAGAC TGAGAC TGAGAC TGAGAC TGAGAC
6406 TGAGA
1 TGAGA
6411 GAGTCATCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.15
Consensus pattern (6 bp):
TGAGAC
Found at i:6718 original size:3 final size:3
Alignment explanation
Indices: 6710--6745 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
6700 AATCATTCTC
6710 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6746 AACCATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:7038 original size:17 final size:16
Alignment explanation
Indices: 7012--7046 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
7002 AATAAATTAT
7012 TAAAAAATTTTAAAAA
1 TAAAAAATTTTAAAAA
*
7028 TAAAAATATTTTTAAAA
1 TAAAAA-ATTTTAAAAA
7045 TA
1 TA
7047 GATAAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAAATTTTAAAAA
Found at i:8189 original size:38 final size:38
Alignment explanation
Indices: 8147--8221 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
8137 GAAGGCGATG
* *
8147 GCTAGGGCAAATGGAGAAGGAAGAAGATGAGTAAAGAA
1 GCTAGGGCAAATGGAGAAAGAAGAAGAGGAGTAAAGAA
8185 GCTAGGGCAAATGGAGAAAGAAGAAGAGGAGTAAAGA
1 GCTAGGGCAAATGGAGAAAGAAGAAGAGGAGTAAAGA
8222 GTGAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.48, C:0.05, G:0.37, T:0.09
Consensus pattern (38 bp):
GCTAGGGCAAATGGAGAAAGAAGAAGAGGAGTAAAGAA
Found at i:15538 original size:5 final size:5
Alignment explanation
Indices: 15525--15559 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
15515 NNNNNNNCCC
* *
15525 CCCTC CCCTT CCCTT CCCTT CCCTT CCCTG CCCTT
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT
15560 TTCTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.63, G:0.03, T:0.34
Consensus pattern (5 bp):
CCCTT
Found at i:19066 original size:91 final size:83
Alignment explanation
Indices: 18965--19136 Score: 272
Period size: 83 Copynumber: 2.0 Consensus size: 83
18955 CAAAACGATC
18965 AAATATTGTTTATAATTTAAAAACAAGACTTTGTTTTCTTTTTCTTTTTTTCCCTAAATACTATT
1 AAATATTGTTTATAATTTAAAAACAAGACTTTG------TTTT-TTTTTTT-CCTAAATACTATT
19030 GAAAATGAGTGGAATTGGACACCTCA
58 GAAAATGAGTGGAATTGGACACCTCA
19056 AAATATTGTTTATAATTTAAAAACAAGACTTTGTTTTTTTTTTTCCTAAATACTATTGAAAATGA
1 AAATATTGTTTATAATTTAAAAACAAGACTTTGTTTTTTTTTTTCCTAAATACTATTGAAAATGA
19121 GTGGAATTGGACACCT
66 GTGGAATTGGACACCT
19137 TATTACTCTC
Statistics
Matches: 81, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
83 37 0.46
84 7 0.09
85 4 0.05
91 33 0.41
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (83 bp):
AAATATTGTTTATAATTTAAAAACAAGACTTTGTTTTTTTTTTTCCTAAATACTATTGAAAATGA
GTGGAATTGGACACCTCA
Found at i:27435 original size:217 final size:218
Alignment explanation
Indices: 27060--27500 Score: 848
Period size: 217 Copynumber: 2.0 Consensus size: 218
27050 CTCGGGGTGA
*
27060 AGATTGTTGAAGGAGAAACTGAAGTGAATAGGGTTGCTTGCGAATATCTTTTCTCTCTTTTTGTT
1 AGATTGTTGAAGGAGAAACTGAAGTGAATAGGGTTGCTTGCGAATATCTTCTCTCTCTTTTTGTT
27125 ACACAGGGAATCGTAAAATTGGATAAGGTTCTTGAGGAAGTTGATAGATGCATTTATGAGGATTT
66 ACACAGGGAATCGTAAAATTGGATAAGGTTCTTGAGGAAGTTGATAGATGCATTTATGAGGATTT
*
27190 GAGGGTATGATTAGATAGGCCTTTCTCAAAGGAGGATTTTCTTATTGCTATAAAGTTTATGAGTC
131 GAGGGTATGATTAGATAGGCCTTTCTCAAAGGAGGATGTTCTTATTGCTATAAAGTTTATGAGTC
27255 CATTAAAGGCTTCA-GGGAAGAC
196 CATTAAAGGCTTCAGGGGAAGAC
*
27277 AGATTGTTGAAGGAGAAACTGAGGTGAATAGGGTTGCTTGCGAATATCTTCTCTCTCTTTTTGTT
1 AGATTGTTGAAGGAGAAACTGAAGTGAATAGGGTTGCTTGCGAATATCTTCTCTCTCTTTTTGTT
27342 ACACAGGGAATCGTAAAATTGGATAAGGTTCTTGAGGAAGTTGATAGATGCATTTATGAGGATTT
66 ACACAGGGAATCGTAAAATTGGATAAGGTTCTTGAGGAAGTTGATAGATGCATTTATGAGGATTT
27407 GAGGGTATGATTAGATAGGCCTTTCTCAAAGGAGGATGTTCTTATTGCTATAAAGTTTATGAGTC
131 GAGGGTATGATTAGATAGGCCTTTCTCAAAGGAGGATGTTCTTATTGCTATAAAGTTTATGAGTC
27472 CATTAAAGGCTTCAGGGGAAGAC
196 CATTAAAGGCTTCAGGGGAAGAC
27495 AGATTG
1 AGATTG
27501 GGTGCAATTT
Statistics
Matches: 220, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
217 206 0.94
218 14 0.06
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.34
Consensus pattern (218 bp):
AGATTGTTGAAGGAGAAACTGAAGTGAATAGGGTTGCTTGCGAATATCTTCTCTCTCTTTTTGTT
ACACAGGGAATCGTAAAATTGGATAAGGTTCTTGAGGAAGTTGATAGATGCATTTATGAGGATTT
GAGGGTATGATTAGATAGGCCTTTCTCAAAGGAGGATGTTCTTATTGCTATAAAGTTTATGAGTC
CATTAAAGGCTTCAGGGGAAGAC
Found at i:29405 original size:24 final size:24
Alignment explanation
Indices: 29373--29564 Score: 231
Period size: 24 Copynumber: 8.0 Consensus size: 24
29363 GCAAGTTCAT
* * *
29373 TACGTTTACACTCATCATCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
29397 TACGTTTACGCTCGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
*
29421 TACGTTTATGCTCGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
* *
29445 TACGTTTACGCTCGTTAACTTATA
1 TACGTTTACGCTCGTCAGCTTATA
*
29469 TACGTTTACGCTTGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
** *
29493 TACGTTTTTTGCTCGTTAGCTTATA
1 TACG-TTTACGCTCGTCAGCTTATA
* * **
29518 TATGTTTATGCTCGTCAGCTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* *
29542 TACGTTTACACTCATCAGCTTAT
1 TACGTTTACGCTCGTCAGCTTAT
29565 CAGGTAAGAA
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
24 123 0.87
25 19 0.13
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (24 bp):
TACGTTTACGCTCGTCAGCTTATA
Found at i:29564 original size:97 final size:96
Alignment explanation
Indices: 29373--29564 Score: 249
Period size: 97 Copynumber: 2.0 Consensus size: 96
29363 GCAAGTTCAT
*
29373 TACGTTTACACTCATCATCTTATATACGTTTACGCTCGTCAGCTTATATACGTTTATGCTCGTCA
1 TACGTTTACACTCATCAGCTTATATACGTTTACGCTCGTCAGCTTATATACGTTTATGCTCGTCA
* * * *
29438 GCTTATATACGTTTACGCTCGTTAACTTATA
66 GCTTACATACGTTTACACTCATCAACTTATA
* ** ** * *
29469 TACGTTTACGCTTGTCAGCTTATATACGTTTTTTGCTCGTTAGCTTATATATGTTTATGCTCGTC
1 TACGTTTACACTCATCAGCTTATATACG-TTTACGCTCGTCAGCTTATATACGTTTATGCTCGTC
* *
29534 AGCTTGCATACGTTTACACTCATCAGCTTAT
65 AGCTTACATACGTTTACACTCATCAACTTAT
29565 CAGGTAAGAA
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
96 24 0.30
97 57 0.70
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (96 bp):
TACGTTTACACTCATCAGCTTATATACGTTTACGCTCGTCAGCTTATATACGTTTATGCTCGTCA
GCTTACATACGTTTACACTCATCAACTTATA
Found at i:41131 original size:19 final size:18
Alignment explanation
Indices: 41090--41132 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
41080 ATTGTAATTC
41090 ACAA-AAAAAAAATACAT
1 ACAATAAAAAAAATACAT
* *
41107 AAAATAAAAAAAATTCAAT
1 ACAATAAAAAAAATAC-AT
41126 ACAATAA
1 ACAATAA
41133 GAACATCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 10 0.48
19 8 0.38
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.16
Consensus pattern (18 bp):
ACAATAAAAAAAATACAT
Found at i:46511 original size:5 final size:6
Alignment explanation
Indices: 46494--46518 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
46484 TTTACCCACA
46494 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
46519 TGAACAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:48389 original size:19 final size:20
Alignment explanation
Indices: 48349--48389 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
48339 AGTGGTCAGA
*
48349 TTTGTCATTAATCCAATTTT
1 TTTGTCATTAATCCAATATT
48369 TTTGTCA-TAAT-CATATATT
1 TTTGTCATTAATCCA-ATATT
48388 TT
1 TT
48390 ACTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 2 0.11
19 10 0.53
20 7 0.37
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTGTCATTAATCCAATATT
Found at i:49442 original size:16 final size:15
Alignment explanation
Indices: 49414--49471 Score: 71
Period size: 16 Copynumber: 3.7 Consensus size: 15
49404 TAAAAAACTC
49414 AAAAATATTTTATTT
1 AAAAATATTTTATTT
* *
49429 AACAATATTTTTATCTC
1 AAAAATA-TTTTAT-TT
49446 AAAAATATTTTATTT
1 AAAAATATTTTATTT
49461 CAAAAATATTT
1 -AAAAATATTT
49472 CTAAAAAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 7 0.19
16 22 0.61
17 7 0.19
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAATATTTTATTT
Found at i:51520 original size:2 final size:2
Alignment explanation
Indices: 51513--51559 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
51503 ACATACAGAA
51513 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
51555 AG AG A
1 AG AG A
51560 AAGATAAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:60727 original size:2 final size:2
Alignment explanation
Indices: 60720--60748 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60710 AACATTGACA
60720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60749 ATTTACATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65137 original size:23 final size:23
Alignment explanation
Indices: 65107--65152 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
65097 TAAGGTAGTG
65107 CAGATATATGAATGAGTTGACCC
1 CAGATATATGAATGAGTTGACCC
65130 CAGATATATGAATGAGTTGACCC
1 CAGATATATGAATGAGTTGACCC
65153 TGGGTCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (23 bp):
CAGATATATGAATGAGTTGACCC
Found at i:72331 original size:21 final size:21
Alignment explanation
Indices: 72305--72350 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
72295 TATTGTAAGC
72305 TTTGTT-GTGAGATTTGATGAT
1 TTTGTTAGTGA-ATTTGATGAT
*
72326 TTTGTTAAGTGATTTTGATGAT
1 TTTGTT-AGTGAATTTGATGAT
72348 TTT
1 TTT
72351 AGGGTTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 12 0.55
23 4 0.18
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.57
Consensus pattern (21 bp):
TTTGTTAGTGAATTTGATGAT
Found at i:73569 original size:21 final size:21
Alignment explanation
Indices: 73543--73611 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
73533 TTAGTATCAA
* *
73543 TAGAAGCATGACTTGTTTTGG
1 TAGAAGCATCACTTGTATTGG
*
73564 TAGAAGTATCACTTGTATTGG
1 TAGAAGCATCACTTGTATTGG
* * * * *
73585 TGGAACCATCCCTAGTATCGG
1 TAGAAGCATCACTTGTATTGG
73606 TAGAAG
1 TAGAAG
73612 TCTGCTACTA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (21 bp):
TAGAAGCATCACTTGTATTGG
Found at i:75890 original size:14 final size:14
Alignment explanation
Indices: 75866--75898 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
75856 TTGGATTCAA
75866 GGTTTATGTTT-AG
1 GGTTTATGTTTAAG
75879 GGTTTAATGTTTAAG
1 GGTTT-ATGTTTAAG
75894 GGTTT
1 GGTTT
75899 GGGGTTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 6 0.33
15 7 0.39
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.52
Consensus pattern (14 bp):
GGTTTATGTTTAAG
Found at i:83159 original size:54 final size:54
Alignment explanation
Indices: 83101--83210 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
83091 GAATTTCTAA
83101 ATGGGATGGAAATAAATTTTTAATTAATTAAAATTTTAAAACCCTACACCATTC
1 ATGGGATGGAAATAAATTTTTAATTAATTAAAATTTTAAAACCCTACACCATTC
83155 ATGGGATGGAAATAAATTTTTAATTAATTAAAATTTTAAAACCCTACACCATTC
1 ATGGGATGGAAATAAATTTTTAATTAATTAAAATTTTAAAACCCTACACCATTC
83209 AT
1 AT
83211 CTCCTCTCCC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (54 bp):
ATGGGATGGAAATAAATTTTTAATTAATTAAAATTTTAAAACCCTACACCATTC
Found at i:90468 original size:28 final size:29
Alignment explanation
Indices: 90398--90472 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
90388 GTTTTAGTTT
*
90398 TGCTTTGTGAGAGC-CTTTTGTTTGGCTC
1 TGCTTTGTGAGAGCTCTTCTGTTTGGCTC
*
90426 TGTTTTGTGTA-AGCTC-TCTGTTTGGCTC
1 TGCTTTGTG-AGAGCTCTTCTGTTTGGCTC
*
90454 TGCTTTGTGCGAGCT-TTCT
1 TGCTTTGTGAGAGCTCTTCT
90473 ATTCTATGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.07, C:0.19, G:0.27, T:0.48
Consensus pattern (29 bp):
TGCTTTGTGAGAGCTCTTCTGTTTGGCTC
Found at i:94744 original size:47 final size:47
Alignment explanation
Indices: 94675--94773 Score: 180
Period size: 47 Copynumber: 2.1 Consensus size: 47
94665 CTAAAAATAA
*
94675 TAAAATTTAAATAGGAAAGTAAAATTAAATTAGGTGGAATTAAACTT
1 TAAAATTTAAATAGGAAAGTAAAATTAAATCAGGTGGAATTAAACTT
*
94722 TAAAATTTAAATAGGAAAGTAAAATTAAATCAGGTGTAATTAAACTT
1 TAAAATTTAAATAGGAAAGTAAAATTAAATCAGGTGGAATTAAACTT
94769 TAAAA
1 TAAAA
94774 CAAGATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.31
Consensus pattern (47 bp):
TAAAATTTAAATAGGAAAGTAAAATTAAATCAGGTGGAATTAAACTT
Found at i:96017 original size:3 final size:3
Alignment explanation
Indices: 96009--96040 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
95999 CAAAGAAGTG
96009 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
96041 GAATTCACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:102513 original size:2 final size:2
Alignment explanation
Indices: 102506--102545 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
102496 GTTATTTCTT
102506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.