Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015313.1 Kokia drynarioides strain JFW-HI SEQ_130358, 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: 65849
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--30 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31 TTACATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:961 original size:9 final size:9
Alignment explanation
Indices: 932--1036 Score: 54
Period size: 10 Copynumber: 11.2 Consensus size: 9
922 AAAAAAATAT
*
932 AAATAATAA
1 AAATTATAA
*
941 TAAATAATAA
1 -AAATTATAA
*
951 AAGTTATAA
1 AAATTATAA
960 AAATTATTAA
1 AAATTA-TAA
*
970 AATTTAATAA
1 AAATT-ATAA
980 AGAA-TATAA
1 A-AATTATAA
989 AATATT-TAA
1 AA-ATTATAA
*
998 AATTTATTAA
1 AAATTA-TAA
*
1008 AATATTAAAA
1 AA-ATTATAA
*
1018 AAAATA-AA
1 AAATTATAA
*
1026 AAATTGTAA
1 AAATTATAA
1035 AA
1 AA
1037 TTTTTATAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
8 9 0.12
9 30 0.40
10 31 0.41
11 5 0.07
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:1018 original size:19 final size:18
Alignment explanation
Indices: 957--1018 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
947 ATAAAAGTTA
957 TAAAAATTATTAAAAT-T
1 TAAAAATTATTAAAATAT
**
974 TAATAAAGAATATAAAATATT
1 TAA-AAATTAT-TAAAATA-T
*
995 TAAAATTTATTAAAATAT
1 TAAAAATTATTAAAATAT
1013 TAAAAA
1 TAAAAA
1019 AAATAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
17 3 0.09
18 11 0.31
19 13 0.37
20 4 0.11
21 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
TAAAAATTATTAAAATAT
Found at i:1018 original size:28 final size:27
Alignment explanation
Indices: 956--1008 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
946 AATAAAAGTT
956 ATAAAAATTATTAAAATTTAATAAAGA
1 ATAAAAATTATTAAAATTTAATAAAGA
*
983 ATATAAAA-TATTTAAAATTTATTAAA
1 ATA-AAAATTA-TTAAAATTTAATAAA
1009 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
ATAAAAATTATTAAAATTTAATAAAGA
Found at i:1047 original size:38 final size:37
Alignment explanation
Indices: 957--1066 Score: 116
Period size: 38 Copynumber: 2.9 Consensus size: 37
947 ATAAAAGTTA
* *
957 TAAAAATTATTAAAAT-TTAATAAAGAATATAAAATATT
1 TAAAATTTATTAAAATATTAA-AAA-AATATAAAAAATT
995 TAAAATTTATTAAAATATTAAAAAAA-ATAAAAAATT
1 TAAAATTTATTAAAATATTAAAAAAATATAAAAAATT
* * *
1031 GTAAAATTTTTATAAAAAACATAAAAAAATATAAAA
1 -TAAAATTTAT-TAAAATA-TTAAAAAAATATAAAA
1067 TGCATCAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
36 9 0.15
37 11 0.18
38 24 0.39
39 12 0.19
40 6 0.10
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (37 bp):
TAAAATTTATTAAAATATTAAAAAAATATAAAAAATT
Found at i:1245 original size:9 final size:9
Alignment explanation
Indices: 1233--1427 Score: 73
Period size: 9 Copynumber: 21.0 Consensus size: 9
1223 TTTTGGTACG
1233 ATAATTTTT
1 ATAATTTTT
1242 ATAATTTTT
1 ATAATTTTT
*
1251 -TACGAATTTT
1 ATA--ATTTTT
*
1261 ATATTTATTT
1 ATAATT-TTT
1271 ATAATTTTTT
1 ATAA-TTTTT
1281 ATAATTTTT
1 ATAATTTTT
*
1290 -TACGA-CTTT
1 ATA--ATTTTT
*
1299 ATAAAATTTT
1 AT-AATTTTT
1309 AT-ATTTTT
1 ATAATTTTT
1317 A-ATATTTTT
1 ATA-ATTTTT
*
1326 ATAAAATTTT
1 AT-AATTTTT
*
1336 AAAATTTTT
1 ATAATTTTT
**
1345 ATTTTTTTT
1 ATAATTTTT
*
1354 CTAATTTTT
1 ATAATTTTT
1363 A-ATATTTTT
1 ATA-ATTTTT
* **
1372 AATTAAACTTCA
1 -A-T-AATTTTT
1384 ATAATTTTT
1 ATAATTTTT
*
1393 ATAACTTTT
1 ATAATTTTT
*
1402 ATTGATTTTT
1 A-TAATTTTT
1412 -T-ATTTTT
1 ATAATTTTT
*
1419 ATCATTTTT
1 ATAATTTTT
1428 GCCATGTGTA
Statistics
Matches: 138, Mismatches: 26, Indels: 44
0.66 0.12 0.21
Matches are distributed among these distances:
7 6 0.04
8 13 0.09
9 69 0.50
10 39 0.28
11 7 0.05
12 3 0.02
13 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:1252 original size:10 final size:10
Alignment explanation
Indices: 1233--1291 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
1223 TTTTGGTACG
1233 ATAA-TTTTT
1 ATAATTTTTT
1242 ATAATTTTTT
1 ATAATTTTTT
*
1252 ACGAA--TTTT
1 A-TAATTTTTT
1261 AT-ATTTATTT
1 ATAATTT-TTT
1271 ATAATTTTTT
1 ATAATTTTTT
1281 ATAATTTTTT
1 ATAATTTTTT
1291 A
1 A
1292 CGACTTTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
7 1 0.02
9 10 0.24
10 25 0.60
11 6 0.14
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:1260 original size:20 final size:20
Alignment explanation
Indices: 1235--1308 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
1225 TTGGTACGAT
1235 AATTTTTATAATTTTTTACG
1 AATTTTTATAATTTTTTACG
*
1255 AA-TTTTAT-ATTTATTTA-T
1 AATTTTTATAATTT-TTTACG
1273 AATTTTTTATAATTTTTTACG
1 AA-TTTTTATAATTTTTTACG
* * *
1294 ACTTTATAAAATTTT
1 AATTTTTATAATTTT
1309 ATATTTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.14
19 10 0.23
20 23 0.52
21 5 0.11
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTTTATAATTTTTTACG
Found at i:1310 original size:38 final size:39
Alignment explanation
Indices: 1233--1362 Score: 114
Period size: 37 Copynumber: 3.5 Consensus size: 39
1223 TTTTGGTACG
**
1233 ATAA-TTTTTATAATTTTTTACGAATTTTATATTTATTT
1 ATAATTTTTTATAATTTTTTACGAATTTTATAAATATTT
*
1271 ATAATTTTTTATAATTTTTTACG-ACTTTATAAA-ATTT
1 ATAATTTTTTATAATTTTTTACGAATTTTATAAATATTT
* * *
1308 -TATATTTTTAAT-ATTTTTATA-AAATTTTA-AAATTTTT
1 ATA-ATTTTTTATAATTTTT-TACGAATTTTATAAATATTT
* *
1345 AT-TTTTTTTCTAATTTTT
1 ATAATTTTTTATAATTTTT
1363 AATATTTTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
36 17 0.23
37 28 0.37
38 12 0.16
39 18 0.24
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (39 bp):
ATAATTTTTTATAATTTTTTACGAATTTTATAAATATTT
Found at i:1326 original size:27 final size:28
Alignment explanation
Indices: 1296--1374 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 28
1286 TTTTTACGAC
1296 TTTATAAAATTTT-ATATTTTTAATATT
1 TTTATAAAATTTTAATATTTTTAATATT
* * *
1323 TTTATAAAATTTTAAAATTTTTATTTTT
1 TTTATAAAATTTTAATATTTTTAATATT
* *
1351 TTTCT-AATTTTTAATATTTTTAAT
1 TTTATAAAATTTTAATATTTTTAAT
1375 TAAACTTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 29 0.66
28 15 0.34
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTATAAAATTTTAATATTTTTAATATT
Found at i:8735 original size:20 final size:20
Alignment explanation
Indices: 8710--8750 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
8700 GCAGAGCATA
8710 TACAATCAAATCAAAGGCTT
1 TACAATCAAATCAAAGGCTT
8730 TACAATCAAATCAAAGGCTT
1 TACAATCAAATCAAAGGCTT
8750 T
1 T
8751 GCACCTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (20 bp):
TACAATCAAATCAAAGGCTT
Found at i:41164 original size:25 final size:25
Alignment explanation
Indices: 41136--41215 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
41126 GTTAAAAGGA
41136 AAACTTAAGTATCGAAGAGATGAAC
1 AAACTTAAGTATCGAAGAGATGAAC
* * *
41161 AAACTATAGGACAT-GAAGA-A-GCTAC
1 AAACT-TAAG-TATCGAAGAGATG-AAC
*
41186 AAAATTAAGTATCGAAGAGATGAAC
1 AAACTTAAGTATCGAAGAGATGAAC
41211 AAACT
1 AAACT
41216 ATAGAAGGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
23 2 0.05
24 9 0.22
25 19 0.46
26 9 0.22
27 2 0.05
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (25 bp):
AAACTTAAGTATCGAAGAGATGAAC
Found at i:41194 original size:50 final size:51
Alignment explanation
Indices: 41135--41245 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 51
41125 TGTTAAAAGG
41135 AAAACTTAAGTATCGAAGAGATGAACAAACTAT-AGGACATGAAGAAGCTAC
1 AAAA-TTAAGTATCGAAGAGATGAACAAACTATAAGGACATGAAGAAGCTAC
41186 AAAATTAAGTATCGAAGAGATGAACAAACTATAGAAGGACATGAAGAAGCTAC
1 AAAATTAAGTATCGAAGAGATGAACAAACTAT--AAGGACATGAAGAAGCTAC
41239 AAAATTA
1 AAAATTA
41246 GAAGAAAATG
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
50 28 0.49
51 4 0.07
53 25 0.44
ACGTcount: A:0.51, C:0.12, G:0.19, T:0.18
Consensus pattern (51 bp):
AAAATTAAGTATCGAAGAGATGAACAAACTATAAGGACATGAAGAAGCTAC
Found at i:52515 original size:29 final size:29
Alignment explanation
Indices: 52483--52575 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
52473 TAAAATGGAA
*
52483 TTTTAGACATTCGAGGGTAAAACGATAAT
1 TTTTAGACATTCGAGGGTAAAAAGATAAT
* * * *
52512 TTTTAGAAAAATCG-GGATAAAAAAATGGAAT
1 TTTTAG-ACATTCGAGGGTAAAAAGAT--AAT
* * *
52543 TTTTGGACATTCAAGGGTAAAATGATAAT
1 TTTTAGACATTCGAGGGTAAAAAGATAAT
52572 TTTT
1 TTTT
52576 GAGAGTTTCG
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
29 22 0.46
30 9 0.19
31 17 0.35
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTTAGACATTCGAGGGTAAAAAGATAAT
Found at i:52605 original size:30 final size:29
Alignment explanation
Indices: 52569--52723 Score: 129
Period size: 29 Copynumber: 5.3 Consensus size: 29
52559 GTAAAATGAT
*
52569 AATTTTTGAGAGTTTCGAGGTCAAAAATGG
1 AATTTTTGAGAGTTTAGAGGT-AAAAATGG
* * *
52599 AATTTTTGA-AGGTTAAGGGGTAAAAATGA
1 AATTTTTGAGA-GTTTAGAGGTAAAAATGG
* **
52628 AATTTTTG-GAAGTTTAGGGGTAAAAATAC
1 AATTTTTGAG-AGTTTAGAGGTAAAAATGG
** *
52657 AATTTTCAAAAGTTTAGAGGTTAAAAATGG
1 AATTTTTGAGAGTTTAGAGG-TAAAAATGG
* *
52687 AATTTTTG-GAAG-TTCGAGGTAAAAATGT
1 AATTTTTGAG-AGTTTAGAGGTAAAAATGG
52715 AATTTTTGA
1 AATTTTTGA
52724 ACAATTTAGA
Statistics
Matches: 100, Mismatches: 18, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
28 16 0.16
29 52 0.52
30 32 0.32
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
AATTTTTGAGAGTTTAGAGGTAAAAATGG
Found at i:52623 original size:59 final size:58
Alignment explanation
Indices: 52532--52724 Score: 189
Period size: 59 Copynumber: 3.3 Consensus size: 58
52522 ATCGGGATAA
*
52532 AAAAATGGAATTTTTGGACA-TTCAA-GGGT-AAAATGATAATTTTT-GAGAGTTTCGAGGT
1 AAAAATGGAATTTTT-GAAAGTT-AAGGGGTAAAAATGA-AATTTTTGGA-AGTTTCGAGGT
* * *
52590 CAAAAATGGAATTTTTGAAGGTTAAGGGGTAAAAATGAAATTTTTGGAAGTTTAGGGGT
1 -AAAAATGGAATTTTTGAAAGTTAAGGGGTAAAAATGAAATTTTTGGAAGTTTCGAGGT
** ** * * *
52649 AAAAATACAATTTTCAAAAGTTTAGAGGTTAAAAATGGAATTTTTGGAAG-TTCGAGGT
1 AAAAATGGAATTTTTGAAAGTTAAG-GGGTAAAAATGAAATTTTTGGAAGTTTCGAGGT
*
52707 AAAAATGTAATTTTTGAA
1 AAAAATGGAATTTTTGAA
52725 CAATTTAGAG
Statistics
Matches: 111, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
58 43 0.39
59 59 0.53
60 9 0.08
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (58 bp):
AAAAATGGAATTTTTGAAAGTTAAGGGGTAAAAATGAAATTTTTGGAAGTTTCGAGGT
Found at i:52649 original size:88 final size:87
Alignment explanation
Indices: 52532--52722 Score: 217
Period size: 88 Copynumber: 2.2 Consensus size: 87
52522 ATCGGGATAA
* * ** * *
52532 AAAAATGGAATTTTTGGACATTCAAGGGT-AAAATGATAATTTTTGAGAGTTTCGAGGTCAAAAA
1 AAAAATGAAATTTTTGGACATTCAAGGGTAAAAAT-ACAATTTTCAAAAGTTTAGAGGTCAAAAA
*
52596 TGGAATTTTT-GAAGGTTAAGGGGT
65 TGGAATTTTTGGAA-GTT-AGAGGT
* * *
52620 AAAAATGAAATTTTTGGA-AGTTTAGGGGTAAAAATACAATTTTCAAAAGTTTAGAGGTTAAAAA
1 AAAAATGAAATTTTTGGACA-TTCAAGGGTAAAAATACAATTTTCAAAAGTTTAGAGGTCAAAAA
*
52684 TGGAATTTTTGGAAGTTCGAGGT
65 TGGAATTTTTGGAAGTTAGAGGT
*
52707 AAAAATGTAATTTTTG
1 AAAAATGAAATTTTTG
52723 AACAATTTAG
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
87 20 0.23
88 60 0.68
89 8 0.09
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.34
Consensus pattern (87 bp):
AAAAATGAAATTTTTGGACATTCAAGGGTAAAAATACAATTTTCAAAAGTTTAGAGGTCAAAAAT
GGAATTTTTGGAAGTTAGAGGT
Found at i:53844 original size:12 final size:12
Alignment explanation
Indices: 53790--53913 Score: 65
Period size: 12 Copynumber: 10.1 Consensus size: 12
53780 TATTAAAATT
*
53790 TATTAATATTAA
1 TATTATTATTAA
*
53802 TATTA--ATTAT
1 TATTATTATTAA
53812 TATTATTATTGAAA
1 TATTATTATT--AA
*
53826 CAGTTATTATTAA
1 TA-TTATTATTAA
*
53839 TATTATTAATGTCA
1 TATTATT-AT-TAA
* *
53853 T-TTATTACTAC
1 TATTATTATTAA
*
53864 TGTTTATTATTAA
1 T-ATTATTATTAA
* **
53877 TGTTATTAAAAA
1 TATTATTATTAA
53889 TATTATTATTAA
1 TATTATTATTAA
**
53901 TGCTATTATTAA
1 TATTATTATTAA
53913 T
1 T
53914 GATGATATTA
Statistics
Matches: 85, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
10 9 0.11
11 2 0.02
12 42 0.49
13 19 0.22
14 5 0.06
15 8 0.09
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:53914 original size:12 final size:12
Alignment explanation
Indices: 53828--53914 Score: 68
Period size: 12 Copynumber: 7.1 Consensus size: 12
53818 TATTGAAACA
53828 GTTATTATTAAT
1 GTTATTATTAAT
* *
53840 ATTATTAATGTCAT
1 GTTATT-AT-TAAT
* *
53854 -TTATTACTACT
1 GTTATTATTAAT
53865 GTTTATTATTAAT
1 G-TTATTATTAAT
**
53878 GTTATTAAAAAT
1 GTTATTATTAAT
*
53890 ATTATTATTAAT
1 GTTATTATTAAT
*
53902 GCTATTATTAAT
1 GTTATTATTAAT
53914 G
1 G
53915 ATGATATTAA
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
11 2 0.04
12 35 0.61
13 17 0.30
14 3 0.05
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.53
Consensus pattern (12 bp):
GTTATTATTAAT
Found at i:54604 original size:6 final size:6
Alignment explanation
Indices: 54593--54651 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
54583 TATAATAAGT
* * *
54593 TTTAAA TTTAAA TATAAA TCTAAA TTTAAA --CAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
54639 -ATAAA TTTAAA TT
1 TTTAAA TTTAAA TT
54652 CAAAATCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
4 3 0.07
5 4 0.09
6 36 0.84
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:54628 original size:28 final size:27
Alignment explanation
Indices: 54596--54649 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
54586 AATAAGTTTT
*
54596 AAATTTAAATATAAATCTAAATTTAAAC
1 AAATTTAAATATAAA-ATAAATTTAAAC
*
54624 AAATTTAAATTTAAAATAAATTTAAA
1 AAATTTAAATATAAAATAAATTTAAA
54650 TTCAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (27 bp):
AAATTTAAATATAAAATAAATTTAAAC
Found at i:54646 original size:17 final size:17
Alignment explanation
Indices: 54593--54684 Score: 107
Period size: 17 Copynumber: 5.4 Consensus size: 17
54583 TATAATAAGT
54593 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* *
54611 TCTAAATTT-AAACAAA
1 TTTAAATTTAAAATAAA
54627 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
54644 TTTAAATTCAAAATCAA
1 TTTAAATTTAAAATAAA
54661 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
54678 TCTTAAA
1 T-TTAAA
54685 ATTGGTTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
16 15 0.24
17 35 0.56
18 10 0.16
19 2 0.03
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:55009 original size:147 final size:147
Alignment explanation
Indices: 54740--55029 Score: 458
Period size: 147 Copynumber: 2.0 Consensus size: 147
54730 AATTTATTTA
* * * *
54740 CTTAGTGTTTTATTCCGTATAAATCCCTAAATTATGCTAATACCTCTATTTAAGCATAAAAGCAG
1 CTTAGTATTTTATTCCGTAGAAATCCCTAAATTATGCTAATACCTCTATTCAAGCATAAAAGCAA
* *
54805 CCGACTCTAAGTTGATTAATTGAAATTTCTTTCTAATTAAAACCCCTATTGTGGCATTAATT-TG
66 CCGACCCTAAGTTGATTAATTGAAATTTCTTTCTAATTAAAACCCCTATTGTCGCATTAATTCT-
54869 ATCCATGGATTCCCTTAT
130 ATCCATGGATTCCCTTAT
*
54887 CTTAGTATTTTATTCTGTAGAAATCCCTAAATTATGCTAATACCTCTATTCAAGCATAAAAGCAA
1 CTTAGTATTTTATTCCGTAGAAATCCCTAAATTATGCTAATACCTCTATTCAAGCATAAAAGCAA
* * *
54952 CTGACCCT-AGATTGATTAATTGAATTTTCTTTCTAATTAAAATCCCTATTGTCGCATTAATTCT
66 CCGACCCTAAG-TTGATTAATTGAAATTTCTTTCTAATTAAAACCCCTATTGTCGCATTAATTCT
55016 ATCCATGGATTCCC
130 ATCCATGGATTCCC
55030 CTATTAGATT
Statistics
Matches: 131, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
146 2 0.02
147 128 0.98
148 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (147 bp):
CTTAGTATTTTATTCCGTAGAAATCCCTAAATTATGCTAATACCTCTATTCAAGCATAAAAGCAA
CCGACCCTAAGTTGATTAATTGAAATTTCTTTCTAATTAAAACCCCTATTGTCGCATTAATTCTA
TCCATGGATTCCCTTAT
Found at i:55605 original size:25 final size:23
Alignment explanation
Indices: 55577--55622 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
55567 GTTGGATCCA
55577 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
55602 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
55623 TTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:59239 original size:28 final size:30
Alignment explanation
Indices: 59184--59241 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
59174 TATTTGTTGC
*
59184 TAAATTTATTTTTTTATATTAAATAAATAAA
1 TAAATTTA-TTTTTTATATTAAAGAAATAAA
*
59215 TAAATTTA-TTTTTA-ATTAACGAAATAA
1 TAAATTTATTTTTTATATTAAAGAAATAA
59242 TCAAACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 6 0.24
31 8 0.32
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TAAATTTATTTTTTATATTAAAGAAATAAA
Found at i:61846 original size:21 final size:20
Alignment explanation
Indices: 61817--61855 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
61807 ACGCCTACGA
61817 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
61837 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
61856 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:61980 original size:15 final size:17
Alignment explanation
Indices: 61960--61993 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
61950 AGGATTTGGT
61960 TTGTTTATT-T-TATTA
1 TTGTTTATTCTATATTA
61975 TTGTTTATTCTATATTA
1 TTGTTTATTCTATATTA
61992 TT
1 TT
61994 AATATAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 1 0.06
17 7 0.41
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TTGTTTATTCTATATTA
Found at i:62039 original size:12 final size:11
Alignment explanation
Indices: 61995--62045 Score: 70
Period size: 12 Copynumber: 4.6 Consensus size: 11
61985 TATATTATTA
61995 ATATAGAATAAT
1 ATATA-AATAAT
62007 ATATAAATAAT
1 ATATAAATAAT
62018 AT-T-AATAAT
1 ATATAAATAAT
62027 ATATAAATAAAT
1 ATATAAAT-AAT
62039 ATATAAA
1 ATATAAA
62046 GAAAATATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.22
10 2 0.06
11 11 0.31
12 15 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
ATATAAATAAT
Found at i:62489 original size:17 final size:17
Alignment explanation
Indices: 62467--62500 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
62457 CTAACTCAAA
62467 ACCAAATCCTGAAAGAT
1 ACCAAATCCTGAAAGAT
62484 ACCAAATCCTGAAAGAT
1 ACCAAATCCTGAAAGAT
62501 TTCGTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (17 bp):
ACCAAATCCTGAAAGAT
Found at i:62524 original size:13 final size:13
Alignment explanation
Indices: 62508--62532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62498 GATTTCGTTG
62508 AAATCAATATAGT
1 AAATCAATATAGT
62521 AAATCAATATAG
1 AAATCAATATAG
62533 ATTTATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
AAATCAATATAGT
Found at i:62946 original size:12 final size:12
Alignment explanation
Indices: 62929--62953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62919 CAGAGGCTAT
62929 TAACAATATTTA
1 TAACAATATTTA
62941 TAACAATATTTA
1 TAACAATATTTA
62953 T
1 T
62954 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:65591 original size:21 final size:20
Alignment explanation
Indices: 65562--65600 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
65552 ACGCCTACGA
65562 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
65582 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
65601 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:65725 original size:15 final size:17
Alignment explanation
Indices: 65705--65738 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
65695 AGGATTTGGT
65705 TTGTTTATT-T-TATTA
1 TTGTTTATTCTATATTA
65720 TTGTTTATTCTATATTA
1 TTGTTTATTCTATATTA
65737 TT
1 TT
65739 AATATAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 1 0.06
17 7 0.41
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TTGTTTATTCTATATTA
Found at i:65784 original size:12 final size:11
Alignment explanation
Indices: 65740--65790 Score: 70
Period size: 12 Copynumber: 4.6 Consensus size: 11
65730 TATATTATTA
65740 ATATAGAATAAT
1 ATATA-AATAAT
65752 ATATAAATAAT
1 ATATAAATAAT
65763 AT-T-AATAAT
1 ATATAAATAAT
65772 ATATAAATAAAT
1 ATATAAAT-AAT
65784 ATATAAA
1 ATATAAA
65791 GAAAATATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.22
10 2 0.06
11 11 0.31
12 15 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
ATATAAATAAT
Done.