Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007871.1 Kokia drynarioides strain JFW-HI SEQ_122512, 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: 48525
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1151 original size:21 final size:21
Alignment explanation
Indices: 1125--1175 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1115 AGAATGATTT
1125 TTAAAAATATATTTTTTTCAA
1 TTAAAAATATATTTTTTTCAA
1146 TTAAAAATATATTTTTTTCAA
1 TTAAAAATATATTTTTTTCAA
1167 TTAAAAATA
1 TTAAAAATA
1176 CTCAAGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAAAATATATTTTTTTCAA
Found at i:2088 original size:21 final size:21
Alignment explanation
Indices: 2049--2097 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2039 ATAGTGCAAA
* **
2049 CTTCTACCGATACCTGTGACAG
1 CTTCTACCAATACAAGTGA-AG
2071 -TTCTACCAATACAAGTGAAG
1 CTTCTACCAATACAAGTGAAG
2091 CTTCTAC
1 CTTCTAC
2098 TGAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (21 bp):
CTTCTACCAATACAAGTGAAG
Found at i:3217 original size:192 final size:194
Alignment explanation
Indices: 2878--3318 Score: 550
Period size: 192 Copynumber: 2.3 Consensus size: 194
2868 CCAGTACTTT
* * * * *
2878 ATGCTGCTCACACGAGCTGTCGAGGACTCGTAACGTATGTAGTACCCCATCCATCGGCACGGTAT
1 ATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCAGTACCACAGCCATCGGCACGGTAT
*** * * * * *
2943 CTATTTGTAAACTGTCCCCTAACGATGCTGCTCACACTAGCTGTTGAGAATATGCATTTAAGCAT
66 CTATGCATAAACTATCCCCTAACGATGCTGCTCACACGAGCTGTCGAAAATATGCACTTAAGCAT
**
3008 AAATCCCAGCCATCGTAGGGCCTATAATCCATT-TAGGATTCATATA-TC-TTTTTCGACTCACG
131 AAATCCCAGCCATCGTAGGGCCTATAATCCATTCTAGGATTC-TATACTCATTTCCCGACTCACG
* * * *
3070 ATGCTGCTCACACGAGGTGTCGAGGACTCGCAACATATGCGGTACCACAGCCATCGGTATGGTAT
1 ATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCAGTACCACAGCCATCGGCACGGTAT
* * * * *
3135 CTGTGCATATATTATTCCCTAACGATGCTGCTCACACGAGCTGTCGAAAATATGCACTTATGCAT
66 CTATGCATAAACTATCCCCTAACGATGCTGCTCACACGAGCTGTCGAAAATATGCACTTAAGCAT
* * * * * *
3200 AAATCTCAGCTATCGTAGGGCCTGTAATTCATTCTTGGATTCTTTACTCATTTCCCGACTCACG
131 AAATCCCAGCCATCGTAGGGCCTATAATCCATTCTAGGATTCTATACTCATTTCCCGACTCACG
*
3264 ATGCTGCTCACACGAGCAGTCGAGGACTCGCAACATATGCAGT-CC-CTAGCCATCG
1 ATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCAGTACCAC-AGCCATCG
3319 CATCGATTTC
Statistics
Matches: 212, Mismatches: 33, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
192 141 0.67
193 19 0.09
194 52 0.25
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (194 bp):
ATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCAGTACCACAGCCATCGGCACGGTAT
CTATGCATAAACTATCCCCTAACGATGCTGCTCACACGAGCTGTCGAAAATATGCACTTAAGCAT
AAATCCCAGCCATCGTAGGGCCTATAATCCATTCTAGGATTCTATACTCATTTCCCGACTCACG
Found at i:6565 original size:36 final size:37
Alignment explanation
Indices: 6516--6619 Score: 160
Period size: 36 Copynumber: 2.9 Consensus size: 37
6506 ATATAATTAG
6516 TCACATGGCATGAAGAACATACCCACATATTCTTTGT
1 TCACATGGCATGAAGAACATACCCACATATTCTTTGT
*
6553 T-ACATGGCATGAAGAACATACCCACATATT-TTTTT
1 TCACATGGCATGAAGAACATACCCACATATTCTTTGT
*
6588 TCACATGG-ATTGAAGAACATACTCACATATTC
1 TCACATGGCA-TGAAGAACATACCCACATATTC
6620 ACTTTCAGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
35 6 0.10
36 55 0.89
37 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (37 bp):
TCACATGGCATGAAGAACATACCCACATATTCTTTGT
Found at i:6859 original size:29 final size:23
Alignment explanation
Indices: 6698--6983 Score: 401
Period size: 23 Copynumber: 12.4 Consensus size: 23
6688 ATCTTAATTC
*
6698 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
6721 TTTAATCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
6744 TTTAAGCACAAGTCACAGTAATA
1 TTTAAGCATAAATCACATTAATA
6767 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * * *
6790 TTTGAGCACAAACCATATTAATA
1 TTTAAGCATAAATCACATTAATA
6813 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
6836 TTTAAGCATAAATCATATTAACA
1 TTTAAGCATAAATCACATTAATA
* *
6859 TTTAAGCATGAATCACAGTAATA
1 TTTAAGCATAAATCACATTAATA
6882 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
*
6905 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
*
6928 TTTAAACATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
6951 TTTAAGCACAAACCATATTAATA
1 TTTAAGCATAAATCACATTAATA
6974 TTTAAGCATA
1 TTTAAGCATA
6984 GATATATGAA
Statistics
Matches: 228, Mismatches: 35, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 228 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:7406 original size:98 final size:98
Alignment explanation
Indices: 7237--7474 Score: 343
Period size: 98 Copynumber: 2.4 Consensus size: 98
7227 CCACACATCA
* * *
7237 CATGAGTTTTAGACGATATCTAGTCCTTTAAACAAGAGATTTTTTGGATTAGTGTCAAGGCTCAT
1 CATGAGTTTTAGACGATATCTAGTCCTTTAAACATGAGTTTTTTTGGATTAGTGTCAAAGCTCAT
* *
7302 TTTTCTTCAAGAAAAGGTAACCAAACTACTTTC
66 TTTTCTTCAAGAAAAAGTAACCAAACGACTTTC
* * * **
7335 CATGAGTTTTAGACGTTATGTAGTCCTTTAAACATGAGTTTTTTTGGATTAGTGTCAAATCTTGT
1 CATGAGTTTTAGACGATATCTAGTCCTTTAAACATGAGTTTTTTTGGATTAGTGTCAAAGCTCAT
* *
7400 TTTTCTTTAAGAAAAAGTAACCAATCGACTTTC
66 TTTTCTTCAAGAAAAAGTAACCAAACGACTTTC
* *
7433 CATGAGTTTTAAACGATATCTAGTCCTTTAAAC-TAAGTTTTT
1 CATGAGTTTTAGACGATATCTAGTCCTTTAAACATGAGTTTTT
7475 AGCCATTAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
97 8 0.06
98 116 0.94
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (98 bp):
CATGAGTTTTAGACGATATCTAGTCCTTTAAACATGAGTTTTTTTGGATTAGTGTCAAAGCTCAT
TTTTCTTCAAGAAAAAGTAACCAAACGACTTTC
Found at i:10643 original size:7 final size:7
Alignment explanation
Indices: 10633--10766 Score: 85
Period size: 7 Copynumber: 19.3 Consensus size: 7
10623 AAGTCAATGA
10633 TCAACAG
1 TCAACAG
10640 TCAA-AG
1 TCAACAG
*
10646 TCAACAA
1 TCAACAG
**
10653 TCAATGG
1 TCAACAG
* *
10660 TTAACGG
1 TCAACAG
10667 TCAACAG
1 TCAACAG
10674 TCAACAG
1 TCAACAG
* **
10681 TTAATGG
1 TCAACAG
10688 TCAACTA-
1 TCAAC-AG
*
10695 TCAACGG
1 TCAACAG
10702 TCAACAG
1 TCAACAG
10709 TCAACAG
1 TCAACAG
**
10716 TCAATGG
1 TCAACAG
10723 TCAACTA-
1 TCAAC-AG
*
10730 TCAACGG
1 TCAACAG
*
10737 TCAATAG
1 TCAACAG
*
10744 TCAACTG
1 TCAACAG
**
10751 TCAATGG
1 TCAACAG
10758 TCAACAG
1 TCAACAG
10765 TC
1 TC
10767 GGTCAACGAT
Statistics
Matches: 93, Mismatches: 29, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
6 6 0.06
7 87 0.94
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (7 bp):
TCAACAG
Found at i:10686 original size:28 final size:28
Alignment explanation
Indices: 10624--10766 Score: 119
Period size: 28 Copynumber: 5.1 Consensus size: 28
10614 TCAACGGTAA
* *
10624 AGTCAATGATCAACAGTCAA-AGTCAAC
1 AGTCAATGGTCAACGGTCAACAGTCAAC
* *
10651 AATCAATGGTTAACGGTCAACAGTCAAC
1 AGTCAATGGTCAACGGTCAACAGTCAAC
* ** *
10679 AGTTAATGGTCAACTATCAACGGTCAAC
1 AGTCAATGGTCAACGGTCAACAGTCAAC
** *
10707 AGTCAACAGTCAATGGTCAACTA-TCAAC
1 AGTCAATGGTCAACGGTCAAC-AGTCAAC
* * * **
10735 GGTCAATAGTCAACTGTCAATGGTCAAC
1 AGTCAATGGTCAACGGTCAACAGTCAAC
10763 AGTC
1 AGTC
10767 GGTCAACGAT
Statistics
Matches: 89, Mismatches: 24, Indels: 5
0.75 0.20 0.04
Matches are distributed among these distances:
27 16 0.18
28 73 0.82
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (28 bp):
AGTCAATGGTCAACGGTCAACAGTCAAC
Found at i:10707 original size:35 final size:35
Alignment explanation
Indices: 10662--10762 Score: 175
Period size: 35 Copynumber: 2.9 Consensus size: 35
10652 ATCAATGGTT
*
10662 AACGGTCAACAGTCAACAGTTAATGGTCAACTATC
1 AACGGTCAACAGTCAACAGTCAATGGTCAACTATC
10697 AACGGTCAACAGTCAACAGTCAATGGTCAACTATC
1 AACGGTCAACAGTCAACAGTCAATGGTCAACTATC
* *
10732 AACGGTCAATAGTCAACTGTCAATGGTCAAC
1 AACGGTCAACAGTCAACAGTCAATGGTCAAC
10763 AGTCGGTCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (35 bp):
AACGGTCAACAGTCAACAGTCAATGGTCAACTATC
Found at i:14038 original size:18 final size:17
Alignment explanation
Indices: 14004--14038 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
13994 TATGATTTTA
*
14004 TCTAATTAAATTAATTT
1 TCTAATTAAAATAATTT
14021 TCTAATTAAACATAATTT
1 TCTAATTAAA-ATAATTT
14039 AACTAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
TCTAATTAAAATAATTT
Found at i:14242 original size:21 final size:21
Alignment explanation
Indices: 14183--14243 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
14173 GGCTAGACTT
* *
14183 TTATTTATTTTTAATATGATTA
1 TTATTTA-TTTTAATTTTATTA
14205 -TA-TT-TTTTAATAATTTATTA
1 TTATTTATTTTAAT--TTTATTA
14225 TTATTTATTTTAATTTTAT
1 TTATTTATTTTAATTTTAT
14244 ACATTACGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
18 7 0.22
20 7 0.22
21 9 0.28
22 2 0.06
23 7 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTTATTTTAATTTTATTA
Found at i:17507 original size:17 final size:17
Alignment explanation
Indices: 17487--17519 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17477 TTTTTAATTT
17487 AATCCTTAATT-TAAATC
1 AATCC-TAATTCTAAATC
17504 AATCCTAATTCTAAAT
1 AATCCTAATTCTAAAT
17520 AAATTACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (17 bp):
AATCCTAATTCTAAATC
Found at i:17847 original size:29 final size:29
Alignment explanation
Indices: 17809--17867 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
17799 TTTGTGTATG
* * *
17809 ACCCCCTATATGCGAGCCCCTGTATGCAA
1 ACCCCATATAGGCGAACCCCTGTATGCAA
*
17838 ACCCCATATAGGCGAACCCTTGTATGCAA
1 ACCCCATATAGGCGAACCCCTGTATGCAA
17867 A
1 A
17868 TCCTTATGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (29 bp):
ACCCCATATAGGCGAACCCCTGTATGCAA
Found at i:18042 original size:23 final size:23
Alignment explanation
Indices: 18016--18246 Score: 97
Period size: 23 Copynumber: 10.2 Consensus size: 23
18006 TTATGTGAAT
18016 CCTACATGTTTATACATGCAAAC
1 CCTACATGTTTATACATGCAAAC
*
18039 CCTAC-T-TATACTA-ATGTGCAAAC
1 CCTACATGTTTA-TACA--TGCAAAC
* * * ***
18062 CTTATATGTTTATCCATGTGCA-
1 CCTACATGTTTATACATGCAAAC
*
18084 CCTAACATG-TTATACATTCAAAC
1 CCT-ACATGTTTATACATGCAAAC
* * **
18107 CCTACTTATATTA-ATGTGCAAAC
1 CCTACATGT-TTATACATGCAAAC
* * * *
18130 CTTATATGTTTATTCTCGTGC--AC
1 CCTACATGTTTA-T-ACATGCAAAC
* * *
18153 CTTCCATG-TTATACATTCAAAC
1 CCTACATGTTTATACATGCAAAC
* *
18175 CCTATATGTTTATTCATGCAAAC
1 CCTACATGTTTATACATGCAAAC
*
18198 CTTACATG-TTATACATGCAAAC
1 CCTACATGTTTATACATGCAAAC
**
18220 CCTATTTGTTTACT-CATGCAAAC
1 CCTACATGTTTA-TACATGCAAAC
18243 CCTA
1 CCTA
18247 GAAGTGTGAA
Statistics
Matches: 148, Mismatches: 42, Indels: 36
0.65 0.19 0.16
Matches are distributed among these distances:
20 3 0.02
21 5 0.03
22 47 0.32
23 79 0.53
24 6 0.04
25 8 0.05
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (23 bp):
CCTACATGTTTATACATGCAAAC
Found at i:18097 original size:68 final size:68
Alignment explanation
Indices: 18019--18178 Score: 250
Period size: 68 Copynumber: 2.3 Consensus size: 68
18009 TGTGAATCCT
*
18019 ACATGTTTATACATGCAAACCCTACTTATACTAATGTGCAAACCTTATATGTTTATCCAT-GTGC
1 ACATG-TTATACATTCAAACCCTACTTATACTAATGTGCAAACCTTATATGTTTATCC-TCGTGC
18083 ACCTA
64 ACCTA
* *
18088 ACATGTTATACATTCAAACCCTACTTATATTAATGTGCAAACCTTATATGTTTATTCTCGTGCAC
1 ACATGTTATACATTCAAACCCTACTTATACTAATGTGCAAACCTTATATGTTTATCCTCGTGCAC
*
18153 CTT
66 CTA
*
18156 CCATGTTATACATTCAAACCCTA
1 ACATGTTATACATTCAAACCCTA
18179 TATGTTTATT
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
67 1 0.01
68 79 0.93
69 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (68 bp):
ACATGTTATACATTCAAACCCTACTTATACTAATGTGCAAACCTTATATGTTTATCCTCGTGCAC
CTA
Found at i:18183 original size:22 final size:22
Alignment explanation
Indices: 18158--18246 Score: 99
Period size: 23 Copynumber: 4.0 Consensus size: 22
18148 TGCACCTTCC
*
18158 ATGTTATACATTCAAACCCTAT
1 ATGTTATACATGCAAACCCTAT
* * *
18180 ATGTTTATTCATGCAAACCTTAC
1 ATG-TTATACATGCAAACCCTAT
18203 ATGTTATACATGCAAACCCTAT
1 ATGTTATACATGCAAACCCTAT
*
18225 TTGTT-TACTCATGCAAACCCTA
1 ATGTTATA--CATGCAAACCCTA
18247 GAAGTGTGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
21 2 0.04
22 23 0.41
23 31 0.55
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.36
Consensus pattern (22 bp):
ATGTTATACATGCAAACCCTAT
Found at i:18195 original size:68 final size:67
Alignment explanation
Indices: 18019--18207 Score: 220
Period size: 68 Copynumber: 2.8 Consensus size: 67
18009 TGTGAATCCT
* * *
18019 ACATGTTTATACATGCAAACCCTACTTATACTAATGTGCAAACCTTATATGTTTATCCATGTGCA
1 ACATG-TTATACATTCAAACCCTAC-TATATTAATATGCAAACCTTATATGTTTATCCATGTGCA
18084 CCTA
64 CCTA
* *
18088 ACATGTTATACATTCAAACCCTACTTATATTAATGTGCAAACCTTATATGTTTATTC-TCGTGCA
1 ACATGTTATACATTCAAACCCTAC-TATATTAATATGCAAACCTTATATGTTTATCCAT-GTGCA
*
18152 CCTT
64 CCTA
* * * *
18156 CCATGTTATACATTCAAACCCTA-TATGTTTATTCATGCAAACCTTACATGTT
1 ACATGTTATACATTCAAACCCTACTAT-ATTAAT-ATGCAAACCTTATATGTT
18208 ATACATGCAA
Statistics
Matches: 108, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
66 3 0.03
67 5 0.05
68 95 0.88
69 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.38
Consensus pattern (67 bp):
ACATGTTATACATTCAAACCCTACTATATTAATATGCAAACCTTATATGTTTATCCATGTGCACC
TA
Found at i:18241 original size:45 final size:45
Alignment explanation
Indices: 18123--18243 Score: 156
Period size: 45 Copynumber: 2.7 Consensus size: 45
18113 TATATTAATG
* * *
18123 TGCAAACCTTATATGTTTATTCTCGTGC--ACCTTCCATGTTATACA
1 TGCAAACCCTATATGTTTA--CTCATGCAAACCTTACATGTTATACA
* *
18168 TTCAAACCCTATATGTTTATTCATGCAAACCTTACATGTTATACA
1 TGCAAACCCTATATGTTTACTCATGCAAACCTTACATGTTATACA
*
18213 TGCAAACCCTATTTGTTTACTCATGCAAACC
1 TGCAAACCCTATATGTTTACTCATGCAAACC
18244 CTAGAAGTGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.08
45 61 0.92
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (45 bp):
TGCAAACCCTATATGTTTACTCATGCAAACCTTACATGTTATACA
Found at i:18394 original size:15 final size:16
Alignment explanation
Indices: 18355--18394 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
18345 AAGTTTTAGT
18355 TATATGAA-GAAATTG
1 TATATGAATGAAATTG
18370 TATATG--TGAAATTG
1 TATATGAATGAAATTG
18384 -ATATGAATGAA
1 TATATGAATGAA
18395 TGCATGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (16 bp):
TATATGAATGAAATTG
Found at i:33832 original size:34 final size:34
Alignment explanation
Indices: 33794--33859 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
33784 GCTTAGTATA
*
33794 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
*
33828 ATTGTCCCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
33860 CCATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:33833 original size:17 final size:17
Alignment explanation
Indices: 33802--33859 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
33792 TAATTGTCCC
* *
33802 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
33819 TGCATTTTTATTGTCCC
1 TGCATTTTTATTGTCAT
* **
33836 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
33853 TGCATTT
1 TGCATTT
33860 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:46974 original size:28 final size:27
Alignment explanation
Indices: 46934--47074 Score: 122
Period size: 28 Copynumber: 5.0 Consensus size: 27
46924 TACGACCCCT
* *
46934 TGTATGCGAACCCCTATAGGCAAACTCC
1 TGTATGTGAACCCCTATAAGCAAAC-CC
*
46962 TGTATGTGAACCCTTATAAGCAAACCCC
1 TGTATGTGAACCCCTATAAGCAAA-CCC
* *
46990 TATATGCGAACCCCTATAAGCAAACCC
1 TGTATGTGAACCCCTATAAGCAAACCC
* * *
47017 T-TATATACGAACCCCCTATAGGCGAACACC
1 TGTATGT--GAA-CCCCTATAAGCAAAC-CC
* * *
47047 TGTATGTGAACCCTTATATGCGAACCC
1 TGTATGTGAACCCCTATAAGCAAACCC
47074 T
1 T
47075 AGGAGAAAAC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.03
27 7 0.07
28 60 0.64
29 17 0.18
30 3 0.03
31 4 0.04
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.23
Consensus pattern (27 bp):
TGTATGTGAACCCCTATAAGCAAACCC
Found at i:46993 original size:14 final size:14
Alignment explanation
Indices: 46942--47021 Score: 70
Period size: 14 Copynumber: 5.7 Consensus size: 14
46932 CTTGTATGCG
*
46942 AACCCCTATAGGCA
1 AACCCCTATAAGCA
* * * **
46956 AACTCCTGTATGTG
1 AACCCCTATAAGCA
*
46970 AACCCTTATAAGCA
1 AACCCCTATAAGCA
* *
46984 AACCCCTATATGCG
1 AACCCCTATAAGCA
46998 AACCCCTATAAGCA
1 AACCCCTATAAGCA
*
47012 AACCCTTATA
1 AACCCCTATA
47022 TACGAACCCC
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 49 1.00
ACGTcount: A:0.35, C:0.31, G:0.11, T:0.23
Consensus pattern (14 bp):
AACCCCTATAAGCA
Done.