Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009982.1 Kokia drynarioides strain JFW-HI SEQ_124734, 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: 111890
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Warning! 131 characters in sequence are not A, C, G, or T
Found at i:30 original size:23 final size:23
Alignment explanation
Indices: 1--64 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
*
1 TCTCTGTTTAGCACTTTGTGTGC
1 TCTCTGTTTAGCACTTTATGTGC
*
24 TCTCTGTTGCCCAGCAC-TTATGTGC
1 TCTCTGTT---TAGCACTTTATGTGC
*
49 TCTCTGTTTAGTACTT
1 TCTCTGTTTAGCACTT
65 CGGTACTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 4 0.12
23 9 0.27
25 15 0.45
26 5 0.15
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (23 bp):
TCTCTGTTTAGCACTTTATGTGC
Found at i:944 original size:17 final size:16
Alignment explanation
Indices: 918--958 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
908 TTGGGACATT
*
918 ATTTAAATAAATTTAA
1 ATTTAAATAAACTTAA
934 ATTTAAAATAAACTTAA
1 ATTT-AAATAAACTTAA
*
951 ATTCAAAT
1 ATTTAAAT
959 TCTGTTGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTAAATAAACTTAA
Found at i:1530 original size:50 final size:50
Alignment explanation
Indices: 1440--1830 Score: 256
Period size: 50 Copynumber: 7.9 Consensus size: 50
1430 TCCTCTTGCG
* * * * * * *
1440 TCTTCGCGGTACTGGATACGTCGTTACGACTTAAACCTTTCCCTTTTGTA
1 TCTTTGCGGTACTGTATCCGCCGTTGCGACTTAGATCTTTCCCTTTTGTA
* *
1490 TCTTTGCGGTACTGTATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATG--
1 TCTTTGCGGTACTGTATCCGCCGTTGCGACTTAGATCTTTCCCTT-TTGTA
* * *
1539 TCTCTGAGGTACTAGGT-T-CGTCGTTGCGACTTA-ATCCTTTCCCTTTTGTA
1 TCTTTGCGGTACT--GTATCCGCCGTTGCGACTTAGAT-CTTTCCCTTTTGTA
* * * *
1589 TATTTGTGGTACTGTATCCGCCATTGCGACTTAGATCTTTCCCTTCATG--
1 TCTTTGCGGTACTGTATCCGCCGTTGCGACTTAGATCTTTCCCTT-TTGTA
* * * ** * *
1638 TCTCTGAGGTACTAGGT-T-TGTTGTTACGACTTA-ATCCTTTCCCTTTTATA
1 TCTTTGCGGTACT--GTATCCGCCGTTGCGACTTAGAT-CTTTCCCTTTTGTA
* * * * *
1688 TCTTTGCGGTA-TGGATCCGCCATTGCGGCTTAGATATTTCCCTTCATGT-
1 TCTTTGCGGTACTGTATCCGCCGTTGCGACTTAGATCTTTCCCTT-TTGTA
* * * *
1737 T-TTTGAGGTA-T-TAAGTTCGTCGTTACGACTTA-ATCCTTTCCCTTTTGTA
1 TCTTTGCGGTACTGT-A-TCCGCCGTTGCGACTTAGAT-CTTTCCCTTTTGTA
* *
1786 TCTTTGCGATACTGGATCCGCCGTTGCGACTTAGATCTTTCCCTT
1 TCTTTGCGGTACTGTATCCGCCGTTGCGACTTAGATCTTTCCCTT
1831 CATGTTTCTG
Statistics
Matches: 257, Mismatches: 57, Indels: 54
0.70 0.15 0.15
Matches are distributed among these distances:
47 1 0.00
48 25 0.10
49 103 0.40
50 114 0.44
51 14 0.05
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.41
Consensus pattern (50 bp):
TCTTTGCGGTACTGTATCCGCCGTTGCGACTTAGATCTTTCCCTTTTGTA
Found at i:1564 original size:49 final size:49
Alignment explanation
Indices: 1508--1931 Score: 296
Period size: 49 Copynumber: 8.6 Consensus size: 49
1498 GTACTGTATC
* *
1508 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
1 CGCCGTTGCGACTTAGATCTTTCCCTTCATGTCTTTGAGGTACTAGGTT
* * * *
1557 CGTCGTTGCGACTTA-ATCCTTTCCCTT-TTGTATATTTGTGGTACT--GTAT
1 CGCCGTTGCGACTTAGAT-CTTTCCCTTCATG--TCTTTGAGGTACTAGGT-T
* *
1606 CCGCCATTGCGACTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
1 -CGCCGTTGCGACTTAGATCTTTCCCTTCATGTCTTTGAGGTACTAGGTT
* ** * * * * *
1656 TGTTGTTACGACTTA-ATCCTTTCCCTTTTATATCTTTGCGGTA-T-GGATC
1 CGCCGTTGCGACTTAGAT-CTTTCCC-TTCATGTCTTTGAGGTACTAGG-TT
* * * * * *
1705 CGCCATTGCGGCTTAGATATTTCCCTTCATGTTTTTGAGGTATTAAGTT
1 CGCCGTTGCGACTTAGATCTTTCCCTTCATGTCTTTGAGGTACTAGGTT
* * * * * *
1754 CGTCGTTACGACTTA-ATCCTTTCCCTT-TTGTATCTTTGCGATACT-GGATC
1 CGCCGTTGCGACTTAGAT-CTTTCCCTTCATG--TCTTTGAGGTACTAGG-TT
1804 CGCCGTTGCGACTTAGATCTTTCCCTTCATGT-TTCTGAGGTACTAGGTT
1 CGCCGTTGCGACTTAGATCTTTCCCTTCATGTCTT-TGAGGTACTAGGTT
* * * * * *
1853 CGCCATTGCGACTTAAACCTTTCCCTTTATGTC-TTCATGGTACTAGATT
1 CGCCGTTGCGACTTAGATCTTTCCCTTCATGTCTTTGA-GGTACTAGGTT
* * * *
1902 CACCGTTGCGACCTAAATTTTTCCCTTCAT
1 CGCCGTTGCGACTTAGATCTTTCCCTTCAT
1932 CTTTCATGGT
Statistics
Matches: 285, Mismatches: 65, Indels: 50
0.71 0.16 0.12
Matches are distributed among these distances:
48 31 0.11
49 161 0.56
50 83 0.29
51 10 0.04
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (49 bp):
CGCCGTTGCGACTTAGATCTTTCCCTTCATGTCTTTGAGGTACTAGGTT
Found at i:1622 original size:99 final size:99
Alignment explanation
Indices: 1458--1880 Score: 623
Period size: 99 Copynumber: 4.3 Consensus size: 99
1448 GTACTGGATA
* * * *
1458 CGTCGTTACGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGTATCCGCCGTTGCGGCTTA
1 CGTCGTTACGACTTAATCCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGACTTA
1523 GATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
66 GATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
* * * *
1557 CGTCGTTGCGACTTAATCCTTTCCCTTTTGTATATTTGTGGTACTGTATCCGCCATTGCGACTTA
1 CGTCGTTACGACTTAATCCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGACTTA
1622 GATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
66 GATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
* * * *
1656 TGTTGTTACGACTTAATCCTTTCCCTTTTATATCTTTGCGGTA-TGGATCCGCCATTGCGGCTTA
1 CGTCGTTACGACTTAATCCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGACTTA
* * * * *
1720 GATATTTCCCTTCATGTTTTTGAGGTATTAAGTT
66 GATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
* *
1754 CGTCGTTACGACTTAATCCTTTCCCTTTTGTATCTTTGCGATACTGGATCCGCCGTTGCGACTTA
1 CGTCGTTACGACTTAATCCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGACTTA
*
1819 GATCTTTCCCTTCATGTTTCTGAGGTACTAGGTT
66 GATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
* * * *
1853 CGCCATTGCGACTTAAACCTTTCCCTTT
1 CGTCGTTACGACTTAATCCTTTCCCTTT
1881 ATGTCTTCAT
Statistics
Matches: 290, Mismatches: 33, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
98 87 0.30
99 203 0.70
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.41
Consensus pattern (99 bp):
CGTCGTTACGACTTAATCCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGACTTA
GATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
Found at i:1807 original size:197 final size:198
Alignment explanation
Indices: 1461--1880 Score: 644
Period size: 197 Copynumber: 2.1 Consensus size: 198
1451 CTGGATACGT
* * *
1461 CGTTACGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGTATCCGCCGTTGCGGCTTAGAT
1 CGTTACGACTTAAACCTTTCCCTTTTATATCTTTGCGGTACTGGATCCGCCATTGCGGCTTAGAT
* * *
1526 CTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGTCGTTGCGACTTAATCCTTTCCCTTTTGTATA
66 ATTTCCCTTCATGTCTCTGAGGTACTAAGTTCGTCGTTACGACTTAATCCTTTCCCTTTTGTATA
* * *
1591 TTTGTGGTACTGTATCCGCCATTGCGACTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
131 TTTGCGATACTGGATCCGCCATTGCGACTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
* *
1656 TGT
196 CGC
* *
1659 TGTTACGACTTAATCCTTTCCCTTTTATATCTTTGCGGTA-TGGATCCGCCATTGCGGCTTAGAT
1 CGTTACGACTTAAACCTTTCCCTTTTATATCTTTGCGGTACTGGATCCGCCATTGCGGCTTAGAT
* * * *
1723 ATTTCCCTTCATGTTTTTGAGGTATTAAGTTCGTCGTTACGACTTAATCCTTTCCCTTTTGTATC
66 ATTTCCCTTCATGTCTCTGAGGTACTAAGTTCGTCGTTACGACTTAATCCTTTCCCTTTTGTATA
* *
1788 TTTGCGATACTGGATCCGCCGTTGCGACTTAGATCTTTCCCTTCATGTTTCTGAGGTACTAGGTT
131 TTTGCGATACTGGATCCGCCATTGCGACTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
1853 CGC
196 CGC
* *
1856 CATTGCGACTTAAACCTTTCCCTTT
1 CGTTACGACTTAAACCTTTCCCTTT
1881 ATGTCTTCAT
Statistics
Matches: 199, Mismatches: 23, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
197 162 0.81
198 37 0.19
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.41
Consensus pattern (198 bp):
CGTTACGACTTAAACCTTTCCCTTTTATATCTTTGCGGTACTGGATCCGCCATTGCGGCTTAGAT
ATTTCCCTTCATGTCTCTGAGGTACTAAGTTCGTCGTTACGACTTAATCCTTTCCCTTTTGTATA
TTTGCGATACTGGATCCGCCATTGCGACTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
CGC
Found at i:13012 original size:30 final size:28
Alignment explanation
Indices: 12977--13172 Score: 116
Period size: 30 Copynumber: 6.8 Consensus size: 28
12967 ACATCTGAGA
* *
12977 GTAAAATGGTACTTTTTGGAAGAATTTG-G
1 GTAAAATGGTAATTTTTGGAAG--TTCGAG
13006 GTTAAAAATGG-AATTTTTGGAAGTTCGAG
1 G-T-AAAATGGTAATTTTTGGAAGTTCGAG
**
13035 GTAAAATGGTAATTTTTGGAAAAATCG-G
1 GTAAAATGGTAATTTTTGG-AAGTTCGAG
* *
13063 AGTAAAAAATGG-AA-TTTTGAAAAGTTCGGGG
1 -GT--AAAATGGTAATTTTTG-GAAGTTC-GAG
** *
13094 GTAAAATGGTAATTTTTGGAAAAATCAAG
1 GTAAAATGGTAATTTTTGG-AAGTTCGAG
* * *
13123 GTTAAAAATGG-AATTTTTGAAAGTTTGGG
1 G-T-AAAATGGTAATTTTTGGAAGTTCGAG
*
13152 GTAAAATGGTGATTTTTGGAA
1 GTAAAATGGTAATTTTTGGAA
13173 AAAAATCGGG
Statistics
Matches: 130, Mismatches: 20, Indels: 35
0.70 0.11 0.19
Matches are distributed among these distances:
27 14 0.11
28 31 0.24
29 28 0.22
30 35 0.27
31 22 0.17
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (28 bp):
GTAAAATGGTAATTTTTGGAAGTTCGAG
Found at i:13020 original size:59 final size:57
Alignment explanation
Indices: 12921--13174 Score: 228
Period size: 58 Copynumber: 4.4 Consensus size: 57
12911 ACTTGAGGGC
* * * **
12921 AAAATGGTAATTTTAGG-AAATTAAGAGTCAAAAACAGAATTTTTAGACA--TCTGAGAGT
1 AAAATGGTAATTTTTGGAAAATT-AGGGTTAAAAATGGAATTTTTAGA-AGTTC-GAG-GT
* * *
12979 AAAATGGTACTTTTTGGAAGAATTTGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGT
1 AAAATGGTAATTTTTGGAA-AATTAGGGTTAAAAATGGAATTTTTAGAAGTTCGAGGT
* * * * * *
13037 AAAATGGTAATTTTTGGAAAAATCGGAGTAAAAAATGGAATTTTGAAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAATTAGG-GTTAAAAATGGAATTTTTAGAAGTTC-GAGGT
* * * *
13096 AAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTT-GAAAGTTTGGGGT
1 AAAATGGTAATTTTTGG-AAAATTAGGGTTAAAAATGGAATTTTTAG-AAGTTCGAGGT
*
13154 AAAATGGTGATTTTTGGAAAA
1 AAAATGGTAATTTTTGGAAAA
13175 AAATCGGGGC
Statistics
Matches: 163, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
57 9 0.06
58 79 0.48
59 64 0.39
60 11 0.07
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (57 bp):
AAAATGGTAATTTTTGGAAAATTAGGGTTAAAAATGGAATTTTTAGAAGTTCGAGGT
Found at i:13039 original size:58 final size:57
Alignment explanation
Indices: 12977--13174 Score: 245
Period size: 58 Copynumber: 3.4 Consensus size: 57
12967 ACATCTGAGA
* * * *
12977 GTAAAATGGTACTTTTTGGAAGAATTTGGGTTAAAAATGGAATTTTTGGAAGTTCGAG
1 GTAAAATGGTAATTTTTGGAA-AATTAGGGTTAAAAATGGAATTTTTGAAAGTTCGGG
* * *
13035 GTAAAATGGTAATTTTTGGAAAAATCGGAGTAAAAAATGGAA-TTTTGAAAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAAATTAGG-GTTAAAAATGGAATTTTTG-AAAGTTC-GGG
* * *
13094 GTAAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTTGAAAGTTTGGG
1 GTAAAATGGTAATTTTTGG-AAAATTAGGGTTAAAAATGGAATTTTTGAAAGTTCGGG
*
13152 GTAAAATGGTGATTTTTGGAAAA
1 GTAAAATGGTAATTTTTGGAAAA
13175 AAATCGGGGC
Statistics
Matches: 122, Mismatches: 13, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
57 14 0.11
58 59 0.48
59 39 0.32
60 10 0.08
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (57 bp):
GTAAAATGGTAATTTTTGGAAAATTAGGGTTAAAAATGGAATTTTTGAAAGTTCGGG
Found at i:13176 original size:59 final size:57
Alignment explanation
Indices: 12977--13207 Score: 277
Period size: 59 Copynumber: 3.9 Consensus size: 57
12967 ACATCTGAGA
* * * * *
12977 GTAAAATGGTACTTTTTGGAAGAATTTGGGTTAAAAATGGAATTTTTGGAAGTTCGAG
1 GTAAAATGGTAATTTTTGGAA-AAATCGGGTTAAAAATGGAATTTTTGAAAGTTCGGG
*
13035 GTAAAATGGTAATTTTTGGAAAAATCGGAGTAAAAAATGGAA-TTTTGAAAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAAAATCGG-GTTAAAAATGGAATTTTTG-AAAGTTC-GGG
* *
13094 GTAAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTTGAAAGTTTGGG
1 GTAAAATGGTAATTTTTGGAAAAATC-GGGTTAAAAATGGAATTTTTGAAAGTTCGGG
* * *
13152 GTAAAATGGTGATTTTTGGAAAAAAATCGGGGCT-AAGATGGAATTTTTGAAAGTTC
1 GTAAAATGGTAATTTTTGG--AAAAATC-GGGTTAAAAATGGAATTTTTGAAAGTTC
13208 AGGGATCAAA
Statistics
Matches: 151, Mismatches: 15, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
57 10 0.07
58 59 0.39
59 66 0.44
60 16 0.11
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (57 bp):
GTAAAATGGTAATTTTTGGAAAAATCGGGTTAAAAATGGAATTTTTGAAAGTTCGGG
Found at i:14388 original size:3 final size:3
Alignment explanation
Indices: 14380--14431 Score: 79
Period size: 3 Copynumber: 17.0 Consensus size: 3
14370 GTTTCCTTTT
14380 TTA TTA TTA TTGA -TA CTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14426 TTA TTA
1 TTA TTA
14432 ATGCCGTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 42 0.91
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:15088 original size:6 final size:6
Alignment explanation
Indices: 15077--15152 Score: 54
Period size: 6 Copynumber: 13.2 Consensus size: 6
15067 ATTATTTAAA
* *
15077 TAAATT TAAATT TAAATT T--ATGA TAAATT TAAATTT TCAA-T T-AATT
1 TAAATT TAAATT TAAATT TAAAT-T TAAATT TAAA-TT TAAATT TAAATT
* * *
15123 TAAATT TAAA-A TAAACT TAAATT CAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT T
15153 TGTTGAGCCC
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
4 4 0.07
5 9 0.16
6 35 0.64
7 7 0.13
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:15105 original size:17 final size:17
Alignment explanation
Indices: 15083--15145 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
15073 TAAATAAATT
*
15083 TAAATTTAAATTTATGA
1 TAAATTTAAATTTATAA
15100 TAAATTTAAATTT-TCAA
1 TAAATTTAAATTTAT-AA
* *
15117 TTAATTTAAATTTAAAA
1 TAAATTTAAATTTATAA
*
15134 TAAACTTAAATT
1 TAAATTTAAATT
15146 CAAATTTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
16 1 0.03
17 38 0.97
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:15126 original size:23 final size:23
Alignment explanation
Indices: 15076--15132 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
15066 CATTATTTAA
*
15076 ATAAATTTAAATTTAAATTTATG
1 ATAAATTTAAATTTAAATTAATG
*
15099 ATAAATTTAAATTTTCAATTAAT-
1 ATAAATTTAAA-TTTAAATTAATG
*
15122 TTAAATTTAAA
1 ATAAATTTAAA
15133 ATAAACTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAAATTTAAATTTAAATTAATG
Found at i:22508 original size:24 final size:23
Alignment explanation
Indices: 22456--22509 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
22446 TTTACAAGTA
*
22456 ATTTTAAAAATTTATCATTTTTCT
1 ATTTTAAAAATTTAT-ATTTTTAT
*
22480 TTTTTAAAATATTTAT-TTTTTAAT
1 ATTTTAAAA-ATTTATATTTTT-AT
22504 ATTTTA
1 ATTTTA
22510 TTATACTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 5 0.20
24 14 0.56
25 6 0.24
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTTAAAAATTTATATTTTTAT
Found at i:24809 original size:36 final size:36
Alignment explanation
Indices: 24747--24843 Score: 90
Period size: 36 Copynumber: 2.7 Consensus size: 36
24737 AAGTCATTAG
* * * *
24747 TTGGCAATATAAAATGTAAGAGATGCA-ACTCAT-TCA
1 TTGGTAATATAAAACGCAAGAAATGCATACT-ATCT-A
* *
24783 TTGGTAATATGAAACGCGAGAAATGCATACTATCTA
1 TTGGTAATATAAAACGCAAGAAATGCATACTATCTA
* *
24819 TTGGTGATATAAAACGTAAGAAATG
1 TTGGTAATATAAAACGCAAGAAATG
24844 TGCACTATCC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
36 45 0.92
37 4 0.08
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (36 bp):
TTGGTAATATAAAACGCAAGAAATGCATACTATCTA
Found at i:25176 original size:58 final size:58
Alignment explanation
Indices: 25099--25240 Score: 164
Period size: 58 Copynumber: 2.4 Consensus size: 58
25089 GAAGATGATG
*
25099 TGCCTCACC-TCTGTTGAGAGCCCGAACA-G-TTCACGAAGGGGCCCGAATGTTAAAGATA
1 TGCCTCACCTTC-GTCGAGAGCCC-AA-ATGATTCACGAAGGGGCCCGAATGTTAAAGATA
* * *
25157 TGCCTCACCTTCGTCGAGAGCCCAAATGATTCACGGAGGGGCCCGAATGTTGATGATA
1 TGCCTCACCTTCGTCGAGAGCCCAAATGATTCACGAAGGGGCCCGAATGTTAAAGATA
* * * *
25215 TACCTCATCTCCGCCGAGAGCCCAAA
1 TGCCTCACCTTCGTCGAGAGCCCAAA
25241 GGGCTCATGG
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
56 1 0.01
57 3 0.04
58 67 0.92
59 2 0.03
ACGTcount: A:0.26, C:0.29, G:0.25, T:0.20
Consensus pattern (58 bp):
TGCCTCACCTTCGTCGAGAGCCCAAATGATTCACGAAGGGGCCCGAATGTTAAAGATA
Found at i:26288 original size:20 final size:21
Alignment explanation
Indices: 26244--26288 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
26234 GAAATGCACT
26244 TTTTAATATTTCAAAATAACAA
1 TTTTAATATTTCAAAAT-ACAA
26266 TTTTAATA-TTCTAAAAT-CAA
1 TTTTAATATTTC-AAAATACAA
26286 TTT
1 TTT
26289 CAATTAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.27
21 3 0.14
22 13 0.59
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTAATATTTCAAAATACAA
Found at i:27109 original size:60 final size:61
Alignment explanation
Indices: 27043--27187 Score: 159
Period size: 61 Copynumber: 2.4 Consensus size: 61
27033 TCCTTTTTAA
* * * *
27043 TTTTTAGAGTTAGGATTAAATTGGCAGATTTTGTAAA-ATCGAGGGCCAAATTTATTG-AT
1 TTTTTAGAATTAGGATTAAATTGACAAATATTGTAAACATCGAGGGCCAAATTTATTGAAT
* * * * *
27102 TATTTTAGAATTAGAACTAAAATGACAAATATTGTAAACATTGAGGGCTAAATTTATTGAAT
1 T-TTTTAGAATTAGGATTAAATTGACAAATATTGTAAACATCGAGGGCCAAATTTATTGAAT
* * *
27164 TTTTTATATTTAGGATCAAATTGA
1 TTTTTAGAATTAGGATTAAATTGA
27188 TAGAATGTGT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
59 1 0.01
60 29 0.43
61 35 0.51
62 3 0.04
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.39
Consensus pattern (61 bp):
TTTTTAGAATTAGGATTAAATTGACAAATATTGTAAACATCGAGGGCCAAATTTATTGAAT
Found at i:31070 original size:16 final size:17
Alignment explanation
Indices: 31040--31076 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
31030 GTTTAAAATT
31040 TTTAATTAATTAAATTTA
1 TTTAATTAA-TAAATTTA
31058 TTTAATTAA-AAATTTA
1 TTTAATTAATAAATTTA
31074 TTT
1 TTT
31077 TCATTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTAATAAATTTA
Found at i:34137 original size:25 final size:25
Alignment explanation
Indices: 34105--34183 Score: 158
Period size: 25 Copynumber: 3.2 Consensus size: 25
34095 CCTTTTTACT
34105 ACACTGAGTGAATGATTTCATGCAC
1 ACACTGAGTGAATGATTTCATGCAC
34130 ACACTGAGTGAATGATTTCATGCAC
1 ACACTGAGTGAATGATTTCATGCAC
34155 ACACTGAGTGAATGATTTCATGCAC
1 ACACTGAGTGAATGATTTCATGCAC
34180 ACAC
1 ACAC
34184 CAGGCACTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (25 bp):
ACACTGAGTGAATGATTTCATGCAC
Found at i:48001 original size:23 final size:22
Alignment explanation
Indices: 47966--48017 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
47956 ATTGATTTTA
*
47966 AAATTTAGAAAGTATA-GGATT
1 AAATTTAGAAAGTAGAGGGATT
*
47987 GAATTTGAGCAAAGTAGAGGGATT
1 AAATTT-AG-AAAGTAGAGGGATT
48011 AAATTTA
1 AAATTTA
48018 ATTTTTGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 5 0.20
22 2 0.08
23 8 0.32
24 10 0.40
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.31
Consensus pattern (22 bp):
AAATTTAGAAAGTAGAGGGATT
Found at i:50968 original size:76 final size:76
Alignment explanation
Indices: 50820--50976 Score: 192
Period size: 76 Copynumber: 2.1 Consensus size: 76
50810 AAATTATGTA
* * * *
50820 TGCAAGTTATTTAAAGCCATCTTTGGGCTTAAGCAAGCCCTACAACAATGGTATTAAAAAACCAC
1 TGCAAGTTATTTAAAGCCATCTATGGACTCAAGCAAGCCCTACAACAATGGCATTAAAAAACCAC
50885 CAAAGTTCTCC
66 CAAAGTTCTCC
* * *
50896 TGCAAGTTATTTAAGGCTATCTATGGACTCAAGCAAGCTCC-ACAACAATGGCA-TAAAGAAGCC
1 TGCAAGTTATTTAAAGCCATCTATGGACTCAAGCAAGC-CCTACAACAATGGCATTAAA-AAACC
* * *
50959 TCCAGAGTTCTCT
64 ACCAAAGTTCTCC
50972 TGCAA
1 TGCAA
50977 ATGGTGTTTC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
75 4 0.06
76 63 0.91
77 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (76 bp):
TGCAAGTTATTTAAAGCCATCTATGGACTCAAGCAAGCCCTACAACAATGGCATTAAAAAACCAC
CAAAGTTCTCC
Found at i:57972 original size:7 final size:7
Alignment explanation
Indices: 57960--57994 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
57950 TCCTAGATTT
57960 TGGAAAA
1 TGGAAAA
57967 TGGAAAA
1 TGGAAAA
57974 TGGAAAA
1 TGGAAAA
57981 TGGAAAA
1 TGGAAAA
*
57988 TTGAAAA
1 TGGAAAA
57995 AGATTGGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (7 bp):
TGGAAAA
Found at i:59838 original size:29 final size:28
Alignment explanation
Indices: 59806--59868 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
59796 AAAATGAGAC
59806 TTTGGA-TACCCGAGGGGCAAAATGGTAAT
1 TTTGGACT-CCCGA-GGGCAAAATGGTAAT
* *
59835 TTTGGACTCTCGAGGGTAAAATGGTAAT
1 TTTGGACTCCCGAGGGCAAAATGGTAAT
59863 TTTGGA
1 TTTGGA
59869 AAATTTTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 20 0.65
29 10 0.32
30 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (28 bp):
TTTGGACTCCCGAGGGCAAAATGGTAAT
Found at i:59895 original size:58 final size:57
Alignment explanation
Indices: 59832--60166 Score: 264
Period size: 58 Copynumber: 5.8 Consensus size: 57
59822 GCAAAATGGT
* *
59832 AATTTTGGAC-TCTCGAGGGTAAAATGGTAATTTTGGAAAATTTTGGGGTTTAAAATAG
1 AATTTTGGACAT-TCGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGG-TTAAAATAG
* * * * ** * * * **
59890 AATTTTAGACATTTGAGGGTAAAACGGTAATTTTAGAAA-AATCGGGATAGAAAACGG
1 AATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGT-TAAAATAG
* * * * *
59947 AATTTTTGGACATTTGGGGGTTAAAATGGTAATTTTTGAGAGTTTTGAGGTTAAAATTGG
1 AA-TTTTGGACATTCGAGGG-TAAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAA-TAG
* * * *
60007 AGTTTTTAGACATTCGAGGGTAAAATGGTAATTTTTTGAAAGTTTTGGGGTCAAAATAA
1 A-ATTTTGGACATTCGAGGGTAAAATGGTAA-TTTTTGAAAGTTTTGGGGTTAAAATAG
* ** * * *
60066 AATTTTGAAGGTTCGGGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTAAAAATAG
1 AATTTTGGACATTCGAGGGT-AAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAATAG
* **
60123 AATTTTTGGA-AGCTCGAGGGTAAAATTATAATTTTTGAAAGTTT
1 AA-TTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTGAAAGTTT
60167 CGGAGTCAAA
Statistics
Matches: 218, Mismatches: 47, Indels: 24
0.75 0.16 0.08
Matches are distributed among these distances:
56 1 0.00
57 42 0.19
58 93 0.43
59 40 0.18
60 42 0.19
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (57 bp):
AATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAATAG
Found at i:60113 original size:29 final size:29
Alignment explanation
Indices: 60019--60217 Score: 165
Period size: 29 Copynumber: 6.8 Consensus size: 29
60009 TTTTTAGACA
*
60019 TTCGAGGGT-AAAATGGTAATTTTTTGAAAGT
1 TTCG-GGGTAAAAAT-GTAA-TTTTTGGAAGT
* * * * *
60050 TTTGGGGTCAAAAT-AAAATTTT-GAAGG
1 TTCGGGGTAAAAATGTAATTTTTGGAAGT
60077 TTCGGGGGTAAAAATGTAATTTTTGGAAGT
1 TTC-GGGGTAAAAATGTAATTTTTGGAAGT
*
60107 TTTGGGGTAAAAATAG-AATTTTTGGAAG-
1 TTCGGGGTAAAAAT-GTAATTTTTGGAAGT
* * * *
60135 CTCGAGGGTAAAATTATAATTTTTGAAAGT
1 TTCG-GGGTAAAAATGTAATTTTTGGAAGT
* *
60165 TTCGGAGTCAAAAATGGAATTTTTGGAAGT
1 TTCGGGGT-AAAAATGTAATTTTTGGAAGT
**
60195 TTAAGGGTAAAAATGTAATTTTT
1 TTCGGGGTAAAAATGTAATTTTT
60218 AGACAATTTA
Statistics
Matches: 133, Mismatches: 26, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
27 5 0.04
28 16 0.12
29 68 0.51
30 36 0.27
31 8 0.06
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
TTCGGGGTAAAAATGTAATTTTTGGAAGT
Found at i:63651 original size:17 final size:18
Alignment explanation
Indices: 63629--63662 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63619 ATTTAAGAGT
63629 TTAAATA-AAAAAATTTA
1 TTAAATACAAAAAATTTA
*
63646 TTAAATACAAAATATTT
1 TTAAATACAAAAAATTT
63663 TATTTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATACAAAAAATTTA
Found at i:67158 original size:18 final size:18
Alignment explanation
Indices: 67135--67182 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
67125 CATCACTGGT
67135 TTGAATTTTTAAAACACA
1 TTGAATTTTTAAAACACA
** *
67153 TTGAATGGTAAAAACACA
1 TTGAATTTTTAAAACACA
* *
67171 TTAAAATTTTAA
1 TTGAATTTTTAA
67183 TCCGAGCAAA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (18 bp):
TTGAATTTTTAAAACACA
Found at i:67569 original size:16 final size:17
Alignment explanation
Indices: 67539--67583 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
67529 AAAAGAAAAA
67539 TTATATTTTTCATCTTT
1 TTATATTTTTCATCTTT
*
67556 TTAT-TTTTTTATCTTT
1 TTATATTTTTCATCTTT
*
67572 TCA-ATTTTTCAT
1 TTATATTTTTCAT
67584 AATTCTAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATTTTTCATCTTT
Found at i:83549 original size:174 final size:175
Alignment explanation
Indices: 83257--83604 Score: 486
Period size: 174 Copynumber: 2.0 Consensus size: 175
83247 TGCATATCCG
* * *
83257 TTGTGGTGAGGATCTAGGGTTCCCGCAATGTTGAAATTGTAGTAAGCATCACACAGTTTGGAATT
1 TTGTGGTGAGGATCTAGGGTTCCCACAATGTTGAAAATATAGTAAGCATCACACAGTTTGGAATT
* * * *
83322 TTTGGCCTTGAAATATCCAGTCCTTTTTATGATGTCACTGCAGTTTTCTGTGATGGT-TTTT-TA
66 ATTGGCCTTGAAATATCCAGTCCTTTTGATGATGTCACTGCAGTTTGCTGTGATGGTCTTTTAAA
* *
83385 GTGGAAACATTCTGTGTGGTCACATTCATGCTTTTATTTTGTTCCA
131 ATGGAAACATTCTGTATGGTCAC-TTCATGCTTTTATTTTGTTCCA
* ** ** **
83431 TTGTGGTGAGGATTTAGGGTTCCCACAATGTTGAAAATATAGTAAGCATTTCAGTGTTTGGGGTT
1 TTGTGGTGAGGATCTAGGGTTCCCACAATGTTGAAAATATAGTAAGCATCACACAGTTTGGAATT
* *
83496 ATTGGCCTTGAAATATTCAGT-CTTTCTGATGATGTTACTGCAGTTTGCTGTGATGGTCTTTTAA
66 ATTGGCCTTGAAATATCCAGTCCTTT-TGATGATGTCACTGCAGTTTGCTGTGATGGTCTTTTAA
*
83560 AATGGAAACATTCTGTATGGTCACTTTATGCTTTTATTTTGTTCC
130 AATGGAAACATTCTGTATGGTCACTTCATGCTTTTATTTTGTTCC
83605 TTGCTTGAAG
Statistics
Matches: 152, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
173 4 0.03
174 102 0.67
175 24 0.16
176 22 0.14
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.41
Consensus pattern (175 bp):
TTGTGGTGAGGATCTAGGGTTCCCACAATGTTGAAAATATAGTAAGCATCACACAGTTTGGAATT
ATTGGCCTTGAAATATCCAGTCCTTTTGATGATGTCACTGCAGTTTGCTGTGATGGTCTTTTAAA
ATGGAAACATTCTGTATGGTCACTTCATGCTTTTATTTTGTTCCA
Found at i:90997 original size:15 final size:15
Alignment explanation
Indices: 90979--91008 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
90969 CTTCTTCTAG
90979 TTCTTCCTCTGCATC
1 TTCTTCCTCTGCATC
*
90994 TTCTTCCTTTGCATC
1 TTCTTCCTCTGCATC
91009 CCCATCTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.37, G:0.07, T:0.50
Consensus pattern (15 bp):
TTCTTCCTCTGCATC
Found at i:95344 original size:18 final size:18
Alignment explanation
Indices: 95317--95352 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
95307 TCATAGGAAG
95317 AACGAATGAAACGTGAGC
1 AACGAATGAAACGTGAGC
*
95335 AACGATTGAAACGTGAGC
1 AACGAATGAAACGTGAGC
95353 TTGAAAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.28, T:0.14
Consensus pattern (18 bp):
AACGAATGAAACGTGAGC
Found at i:101819 original size:2 final size:2
Alignment explanation
Indices: 101812--101836 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
101802 TAACATTATC
101812 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 A
101837 AAGTAATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:102818 original size:15 final size:15
Alignment explanation
Indices: 102798--102829 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
102788 ATGAAATTAC
102798 AAAAAAAAG-AAAAG
1 AAAAAAAAGAAAAAG
102812 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
102827 AAA
1 AAA
102830 CAAAGCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:104417 original size:29 final size:30
Alignment explanation
Indices: 104384--104453 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
104374 AAATAAAAAT
104384 TTCATGTATAAAATTGCACA-AAATCAAAG
1 TTCATGTATAAAATTGCACATAAATCAAAG
* *
104413 TTCATGTATACAATTGCACATTAAATCATAG
1 TTCATGTATAAAATTGCACA-TAAATCAAAG
*
104444 TTCGTGTATA
1 TTCATGTATA
104454 GTTTTGGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 19 0.53
31 17 0.47
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (30 bp):
TTCATGTATAAAATTGCACATAAATCAAAG
Found at i:111871 original size:2 final size:2
Alignment explanation
Indices: 111864--111890 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
111854 ATTGTTTTAA
111864 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 A
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.