Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006784.1 Kokia drynarioides strain JFW-HI SEQ_121383, 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: 26957
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:5527 original size:96 final size:97
Alignment explanation
Indices: 5360--5552 Score: 262
Period size: 96 Copynumber: 2.0 Consensus size: 97
5350 AACCTTGAAA
* * *
5360 AAGGGTATTCGACTATCTCGGTTTGAAGAAAAGTCGCGCCTAATAAGTTAAGGCACAAATTTCCA
1 AAGGGTATTCGACTATCTCGGTTTGAAAAAAAATCACGCCTAATAAGTTAAGGCACAAATTTCCA
* *
5425 AAACCCGAGATAAA-AAATATTGCCTCGATTT
66 AAACCCGAAATAAAGAAATATTGCCTCAATTT
* * * ** *
5456 AAGGGTATTCGATTATCTTGGTTTGAAAAAAAATCACGCCTAGTAAGTTAAGGCATGAATTTTCA
1 AAGGGTATTCGACTATCTCGGTTTGAAAAAAAATCACGCCTAATAAGTTAAGGCACAAATTTCCA
* *
5521 AGACCCGAAATAAAGGAATATTGCCTCAATTT
66 AAACCCGAAATAAAGAAATATTGCCTCAATTT
5553 TAAATATTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
96 68 0.82
97 15 0.18
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (97 bp):
AAGGGTATTCGACTATCTCGGTTTGAAAAAAAATCACGCCTAATAAGTTAAGGCACAAATTTCCA
AAACCCGAAATAAAGAAATATTGCCTCAATTT
Found at i:5852 original size:30 final size:29
Alignment explanation
Indices: 5782--6009 Score: 112
Period size: 29 Copynumber: 7.8 Consensus size: 29
5772 AAAAAAAAAG
* *
5782 GGGTCAAAAATG-AAGTTTTGGAGAGTTTGA
1 GGGT-AAAAATGTAA-TTTTGGAAAGTTTAA
*
5812 -GGTTAAAATGTAATTTTGGAAAGTTTTAA
1 GGGTAAAAATGTAATTTTGGAAAG-TTTAA
* * *
5841 GGGTAAAAATGTCATTTTAGGAAAATTT-G
1 GGGTAAAAATGTAATTTT-GGAAAGTTTAA
* * *
5870 GGGTAAAAACATG-ATTTTTGGAAGGTTGAA
1 GGGT-AAAA-ATGTAATTTTGGAAAGTTTAA
** *
5900 -GGTAAAAACATAATTTTTGG-AAG-TTAG
1 GGGTAAAAATGTAA-TTTTGGAAAGTTTAA
* * *
5927 GGGACAAAAATGTAATTTTTGG-AAGTTCAG
1 GGG-TAAAAATGTAA-TTTTGGAAAGTTTAA
* ** **
5957 GGGCAAAAATGTAATTTTTAAGAAGTTCGA
1 GGGTAAAAATGTAATTTTGGA-AAGTTTAA
* *
5987 GGGTCAAAATGTGATTTTGGAAA
1 GGGTAAAAATGTAATTTTGGAAA
6010 AATGTAGGCG
Statistics
Matches: 152, Mismatches: 32, Indels: 29
0.71 0.15 0.14
Matches are distributed among these distances:
27 3 0.02
28 28 0.18
29 59 0.39
30 54 0.36
31 8 0.05
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTGGAAAGTTTAA
Found at i:5935 original size:29 final size:29
Alignment explanation
Indices: 5910--6008 Score: 123
Period size: 29 Copynumber: 3.4 Consensus size: 29
5900 GGTAAAAACA
5910 TAATTTTTGGAAGTT-AGGGGACAAAAATG
1 TAATTTTTGGAAGTTCAGGGG-CAAAAATG
5939 TAATTTTTGGAAGTTCAGGGGCAAAAATG
1 TAATTTTTGGAAGTTCAGGGGCAAAAATG
* *
5968 TAATTTTTAAGAAGTTCGAGGGTC-AAAATG
1 TAATTTTT-GGAAGTTC-AGGGGCAAAAATG
*
5998 TGA-TTTTGGAA
1 TAATTTTTGGAA
6009 AAATGTAGGC
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
28 3 0.05
29 35 0.56
30 20 0.32
31 5 0.08
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.33
Consensus pattern (29 bp):
TAATTTTTGGAAGTTCAGGGGCAAAAATG
Found at i:7814 original size:17 final size:17
Alignment explanation
Indices: 7790--7852 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
7780 TTTAGATTTG
7790 AATAAATTTAAACTTAA
1 AATAAATTTAAACTTAA
* *
7807 AATTAATTTAAATTTAA
1 AATAAATTTAAACTTAA
*
7824 AATAAATTTAAACCTAA
1 AATAAATTTAAACTTAA
* *
7841 AACAAAATTAAA
1 AATAAATTTAAA
7853 AATGAGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAATTTAAACTTAA
Found at i:7823 original size:11 final size:11
Alignment explanation
Indices: 7792--7835 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
7782 TAGATTTGAA
7792 TAAATTTAAACT
1 TAAATTTAAA-T
* *
7804 TAAAATTAATT
1 TAAATTTAAAT
*
7815 TAAATTTAAAA
1 TAAATTTAAAT
7826 TAAATTTAAA
1 TAAATTTAAA
7836 CCTAAAACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 19 0.70
12 8 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:8152 original size:37 final size:37
Alignment explanation
Indices: 8084--8155 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
8074 GCTTCATATC
* * * *
8084 TTGATTCACTTCTTTGTATTTCACTAGGAAGATGAAT
1 TTGATTCACTTCTCTGCATTTCACCAAGAAGATGAAT
8121 TTGATTCACTTCTCTGCATCTT-ACCAAGAAGATGA
1 TTGATTCACTTCTCTGCAT-TTCACCAAGAAGATGA
8156 TCACTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 28 0.93
38 2 0.07
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (37 bp):
TTGATTCACTTCTCTGCATTTCACCAAGAAGATGAAT
Found at i:8335 original size:78 final size:78
Alignment explanation
Indices: 8171--8535 Score: 371
Period size: 78 Copynumber: 4.7 Consensus size: 78
8161 TTATTGCTTC
* * * * * * * *
8171 GAACGACTACAATTTGCCCAATGATCGGGGTAAGAGATTGGCTGATAATGATCTGCCCCAGGCTC
1 GAACGACTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTC
*
8236 AGGGAAAAAGATA
66 AGGGTAAAAGATA
* * * *
8249 GAATGACTGCAATCTGTCCTAGGCTTGGGGTAAGATATTTGCTGATGATGATCTGCCCCAAGCTC
1 GAACGACTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCT-
*
8314 CA-GGTAAAATG-TC
65 CAGGGTAAAA-GATA
* * * * *
8327 GAACGACTGCAATTTGTCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGGCCCAAGCTC
1 GAACGACTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTC
8392 AGGGTAAAAGATA
66 AGGGTAAAAGATA
* * * * * * *
8405 GAATGGCTGAAATCTGCCCTAAGCTCGGGGTAAGAGA-TTGACTGATGTTGATTTG-CCCAGGCT
1 GAACGACTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTTG-CTGATGATGATCTGCCCCAAGCT
**
8468 CAGGGTAAAAGACC
65 CAGGGTAAAAGATA
* * * *
8482 GAACGGCTGCAACCTACCCTAGGCTCGGGGTAAGAGA-TTGACTGATGGTGATCT
1 GAACGACTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTTG-CTGATGATGATCT
8536 ACCTCAGGTT
Statistics
Matches: 241, Mismatches: 41, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
77 71 0.29
78 167 0.69
79 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
GAACGACTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTC
AGGGTAAAAGATA
Found at i:8462 original size:156 final size:155
Alignment explanation
Indices: 8169--8535 Score: 452
Period size: 156 Copynumber: 2.4 Consensus size: 155
8159 CTTTATTGCT
* * * * ** *
8169 TCGAACGACTACAATTTGCCCAATGATCGGGGTAAGAGATTGGCTGATAATGATCTGCCCCAGGC
1 TCGAACGACTGCAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* * * * *
8234 TCAGGGAAAAAGATAGAATGACTGCAATCTGTCCTAGGCTTGGGGTAAGATATTTGCTGATGATG
66 TCAGGGAAAAAGATAGAATGACTGAAATCTGCCCTAAGCTCGGGGTAAGAGATTTGCTGATGATG
8299 ATCTGCCCCAAGCTCCA-GGTAAAATG-
131 ATCTG-CCCAAGCT-CAGGGTAAAA-GA
* *
8325 TCGAACGACTGCAATTTGTCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGGCCCAAGC
1 TCGAACGACTGCAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* * *
8390 TCAGGGTAAAAGATAGAATGGCTGAAATCTGCCCTAAGCTCGGGGTAAGAGA-TTGACTGATGTT
66 TCAGGGAAAAAGATAGAATGACTGAAATCTGCCCTAAGCTCGGGGTAAGAGATTTG-CTGATGAT
* *
8454 GATTTGCCCAGGCTCAGGGTAAAAGA
130 GATCTGCCCAAGCTCAGGGTAAAAGA
* * ** * *
8480 CCGAACGGCTGCAACCTACCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCT
1 TCGAACGACTGCAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCT
8536 ACCTCAGGTT
Statistics
Matches: 182, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
154 3 0.02
155 66 0.36
156 113 0.62
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (155 bp):
TCGAACGACTGCAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
TCAGGGAAAAAGATAGAATGACTGAAATCTGCCCTAAGCTCGGGGTAAGAGATTTGCTGATGATG
ATCTGCCCAAGCTCAGGGTAAAAGA
Found at i:8538 original size:39 final size:39
Alignment explanation
Indices: 8344--8678 Score: 190
Period size: 39 Copynumber: 8.6 Consensus size: 39
8334 TGCAATTTGT
*
8344 CCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGGC
1 CCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCT-GC
* * * *
8384 CC-AAGCTCAGGGTAAAAGATAGA---ATGGCTGAAATCTGC
1 CCTAGGCTCGGGGTAAGAGATTGACTGATGG-TG--ATCTGC
* * *
8422 CCTAAGCTCGGGGTAAGAGATTGACTGATGTTGATTTGC
1 CCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGC
* * ** * * ** * *
8461 CC-AGGCTCAGGGTAAAAGACCGAACGGCT-GCAACCTAC
1 CCTAGGCTCGGGGTAAGAGATTG-ACTGATGGTGATCTGC
*
8499 CCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCT-A
1 CCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGC
* * * * * *
8537 CCTCAGGTTCGAGGTAAGAGATCAGA-TAACT-ATAATCTGC
1 CCT-AGGCTCGGGGTAAGAGAT-TGACTGA-TGGTGATCTGC
* * *
8577 TCC-AGGCTCGGGGTAAGAGATCGAAC-GATTGTAATCTGC
1 -CCTAGGCTCGGGGTAAGAGATTG-ACTGATGGTGATCTGC
* * * *
8616 CCCAGACTTGGGGTAAGAGATTTG-TTGATGGTGATCTGC
1 CCTAGGCTCGGGGTAAGAGA-TTGACTGATGGTGATCTGC
*
8655 CCTAGGGTCGGGGTAAGAGATTGA
1 CCTAGGCTCGGGGTAAGAGATTGA
8679 AATCTTCAAT
Statistics
Matches: 218, Mismatches: 55, Indels: 45
0.69 0.17 0.14
Matches are distributed among these distances:
36 4 0.02
37 2 0.01
38 38 0.17
39 160 0.73
40 7 0.03
41 4 0.02
42 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (39 bp):
CCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGC
Found at i:8553 original size:155 final size:154
Alignment explanation
Indices: 8195--8597 Score: 442
Period size: 155 Copynumber: 2.6 Consensus size: 154
8185 TGCCCAATGA
** * *
8195 TCGGGGTAAGAGATTGGCTGATAATGATCTGCCCCAGGCTCAGGGAAAAAGATAGAATGACTGCA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAGGCTCAGGGTAAAAGATAGAATGACTGAA
* * *
8260 ATCTGTCCTAGGCTTGGGGTAAGATATTTGCTGATGATGATCTGCCCCAAGCTCCAGGTAAAATG
65 ATCTGCCCTAGGCTCGGGGTAAGAGA-TTGCTGATGATGATCTGCCCCAAGCTCCAGGTAAAATG
* ** **
8325 TCGAACGACTGCAATTTGTCCTAGGC
129 CCGAACGACTGCAACCTACCCTAGGC
* *
8351 TCGGGGTAAGAGATTGGCTGATGGTGATCTGGCCCAAGCTCAGGGTAAAAGATAGAATGGCTGAA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCT-GCCCAGGCTCAGGGTAAAAGATAGAATGACTGAA
* * * *
8416 ATCTGCCCTAAGCTCGGGGTAAGAGATTGACTGATGTTGATTTG-CCCAGGCT-CAGGGTAAAA-
65 ATCTGCCCTAGGCTCGGGGTAAGAGATTG-CTGATGATGATCTGCCCCAAGCTCCA-GGTAAAAT
*
8478 GACCGAACGGCTGCAACCTACCCTAGGC
128 G-CCGAACGACTGCAACCTACCCTAGGC
* * * * *
8506 TCGGGGTAAGAGATTGACTGATGGTGATCTACCTCAGGTTC-GAGGTAAGAGATCAG-ATAACT-
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCC-CAGGCTCAG-GGTAAAAGAT-AGAATGACTG
8568 ATAATCTGCTCC-AGGCTCGGGGTAAGAGAT
63 A-AATCTGC-CCTAGGCTCGGGGTAAGAGAT
8598 CGAACGATTG
Statistics
Matches: 211, Mismatches: 27, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
154 7 0.03
155 108 0.51
156 95 0.45
157 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (154 bp):
TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCAGGCTCAGGGTAAAAGATAGAATGACTGAAA
TCTGCCCTAGGCTCGGGGTAAGAGATTGCTGATGATGATCTGCCCCAAGCTCCAGGTAAAATGCC
GAACGACTGCAACCTACCCTAGGC
Found at i:10930 original size:3 final size:3
Alignment explanation
Indices: 10922--10951 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
10912 GGTCATCCCT
*
10922 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
10952 AATATCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:10939 original size:15 final size:15
Alignment explanation
Indices: 10921--10950 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10911 CGGTCATCCC
10921 TTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTT
10936 TTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTT
10951 CAATATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTCTTCTTCTT
Found at i:19960 original size:127 final size:127
Alignment explanation
Indices: 19734--19988 Score: 501
Period size: 127 Copynumber: 2.0 Consensus size: 127
19724 AAAATTTTGA
19734 AAACTCGGATAAGGCTTTAAAGTATGATCCTTAAATGCATAAGTCATGTTTAAGAAAGAAGTCGA
1 AAACTCGGATAAGGCTTTAAAGTATGATCCTTAAATGCATAAGTCATGTTTAAGAAAGAAGTCGA
19799 ATTTTGTTTGGAAGTCTCTCTATTTCGAGGTGATCGAGAGAGAAAGTAATGTCCAGTGAGTT
66 ATTTTGTTTGGAAGTCTCTCTATTTCGAGGTGATCGAGAGAGAAAGTAATGTCCAGTGAGTT
19861 AAACTCGGATAAGGCTTTAAAGTATGATCCTTAAATGCATAAGTCATGTTTAAGAAAGAAGTCGA
1 AAACTCGGATAAGGCTTTAAAGTATGATCCTTAAATGCATAAGTCATGTTTAAGAAAGAAGTCGA
*
19926 TTTTTGTTTGGAAGTCTCTCTATTTCGAGGTGATCGAGAGAGAAAGTAATGTCCAGTGAGTT
66 ATTTTGTTTGGAAGTCTCTCTATTTCGAGGTGATCGAGAGAGAAAGTAATGTCCAGTGAGTT
19988 A
1 A
19989 GGACATAATG
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (127 bp):
AAACTCGGATAAGGCTTTAAAGTATGATCCTTAAATGCATAAGTCATGTTTAAGAAAGAAGTCGA
ATTTTGTTTGGAAGTCTCTCTATTTCGAGGTGATCGAGAGAGAAAGTAATGTCCAGTGAGTT
Found at i:20222 original size:97 final size:98
Alignment explanation
Indices: 20054--20250 Score: 281
Period size: 97 Copynumber: 2.0 Consensus size: 98
20044 AACCTTGAAA
* * * *
20054 AAGGGTATTCGATTATCCCAGTTTGAAGAAAAGTTGCGGCTAGTAAGTTAAGGCACAAATTTCCA
1 AAGGGTATTCGATTATCCCAATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTCCA
*
20119 AAACTCGAGAT-AAAGAAATATTGCCTCGAT-TT
66 AAACTCGAAATAAAAG-AATATTGCCTCGATGTT
* ** *
20151 AAGGGTATTCGATTATCCCAATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCATGAATTTTCA
1 AAGGGTATTCGATTATCCCAATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTCCA
*
20216 AGACTCGAAATAAAAGAATATTGCCTCGATGTT
66 AAACTCGAAATAAAAGAATATTGCCTCGATGTT
20249 AA
1 AA
20251 ATATTTTGGA
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
97 80 0.91
98 8 0.09
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (98 bp):
AAGGGTATTCGATTATCCCAATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTCCA
AAACTCGAAATAAAAGAATATTGCCTCGATGTT
Found at i:20593 original size:29 final size:29
Alignment explanation
Indices: 20495--20811 Score: 220
Period size: 29 Copynumber: 11.0 Consensus size: 29
20485 AGTTCCGGAT
* * *
20495 AGTTTG-GGGTTAAAATGTAATTTTAGAA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
* * *
20523 AGTTTTAGGGGTAAAAATGTCATTTTGGGA
1 AGTTTGA-GGGTAAAAATGTAATTTTTGGA
** * * *
20553 AAATTCAAGGTAAAAATGTGATTTTTGGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
** * *
20582 AGTTTGAGGGTAAAAACATGATTTTTGAA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
* *
20611 AGTTT-AGGGGCAAAAATGTGATTTTTGGA
1 AGTTTGA-GGGTAAAAATGTAATTTTTGGA
* *
20640 AGTTTAAGGGCAAAAATGTAATTTTTGGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
* *
20669 AGTATG-GGG-GAAAATGTAATTTTTGAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTG-GA
* *
20697 AGTTCGAGGG-AAAAATGT-ATTTTTCAAGA
1 AGTTTGAGGGTAAAAATGTAATTTTT--GGA
*
20726 AGTTT-AGGAGT-AAAACGTAATTTTTGGA
1 AGTTTGAGG-GTAAAAATGTAATTTTTGGA
* ** * *
20754 TGTTCAAGGATAAAAATGTAATTTTTAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
** * *
20783 AGTTCAAGGGTTAAAATGTGA-TTTTGGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
20811 A
1 A
20812 AAATGTAAGG
Statistics
Matches: 233, Mismatches: 43, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
27 15 0.06
28 37 0.16
29 152 0.65
30 29 0.12
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AGTTTGAGGGTAAAAATGTAATTTTTGGA
Found at i:20749 original size:114 final size:113
Alignment explanation
Indices: 20565--20785 Score: 268
Period size: 114 Copynumber: 1.9 Consensus size: 113
20555 ATTCAAGGTA
* * * * *
20565 AAAATGTGATTTTTGGAAGTTTGAGGGTAAAAACATGATTTTTGAAAGTTTAGGGGCAAAAATGT
1 AAAATGTAATTTTTGGAAGTTCGAGGG-AAAAACATGATTTTTAAAAGTTTAGGAGCAAAAACGT
* * * *
20630 GATTTTTGGAAGTTTAAGGGCAAAAATGTAATTTTTGGAAGTATGGGGG
65 AATTTTTGGAAGTTCAAGGACAAAAATGTAATTTTTAGAAGTATGGGGG
*
20679 AAAATGTAATTTTTGAGAAGTTCGAGGG-AAAA-ATGTATTTTTCAAGAAGTTTAGGAG-TAAAA
1 AAAATGTAATTTTTG-GAAGTTCGAGGGAAAAACATG-ATTTTT-AA-AAGTTTAGGAGCAAAAA
* *
20741 CGTAATTTTTGGATGTTCAAGGATAAAAATGTAATTTTTAGAAGT
62 CGTAATTTTTGGAAGTTCAAGGACAAAAATGTAATTTTTAGAAGT
20786 TCAAGGGTTA
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
112 3 0.03
113 10 0.11
114 57 0.63
115 21 0.23
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (113 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGAAAAACATGATTTTTAAAAGTTTAGGAGCAAAAACGTA
ATTTTTGGAAGTTCAAGGACAAAAATGTAATTTTTAGAAGTATGGGGG
Found at i:22713 original size:6 final size:6
Alignment explanation
Indices: 22702--22795 Score: 76
Period size: 6 Copynumber: 16.7 Consensus size: 6
22692 TAGATTTGAA
* *
22702 TAAATT TAAATT TAAA-- T-AATT TAAAATT TAAA-A TAAATT TAAACT
1 TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT
* * * *
22747 TAAAAT T-AATT TAAACT TAAAAT T-AATT TAAATT TAAA-A TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
22792 TAAA
1 TAAA
22796 CCTAAAACAA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
3 2 0.03
4 1 0.01
5 17 0.24
6 45 0.64
7 5 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:22788 original size:51 final size:50
Alignment explanation
Indices: 22703--22812 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 50
22693 AGATTTGAAT
* * *
22703 AAATTTAAATTTAAATAATTTAAAATTTAAAATAAATTTAAACTTAAAAT
1 AAATTTAAATTAAAATAATTTAAAATTTAAAATAAATTTAAACCTAAAAC
*
22753 TAATTTAAACTTAAAATTAATTT-AAATTTAAAATAAATTTAAACCTAAAAC
1 AAATTTAAA-TTAAAA-TAATTTAAAATTTAAAATAAATTTAAACCTAAAAC
22804 AAATTTAAA
1 AAATTTAAA
22813 AAATGCGTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 8 0.15
51 39 0.74
52 6 0.11
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (50 bp):
AAATTTAAATTAAAATAATTTAAAATTTAAAATAAATTTAAACCTAAAAC
Found at i:22801 original size:17 final size:17
Alignment explanation
Indices: 22700--22812 Score: 140
Period size: 17 Copynumber: 6.7 Consensus size: 17
22690 TTTAGATTTG
*
22700 AATAAATTTAAA-TTTA
1 AATAAATTTAAACTTAA
*
22716 AAT-AATTTAAAATTTAA
1 AATAAATTT-AAACTTAA
22733 AATAAATTTAAACTTAA
1 AATAAATTTAAACTTAA
*
22750 AATTAATTTAAACTTAA
1 AATAAATTTAAACTTAA
* *
22767 AATTAATTTAAATTTAA
1 AATAAATTTAAACTTAA
*
22784 AATAAATTTAAACCTAA
1 AATAAATTTAAACTTAA
*
22801 AACAAATTTAAA
1 AATAAATTTAAA
22813 AAATGCGTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
15 5 0.06
16 6 0.07
17 70 0.81
18 5 0.06
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATTTAAACTTAA
Done.