Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011172.1 Kokia drynarioides strain JFW-HI SEQ_126148, 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: 38228
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 39 characters in sequence are not A, C, G, or T
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--41 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
42 GCAATAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:108 original size:20 final size:20
Alignment explanation
Indices: 80--119 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
70 AGTTTTTTTT
*
80 TAATGTTTAAATAATAATAA
1 TAATATTTAAATAATAATAA
* *
100 TAATATTTAATTATTAATAA
1 TAATATTTAAATAATAATAA
120 ATAAAAAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TAATATTTAAATAATAATAA
Found at i:1087 original size:30 final size:30
Alignment explanation
Indices: 1042--1442 Score: 224
Period size: 29 Copynumber: 13.6 Consensus size: 30
1032 ACCATTTTAC
1042 CCCT-AAACTTCCAAAAATCTCATTTTTGA
1 CCCTGAAACTTCCAAAAATCTCATTTTTGA
* *
1071 CTCTGAAACTTTCAAAAAT-TACCA-TTTT-A
1 CCCTGAAACTTCCAAAAATCT--CATTTTTGA
*
1100 CCCTCG-AACTTCCAAAAATCCCATTTTTGA
1 CCCT-GAAACTTCCAAAAATCTCATTTTTGA
*
1130 CCCTAAAACTTCCAAAAAT-TACCA-TTTT-A
1 CCCTGAAACTTCCAAAAATCT--CATTTTTGA
* *
1159 CCCCT-AAACTTCTAAAAATCCCATTTTTGA
1 -CCCTGAAACTTCCAAAAATCTCATTTTTGA
** *
1189 CCCCAAAACTTCTAAAAAT-TACCA-TTTT-A
1 CCCTGAAACTTCCAAAAATCT--CATTTTTGA
1218 CCCCT-AAACTTCCAAAAATCTCATTTTTGA
1 -CCCTGAAACTTCCAAAAATCTCATTTTTGA
* * *
1248 CCCCGAAACTTCTAAAAATTATCA-TTTT-A
1 CCCTGAAACTTCCAAAAA-TCTCATTTTTGA
* * *
1277 CCATTG-AATTTCCAAAAATCTTATTTTTGA
1 CC-CTGAAACTTCCAAAAATCTCATTTTTGA
** *
1307 CCCCAAAACTTCTAAAAAT-T-ACTATTTT-A
1 CCCTGAAACTTCCAAAAATCTCA-T-TTTTGA
* *
1336 CCCCT-AAAC-TCCTAAAAATCCCATTTTTAA
1 -CCCTGAAACTTCC-AAAAATCTCATTTTTGA
*
1366 CCCTAAAACTTCCAAAAAT-TACCA-TTTT-A
1 CCCTGAAACTTCCAAAAATCT--CATTTTTGA
* * * *
1395 CCCTCG-AACTTTCGAAAATCCCA-TTTTAA
1 CCCT-GAAACTTCCAAAAATCTCATTTTTGA
*
1424 CCCCGAAACTTCCAAAAAT
1 CCCTGAAACTTCCAAAAAT
1443 TACCATTTTA
Statistics
Matches: 292, Mismatches: 38, Indels: 84
0.71 0.09 0.20
Matches are distributed among these distances:
28 19 0.07
29 135 0.46
30 122 0.42
31 16 0.05
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.33
Consensus pattern (30 bp):
CCCTGAAACTTCCAAAAATCTCATTTTTGA
Found at i:1118 original size:59 final size:59
Alignment explanation
Indices: 1026--1453 Score: 510
Period size: 59 Copynumber: 7.3 Consensus size: 59
1016 AGATTGTCCG
* * **
1026 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACTCTGAAACTTTCA
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCA
* * *
1085 AAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCA
1 AAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCA
*
1144 AAAATTACCATTTTACCCCTAAACTTCTAAAAATCCCATTTTTGACCCCAAAAC-TTCTA
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTC-A
* *
1203 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGAAAC-TTCTA
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTC-A
* ** * * **
1262 AAAATTATCATTTTACCATTGAATTTCCAAAAATCTTATTTTTGACCCCAAAAC-TTCTA
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTC-A
* * * *
1321 AAAATTACTATTTTACCCCTAAAC-TCCTAAAAATCCCATTTTTAACCCTAAAACTTCCA
1 AAAATTACCATTTTACCCCTAAACTTCC-AAAAATCCCATTTTTGACCCCAAAACTTTCA
* * * * * *
1380 AAAATTACCATTTTA-CCCTCGAACTTTCGAAAATCCCA-TTTTAACCCCGAAACTTCCA
1 AAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCA
1438 AAAATTACCATTTTAC
1 AAAATTACCATTTTAC
1454 TCCCGAATGT
Statistics
Matches: 325, Mismatches: 36, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
58 46 0.14
59 271 0.83
60 8 0.02
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCA
Found at i:1326 original size:177 final size:177
Alignment explanation
Indices: 1026--1453 Score: 628
Period size: 177 Copynumber: 2.4 Consensus size: 177
1016 AGATTGTCCG
* *
1026 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACTCTGAAACTT-TCAAAAAT
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTCT-AAAAAT
* *
1090 TACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTACCAT
65 TACCATTTTACCATCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCAT
* * *
1155 TTTACCCCTAAACTTCTAAAAATCCCATTTTTGACCCCAAAACTTCTA
130 TTTACCCCTAAACTCCTAAAAATCCCATTTTTAACCCCAAAACTTCCA
1203 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTCTAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTCTAAAAATT
* * * ** * *
1268 ATCATTTTACCATTGAATTTCCAAAAATCTTATTTTTGACCCCAAAACTTCTAAAAATTACTATT
66 ACCATTTTACCATCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATT
*
1333 TTACCCCTAAACTCCTAAAAATCCCATTTTTAACCCTAAAACTTCCA
131 TTACCCCTAAACTCCTAAAAATCCCATTTTTAACCCCAAAACTTCCA
* * * * * *
1380 AAAATTACCATTTTA-CCCTCGAACTTTCGAAAATCCCA-TTTTAACCCCGAAACTTCCAAAAAT
1 AAAATTACCATTTTACCCCT-AAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTCTAAAAAT
1443 TACCATTTTAC
65 TACCATTTTAC
1454 TCCCGAATGT
Statistics
Matches: 227, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
176 37 0.16
177 189 0.83
178 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (177 bp):
AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGAAACTTCTAAAAATT
ACCATTTTACCATCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATT
TTACCCCTAAACTCCTAAAAATCCCATTTTTAACCCCAAAACTTCCA
Found at i:1477 original size:58 final size:56
Alignment explanation
Indices: 1075--1567 Score: 260
Period size: 59 Copynumber: 8.4 Consensus size: 56
1065 TTTTGACTCT
* *** * *
1075 GAAACTTTCAAAAATTACCATTTTACCCTCGAACT-TCCAAAAATCCCATTTTTGACCCT
1 GAAACTTCCAAAAATTACCATTTTACCC-CGAA-TGTTTGAAAAT-CCA-TTTTAACCCC
* * ** * *
1134 AAAACTTCCAAAAATTACCATTTTACCCCTAAACTTCTAAAAATCCCATTTTTGACCCC
1 GAAACTTCCAAAAATTACCATTTTACCCCGAATGTT-TGAAAAT-CCA-TTTTAACCCC
* * * ** ** *
1193 AAAACTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCC
1 GAAACTTCCAAAAATTACCATTTTACCCCGAATGTT-TGAAAATC-CA-TTTTAACCCC
* * ** ** * *
1252 GAAACTTCTAAAAATTATCATTTTACCATTGAAT-TTCCAAAAATCTTATTTTTGACCCC
1 GAAACTTCCAAAAATTACCATTTTACC-CCGAATGTT-TGAAAATC-CA-TTTTAACCCC
* * * * ** * * *
1311 AAAACTTCTAAAAATTACTATTTTACCCCTAAACTCCTAAAAATCCCATTTTTAACCCT
1 GAAACTTCCAAAAATTACCATTTTACCCCGAATGT-TTGAAAAT-CCA-TTTTAACCCC
* *
1370 AAAACTTCCAAAAATTACCATTTTACCCTCGAACT-TTCGAAAATCCCATTTTAACCCC
1 GAAACTTCCAAAAATTACCATTTTACCC-CGAA-TGTTTGAAAAT-CCATTTTAACCCC
* * *
1428 GAAACTTCCAAAAATTACCATTTTACTCCCGAATGTTTGAAGACTCCATTTTCGACCTC
1 GAAACTTCCAAAAATTACCATTTTAC-CCCGAATGTTTGAA-AATCCATTTT-AACCCC
* * * *
1487 GAAAC-TCTC-AAAGTTACCCTTTTACCCCTGAATGTTT-AAAATTTCATTTTTAACCAC
1 GAAACTTC-CAAAAATTACCATTTTACCCC-GAATGTTTGAAAA-TCCA-TTTTAACCCC
** *
1544 GAATTTTCCCAAAATTACCATTTT
1 GAAACTTCCAAAAATTACCATTTT
1568 GCCTCGTGCA
Statistics
Matches: 364, Mismatches: 51, Indels: 39
0.80 0.11 0.09
Matches are distributed among these distances:
56 1 0.00
57 17 0.05
58 99 0.27
59 240 0.66
60 7 0.02
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (56 bp):
GAAACTTCCAAAAATTACCATTTTACCCCGAATGTTTGAAAATCCATTTTAACCCC
Found at i:10680 original size:20 final size:20
Alignment explanation
Indices: 10655--10712 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
10645 TGTAATTTTT
10655 TTGAAAGTTTAGTGATTGAA
1 TTGAAAGTTTAGTGATTGAA
10675 TTGAAAGTTTAGTGATTGAA
1 TTGAAAGTTTAGTGATTGAA
*
10695 TTGAAAGTTGAGTGATTG
1 TTGAAAGTTTAGTGATTG
10713 TTGGTGTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.40
Consensus pattern (20 bp):
TTGAAAGTTTAGTGATTGAA
Found at i:12063 original size:2 final size:2
Alignment explanation
Indices: 12056--12084 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12046 ATAAATTCTC
12056 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
12085 CCTTCAAATA
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:16632 original size:15 final size:14
Alignment explanation
Indices: 16612--16645 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16602 ATTTAATAGT
16612 TAATTTATAATCTAA
1 TAATTTAT-ATCTAA
*
16627 TAATTTATATTTAA
1 TAATTTATATCTAA
16641 TAATT
1 TAATT
16646 AAATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTTATATCTAA
Found at i:16650 original size:19 final size:18
Alignment explanation
Indices: 16595--16660 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 18
16585 GTTATGACTA
*
16595 AATTTATATTTAATAGTT
1 AATTTATATTTAATAATT
* *
16613 AATTTATA-AT-CTAA-T
1 AATTTATATTTAATAATT
16628 AATTTATATTTAATAATT
1 AATTTATATTTAATAATT
16646 AAATTTATAATTTAA
1 -AATTTAT-ATTTAA
16661 GTATACTAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
15 9 0.24
16 3 0.08
17 4 0.11
18 9 0.24
19 7 0.18
20 6 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
AATTTATATTTAATAATT
Found at i:16655 original size:26 final size:24
Alignment explanation
Indices: 16593--16659 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 24
16583 TAGTTATGAC
16593 TAAATTTAT-ATTTAATAGTTAATT
1 TAAATTTATAATTT-ATAGTTAATT
* *
16617 TATAATCTAATAATTTATATTTAATAAT
1 TA-AAT-TTATAATTTATAGTTAAT--T
16645 TAAATTTATAATTTA
1 TAAATTTATAATTTA
16660 AGTATACTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
24 2 0.06
25 3 0.09
26 20 0.57
27 7 0.20
28 3 0.09
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
TAAATTTATAATTTATAGTTAATT
Found at i:27287 original size:10 final size:11
Alignment explanation
Indices: 27276--27315 Score: 59
Period size: 10 Copynumber: 3.9 Consensus size: 11
27266 TATTTATAAA
27276 TAAATATTAA-
1 TAAATATTAAT
27286 T-AATATTAAT
1 TAAATATTAAT
27296 TAAATA-TAAT
1 TAAATATTAAT
27306 TAAATATTAA
1 TAAATATTAA
27316 ATTTTTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 12 0.44
11 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATATTAAT
Found at i:27738 original size:17 final size:19
Alignment explanation
Indices: 27701--27741 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27691 TATAAATAAA
*
27701 ATAATAAACATGTATTTAT
1 ATAATAAACATATATTTAT
27720 ATAATAAA-ATATATTATAT
1 ATAATAAACATATATT-TAT
27739 ATA
1 ATA
27742 TCATTATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAATAAACATATATTTAT
Found at i:28174 original size:17 final size:17
Alignment explanation
Indices: 28138--28225 Score: 79
Period size: 17 Copynumber: 5.0 Consensus size: 17
28128 AAATTCGTTC
*
28138 AAATTTATTTTTAGATTT
1 AAATTTA-TTTTAAATTT
*
28156 AAATTTATGTTAAATTT
1 AAATTTATTTTAAATTT
28173 AAATTTATCTTTTTAAATTT
1 AAATTTA---TTTTAAATTT
***
28193 AAATTTGCCTTAAATTT
1 AAATTTATTTTAAATTT
*
28210 AAATTTA-ATTAAATTT
1 AAATTTATTTTAAATTT
28226 GAATGGATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
16 8 0.14
17 29 0.49
18 7 0.12
20 15 0.25
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:28194 original size:37 final size:35
Alignment explanation
Indices: 28138--28216 Score: 104
Period size: 37 Copynumber: 2.2 Consensus size: 35
28128 AAATTCGTTC
* **
28138 AAATTTATTTTTAGATTTAAATTTATGTTAAATTT
1 AAATTTATTTTTAAATTTAAATTTACCTTAAATTT
*
28173 AAATTTATCTTTTTAAATTTAAATTTGCCTTAAATTT
1 AAATTTA--TTTTTAAATTTAAATTTACCTTAAATTT
28210 AAATTTA
1 AAATTTA
28217 ATTAAATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 7 0.18
37 31 0.82
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (35 bp):
AAATTTATTTTTAAATTTAAATTTACCTTAAATTT
Found at i:28931 original size:33 final size:33
Alignment explanation
Indices: 28891--28957 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
28881 AAAATACCAT
* * *
28891 TAATAATATTATTAATTAT-ATTGACAATAATAA
1 TAATAATATCACTAA-TATCATTAACAATAATAA
28924 TAATAATATCACTAATATCATTAACAATAATAA
1 TAATAATATCACTAATATCATTAACAATAATAA
28957 T
1 T
28958 GACATCAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (33 bp):
TAATAATATCACTAATATCATTAACAATAATAA
Found at i:28953 original size:30 final size:28
Alignment explanation
Indices: 28919--28983 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
28909 TATTGACAAT
* * *
28919 AATAATAATAATATCACTAATATCATTAAC
1 AATAATAATAACATCAATAATAACATT--C
*
28949 AATAATAATGACATCAATAATAACATTC
1 AATAATAATAACATCAATAATAACATTC
28977 AATAATA
1 AATAATA
28984 GCATTAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 8 0.26
30 23 0.74
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (28 bp):
AATAATAATAACATCAATAATAACATTC
Found at i:30203 original size:59 final size:60
Alignment explanation
Indices: 30061--30240 Score: 294
Period size: 60 Copynumber: 3.0 Consensus size: 60
30051 GAGGTCCCTA
* *
30061 AACCTTCTAGATATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTGACCTCG
1 AACCTTTTAGAAATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTGACCTCG
*
30121 AACCTTTTAGAAATTACCATTTTACCCCTGAACTTCCAAAAATCACATTTTTTGACCTCG
1 AACCTTTTAGAAATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTGACCTCG
*
30181 AACCTTTTA-AAATTACCATTTTACCCCCGAACTTCCAAAAATTC-CA-TTTTTAACCTCG
1 AACCTTTTAGAAATTACCATTTTACCCCCGAACTTCCAAAAA-TCACATTTTTTGACCTCG
30239 AA
1 AA
30241 ACATCCAAAA
Statistics
Matches: 114, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
58 13 0.11
59 33 0.29
60 68 0.60
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (60 bp):
AACCTTTTAGAAATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTGACCTCG
Found at i:30250 original size:30 final size:29
Alignment explanation
Indices: 30073--30255 Score: 86
Period size: 30 Copynumber: 6.2 Consensus size: 29
30063 CCTTCTAGAT
* *
30073 ATTACCATTTTACCCCCGAACTTCCAAAA
1 ATTACCATTTTAACCCCGAACATCCAAAA
* * * * ** *
30102 ATCA-CATTTTTTGACCTCGAACCTTTTAGAA
1 ATTACCA--TTTTAACCCCGAA-CATCCAAAA
*
30133 ATTACCATTTT-ACCCCTGAACTTCCAAAA
1 ATTACCATTTTAACCCC-GAACATCCAAAA
* * * * ***
30162 ATCA-CATTTTTTGACCTCGAACCTTTTAAA
1 ATTACCA--TTTTAACCCCGAACATCCAAAA
* *
30192 ATTACCATTTTACCCCCGAACTTCCAAAA
1 ATTACCATTTTAACCCCGAACATCCAAAA
*
30221 ATT-CCATTTTTAACCTCGAAACATCCAAAA
1 ATTACCA-TTTTAACCCCG-AACATCCAAAA
30251 ATTAC
1 ATTAC
30256 TATCGTACTC
Statistics
Matches: 113, Mismatches: 29, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
28 7 0.06
29 43 0.38
30 45 0.40
31 16 0.14
32 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (29 bp):
ATTACCATTTTAACCCCGAACATCCAAAA
Found at i:30252 original size:59 final size:60
Alignment explanation
Indices: 30073--30255 Score: 255
Period size: 59 Copynumber: 3.1 Consensus size: 60
30063 CCTTCTAGAT
* * *
30073 ATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTGACCTCGAACCTTTTAGAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTGACCTCGAAACATTTAAAA
* * *
30133 ATTACCATTTTACCCCTGAACTTCCAAAAATCACATTTTTTGACCTCG-AACCTTTTAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTGACCTCGAAACATTTAAAA
* **
30192 ATTACCATTTTACCCCCGAACTTCCAAAAATTC-CA-TTTTTAACCTCGAAACATCCAAAA
1 ATTACCATTTTACCCCCGAACTTCCAAAAA-TCACATTTTTTGACCTCGAAACATTTAAAA
30251 ATTAC
1 ATTAC
30256 TATCGTACTC
Statistics
Matches: 110, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
58 11 0.10
59 50 0.45
60 49 0.45
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (60 bp):
ATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTGACCTCGAAACATTTAAAA
Found at i:30311 original size:118 final size:119
Alignment explanation
Indices: 30073--30327 Score: 286
Period size: 118 Copynumber: 2.1 Consensus size: 119
30063 CCTTCTAGAT
* * * ** *
30073 ATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTGACCTCGAACCTTTTAGAAATTAC
1 ATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTAACCTCGAAACATCCAAAAATTAC
** * * * * *
30138 CATTTTACCCCTGAACTTCCAAAAATCACATTTTTTGACCTCGAACCTTTTAAA
66 CATCGTACCCCAGAACTTCCAAAAATCACATTTTTTGACCACGAAACTCTCAAA
30192 ATTACCATTTTACCCCCGAACTTCCAAAAATTC-CA-TTTTTAACCTCGAAACATCCAAAAATTA
1 ATTACCATTTTACCCCCGAACTTCCAAAAA-TCACATTTTTTAACCTCGAAACATCCAAAAATTA
* *
30255 CTATCGTACTCCCAG-A-TGTCCAAAGACTC-CATTTTTTGACCACGAAACTCTCAAA
65 CCATCGTAC-CCCAGAACT-TCCAAA-AATCACATTTTTTGACCACGAAACTCTCAAA
*
30310 ATTACCGTTTTTACCCCC
1 ATTACC-ATTTTACCCCC
30328 CGAATGTTTT
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
117 1 0.01
118 63 0.55
119 49 0.43
120 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (119 bp):
ATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTTAACCTCGAAACATCCAAAAATTAC
CATCGTACCCCAGAACTTCCAAAAATCACATTTTTTGACCACGAAACTCTCAAA
Found at i:34685 original size:29 final size:29
Alignment explanation
Indices: 34652--34714 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
34642 TGCATGATCA
*
34652 ACATGACTACTGTTACTGATAAACTGAGT
1 ACATGACTACTGCTACTGATAAACTGAGT
** * * *
34681 ACATGTTTACTGCTACTGTTAATCTGATT
1 ACATGACTACTGCTACTGATAAACTGAGT
34710 ACATG
1 ACATG
34715 CTAAATATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (29 bp):
ACATGACTACTGCTACTGATAAACTGAGT
Found at i:34981 original size:91 final size:90
Alignment explanation
Indices: 34855--35023 Score: 196
Period size: 91 Copynumber: 1.9 Consensus size: 90
34845 CTTACTCACC
** * ** * * *
34855 GCTTTTATATGCAAACCCATTGTGTCTTCACAACTACTGGTAGTGTATTGACCTGCAAATACTAG
1 GCTTTTATATGCAAACCCATTGTGAATTCACAACTACTGGCAACGTATTAACCTGC-AACACTAA
34920 TGGTTCATCCACAATTTTTACTGGCA
65 TGGTTCATCCACAATTTTTACTGGCA
* * * * *
34946 GCTTTTATCTGCAAA-CTAGTTGTGAATTCATAACTATTGGCAACGTATTAACTTGCAACACTAA
1 GCTTTTATATGCAAACCCA-TTGTGAATTCACAACTACTGGCAACGTATTAACCTGCAACACTAA
35010 TGGTTCATCCACAA
65 TGGTTCATCCACAA
35024 ACTAGAGTGT
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
90 22 0.34
91 42 0.66
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.34
Consensus pattern (90 bp):
GCTTTTATATGCAAACCCATTGTGAATTCACAACTACTGGCAACGTATTAACCTGCAACACTAAT
GGTTCATCCACAATTTTTACTGGCA
Found at i:37270 original size:10 final size:9
Alignment explanation
Indices: 37257--37367 Score: 50
Period size: 9 Copynumber: 12.2 Consensus size: 9
37247 TATTCCAATA
37257 TTTTATATAT
1 TTTTATAT-T
37267 TTTTATATT
1 TTTTATATT
*
37276 TTTTGTATT
1 TTTTATATT
* *
37285 TATTAGAATAT
1 TTTTA-TAT-T
* * *
37296 TTGTAGAGT
1 TTTTATATT
*
37305 TTTTATATGG
1 TTTTATAT-T
*
37315 TTTTATGAAT
1 TTTTAT-ATT
37325 TTTTATA-T
1 TTTTATATT
*
37333 TGTTATA-T
1 TTTTATATT
37341 TTTTA-A-T
1 TTTTATATT
*
37348 TTTTAGATT
1 TTTTATATT
*
37357 TTTTGTATT
1 TTTTATATT
37366 TT
1 TT
37368 AATAAGTTTT
Statistics
Matches: 77, Mismatches: 18, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
7 7 0.09
8 13 0.17
9 29 0.38
10 23 0.30
11 5 0.06
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (9 bp):
TTTTATATT
Found at i:37273 original size:8 final size:8
Alignment explanation
Indices: 37254--37359 Score: 61
Period size: 8 Copynumber: 12.0 Consensus size: 8
37244 ATATATTCCA
37254 ATATTTTAT
1 ATATTTT-T
37263 ATATTTTT
1 ATATTTTT
37271 ATATTTTTT
1 ATA-TTTTT
*
37280 GTATTTATT
1 ATATTT-TT
*
37289 AGAATATTTGT
1 ---ATATTTTT
*
37300 AGAGTTTTT
1 ATA-TTTTT
37309 ATATGGTTTT
1 ATAT--TTTT
37319 ATGAATTTTT
1 AT--ATTTTT
*
37329 ATATTGTT
1 ATATTTTT
37337 ATATTTTT
1 ATATTTTT
37345 A-ATTTTT
1 ATATTTTT
*
37352 AGATTTTT
1 ATATTTTT
37360 TGTATTTTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
7 7 0.09
8 29 0.37
9 22 0.28
10 12 0.15
11 1 0.01
12 7 0.09
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.64
Consensus pattern (8 bp):
ATATTTTT
Found at i:37390 original size:30 final size:31
Alignment explanation
Indices: 37347--37411 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
37337 ATATTTTTAA
* *
37347 TTTTTAGATTTTTTGTAT-TTTAATAAGTTT
1 TTTTTACAATTTTTGTATATTTAATAAGTTT
* *
37377 TTTTTACAATTTTTTTATAGTTTTATAAGTTT
1 TTTTTACAATTTTTGTATA-TTTAATAAGTTT
37409 TTT
1 TTT
37412 AACATTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 15 0.52
32 14 0.48
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.68
Consensus pattern (31 bp):
TTTTTACAATTTTTGTATATTTAATAAGTTT
Done.