Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009461.1 Kokia drynarioides strain JFW-HI SEQ_124168, 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: 49734
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 308 characters in sequence are not A, C, G, or T
Found at i:156 original size:30 final size:27
Alignment explanation
Indices: 92--156 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
82 TTCTGAACGT
*
92 TTTAATAATAATAATAAATATAATAAA
1 TTTATTAATAATAATAAATATAATAAA
** *
119 TACATTAATATTAATAAAATAATAATAAAA
1 TTTATTAATAATAAT-AAAT-ATAAT-AAA
149 TTTATTAA
1 TTTATTAA
157 AAAAAAAGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 11 0.38
28 4 0.14
29 5 0.17
30 9 0.31
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TTTATTAATAATAATAAATATAATAAA
Found at i:1147 original size:59 final size:59
Alignment explanation
Indices: 1051--1469 Score: 461
Period size: 59 Copynumber: 7.1 Consensus size: 59
1041 GAAGGTCTCT
* * * *
1051 AAACTATCCAAAAATTCCA-TTTTACCCCCGAATTTCCAAAAATCCCATTTTTGACCCCA
1 AAACT-TCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * *
1110 AAACTTCTAAAAATTCTATTTTTACCCTTGGACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * *
1169 AAACTTCAAAAAATTTTGTTTTTACACC-CGAACTTCCAAAAATCCCACTTTTGACC-CTA
1 AAACTTCCAAAAATTCTATTTTTAC-CCTCGAACTTCCAAAAATCCCATTTTTGACCTC-A
* * * * * * *
1228 AAATTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATCTCATTTTTAACCCCG
1 AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * * *
1287 AAACTTCCAAAAATT-TCATTTTTACCCACGAACTTCCAAAAATTCTATTTTTGATCTCG
1 AAACTTCCAAAAATTCT-ATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * * *
1346 AAACTTTCAAAAATTCTATTTTTACCCACGAACTTCCAAAAATCCCGTTTTTTATCTCA
1 AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * *
1405 AAACTTCCAAAAATTCTATTTTTTGCCCTCAAACTTCC-AAAATCTCCATTTTCGACCTCA
1 AAACTTCCAAAAATTCTA-TTTTTACCCTCGAACTTCCAAAAATC-CCATTTTTGACCTCA
1465 AAACT
1 AAACT
1470 CTCAAAATTA
Statistics
Matches: 302, Mismatches: 49, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
58 14 0.05
59 252 0.83
60 36 0.12
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
Found at i:1456 original size:29 final size:29
Alignment explanation
Indices: 1051--1456 Score: 290
Period size: 30 Copynumber: 13.8 Consensus size: 29
1041 GAAGGTCTCT
*
1051 AAACTATCCAAAAATTCCA-TTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCTC
* * *
1080 GAATTTCCAAAAATCCCATTTTTGACCC-C
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* * *
1109 AAAACTTCTAAAAATTCTATTTTTACCCTT
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
** *
1139 GGACTTCCAAAAATCCCATTTTTGA-CCTC
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* ***
1168 GAAACTTCAAAAAATTTTGTTTTTACACC-C
1 -AAACTTCCAAAAATTCCATTTTTAC-CCTC
* * * *
1198 GAACTTCCAAAAATCCCACTTTTGACCCTA
1 AAACTTCCAAAAATTCCA-TTTTTACCCTC
* *
1228 AAATTTCCAAAAATTCCATTTTTACCCTT
1 AAACTTCCAAAAATTCCATTTTTACCCTC
*
1257 GAACTTCCAAAAA-TCTCATTTTTAACCC-C
1 AAACTTCCAAAAATTC-CATTTTT-ACCCTC
* *
1286 GAAACTTCCAAAAATTTCATTTTTACCCAC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* * *
1316 GAACTTCCAAAAATTCTATTTTTGA-TCTC
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* * *
1345 GAAACTTTCAAAAATTCTATTTTTACCCAC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* * * *
1375 GAACTTCCAAAAATCCCGTTTTTTA-TCTC
1 AAACTTCCAAAAATTCC-ATTTTTACCCTC
* *
1404 AAAACTTCCAAAAATTCTATTTTTTGCCCTC
1 -AAACTTCCAAAAATTCCA-TTTTTACCCTC
1435 AAACTTCC-AAAATCTCCATTTT
1 AAACTTCCAAAAAT-TCCATTTT
1457 CGACCTCAAA
Statistics
Matches: 291, Mismatches: 63, Indels: 46
0.73 0.16 0.12
Matches are distributed among these distances:
28 14 0.05
29 126 0.43
30 145 0.50
31 6 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:1463 original size:29 final size:30
Alignment explanation
Indices: 1051--1466 Score: 194
Period size: 29 Copynumber: 14.1 Consensus size: 30
1041 GAAGGTCTCT
* *
1051 AAACTATCCAAAAATTCCATTTTAC--CCCC
1 AAACT-TCCAAAAATTCCATTTTTCGACCTC
* * * *
1080 GAATTTCCAAAAATCCCATTTTT-GACCCC
1 AAACTTCCAAAAATTCCATTTTTCGACCTC
* * *
1109 AAAACTTCTAAAAATTCTATTTTT--ACCCTT
1 -AAACTTCCAAAAATTCCATTTTTCGA-CCTC
** *
1139 GGACTTCCAAAAATCCCATTTTT-GACCTC
1 AAACTTCCAAAAATTCCATTTTTCGACCTC
* ***
1168 GAAACTTCAAAAAATTTTGTTTTTAC-ACC-C
1 -AAACTTCCAAAAATTCCATTTTT-CGACCTC
* * * *
1198 GAACTTCCAAAAATCCCACTTTT-GACCCTA
1 AAACTTCCAAAAATTCCATTTTTCGA-CCTC
* *
1228 AAATTTCCAAAAATTCCATTTTT--ACCCTT
1 AAACTTCCAAAAATTCCATTTTTCGA-CCTC
* * *
1257 GAACTTCCAAAAA-TCTCATTTTT-AACCCC
1 AAACTTCCAAAAATTC-CATTTTTCGACCTC
*
1286 GAAACTTCCAAAAATTTCATTTTT--ACC-C
1 -AAACTTCCAAAAATTCCATTTTTCGACCTC
* *
1314 ACGAACTTCCAAAAATTCTATTTTT-GATCTC
1 A--AACTTCCAAAAATTCCATTTTTCGACCTC
* *
1345 GAAACTTTCAAAAATTCTATTTTT--ACC-C
1 -AAACTTCCAAAAATTCCATTTTTCGACCTC
* * * *
1373 ACGAACTTCCAAAAATCCCGTTTTT-TATCTC
1 A--AACTTCCAAAAATTCCATTTTTCGACCTC
* * *
1404 AAAACTTCCAAAAATTCTATTTTTTGCCCTC
1 -AAACTTCCAAAAATTCCATTTTTCGACCTC
1435 AAACTTCC-AAAATCTCCA-TTTTCGACCTC
1 AAACTTCCAAAAAT-TCCATTTTTCGACCTC
1464 AAA
1 AAA
1467 ACTCTCAAAA
Statistics
Matches: 298, Mismatches: 62, Indels: 54
0.72 0.15 0.13
Matches are distributed among these distances:
27 2 0.01
28 21 0.07
29 132 0.44
30 132 0.44
31 9 0.03
32 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTCGACCTC
Found at i:2582 original size:7 final size:7
Alignment explanation
Indices: 2551--2581 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2541 TGCCCTATCA
2551 TTTTCTT
1 TTTTCTT
2558 TTTTCTT
1 TTTTCTT
2565 TTTTCTT
1 TTTTCTT
2572 TTTT-TT
1 TTTTCTT
2578 TTTT
1 TTTT
2582 TATATATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTCTT
Found at i:4799 original size:32 final size:31
Alignment explanation
Indices: 4763--4828 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
4753 AAACATCAAC
*
4763 AATTTCTTTGATAAT-TT-TTTTTATTTATACTT
1 AATTTCTTT-AT-ATGTTATTTTT-TTTATACAT
4795 AATTTCTTTATATGTTATTTTTTTTATACAT
1 AATTTCTTTATATGTTATTTTTTTTATACAT
4826 AAT
1 AAT
4829 GAAAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 2 0.06
31 15 0.48
32 14 0.45
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (31 bp):
AATTTCTTTATATGTTATTTTTTTTATACAT
Found at i:5152 original size:16 final size:16
Alignment explanation
Indices: 5107--5178 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
5097 TCTGCTCATA
*
5107 TTATT-TTTTAATTTT
1 TTATTATTTTAATATT
**
5122 TTAAAATATTT-ATATT
1 TTATTAT-TTTAATATT
5138 TTATTATTTTAATATT
1 TTATTATTTTAATATT
* * *
5154 TAATAATTTTATACATT
1 TTATTATTTTA-ATATT
5171 TT-TTATTT
1 TTATTATTT
5179 ATTGAAAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
15 6 0.14
16 29 0.67
17 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTTTAATATT
Found at i:5156 original size:31 final size:31
Alignment explanation
Indices: 5107--5166 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
5097 TCTGCTCATA
*
5107 TTATTTTTTAATTTTTTAA-AATATTTATATT
1 TTATTTTTTAATTATTTAATAAT-TTTATATT
5138 TTATTATTTTAA-TATTTAATAATTTTATA
1 TTATT-TTTTAATTATTTAATAATTTTATA
5167 CATTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TTATTTTTTAATTATTTAATAATTTTATATT
Found at i:5597 original size:16 final size:16
Alignment explanation
Indices: 5577--5617 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
5567 ATTTTGACAT
5577 AAAAATTATATAT-AA
1 AAAAATTATATATCAA
5592 AGAAAA--ATATATCAA
1 A-AAAATTATATATCAA
5607 AAAAATTATAT
1 AAAAATTATAT
5618 TTGTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 10 0.45
15 4 0.18
16 8 0.36
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
AAAAATTATATATCAA
Found at i:23747 original size:29 final size:28
Alignment explanation
Indices: 23676--23748 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
23666 AATAACCCTT
*
23676 AACCTTATAACCTAAAACCATGAAGCCCA
1 AACCTTAAAACCTAAAACCA-GAAGCCCA
* *
23705 AACC-TAATATCCTAAAACCA-AATCATCCA
1 AACCTTAA-AACCTAAAACCAGAAGC--CCA
23734 AACCTTAAAACCTAA
1 AACCTTAAAACCTAA
23749 TTCGGTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.08
28 2 0.06
29 28 0.78
30 3 0.08
ACGTcount: A:0.48, C:0.30, G:0.03, T:0.19
Consensus pattern (28 bp):
AACCTTAAAACCTAAAACCAGAAGCCCA
Found at i:23853 original size:19 final size:19
Alignment explanation
Indices: 23800--23858 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
23790 GACCGACACG
*
23800 TTGACTTTGATCGTTAACT
1 TTGACTTTGATCGTTGACT
****
23819 TTGACCAAACAT-GTTGACT
1 TTGA-CTTTGATCGTTGACT
23838 TTGACTTTGATCGTTGACT
1 TTGACTTTGATCGTTGACT
23857 TT
1 TT
23859 TTTTTTACTA
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
18 3 0.10
19 23 0.79
20 3 0.10
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (19 bp):
TTGACTTTGATCGTTGACT
Found at i:28114 original size:110 final size:109
Alignment explanation
Indices: 27888--28114 Score: 262
Period size: 110 Copynumber: 2.1 Consensus size: 109
27878 AAACAAAGAA
* ** * * *
27888 CATTCATCGATTTTAAATAGGATGTTCAATTACTTAGGTTCAAAGAAAAAACCATACCTAGCACA
1 CATTTATCGATTTTAAATAGGATACTCAATTACTTAGGCTCAAAGAAAAAACCATACCCAACACA
* * * *
27953 TTATGACACAATTTTTCTAGTCCCCTAAAATAATAGAACATTGAG
66 TTATGACACAATTTCTCGAGTCCCCTAAAATAAAAAAACATT-AG
*
27998 CATTTATCGATTTTAAATAGGATACTCAATTATTTAGGCTCAAAGAAAAAAACCATACCCAACAC
1 CATTTATCGATTTTAAATAGGATACTCAATTACTTAGGCTCAAAG-AAAAAACCATACCCAACAC
* *
28063 GTTA-GAGCACAATTTCTCGAGGT-CCTTAAAATAAAAAAAACATT-G
65 ATTATGA-CACAATTTCTCGA-GTCCCCTAAAAT-AAAAAAACATTAG
*
28108 CCTTTAT
1 CATTTAT
28115 TTTTTAAACA
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
110 49 0.49
111 39 0.39
112 11 0.11
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (109 bp):
CATTTATCGATTTTAAATAGGATACTCAATTACTTAGGCTCAAAGAAAAAACCATACCCAACACA
TTATGACACAATTTCTCGAGTCCCCTAAAATAAAAAAACATTAG
Found at i:29302 original size:29 final size:28
Alignment explanation
Indices: 29270--29331 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
29260 AAAATGCAAT
*
29270 TTTTGGATCA-TTGAGCGGCAAAATGGTAA
1 TTTTGGA-CACTTG-GCGGCAAAATAGTAA
*
29299 TTTTGGACACTTTGGGGGCAAAATAGTAA
1 TTTTGGACAC-TTGGCGGCAAAATAGTAA
29328 TTTT
1 TTTT
29332 CGGAGGTTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 24 0.83
30 3 0.10
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (28 bp):
TTTTGGACACTTGGCGGCAAAATAGTAA
Found at i:29544 original size:30 final size:30
Alignment explanation
Indices: 29289--29684 Score: 224
Period size: 29 Copynumber: 13.5 Consensus size: 30
29279 ATTGAGCGGC
* **
29289 AAAATGGTAA-TTTTGGACACTTTG-GGGGC
1 AAAATGGTAATTTTTGGA-AGTTTGAGGGTA
* * * *
29318 AAAATAGTAATTTTCGGAGGTTCGAGGGTA
1 AAAATGGTAATTTTTGGAAGTTTGAGGGTA
*
29348 AAACA--GTAATTTTTGGACA-TTCGAGGGTCA
1 AAA-ATGGTAATTTTTGGA-AGTTTGAGGGT-A
* * *
29378 AAAATGG-GA-TTTTGGAAATTCGAGGGT-
1 AAAATGGTAATTTTTGGAAGTTTGAGGGTA
* * * * *
29405 AAAATGGTACTTTTTGGGAAG-ATCAAGATCA
1 AAAATGGTAATTTTT-GGAAGTTTGAGGGT-A
* *
29436 AAAAT-G-AAATTTTGGAAGTTTGGGGGT-
1 AAAATGGTAATTTTTGGAAGTTTGAGGGTA
* * * *
29463 AAAAT-GTGATTTTCGAAAAGTTTG-GGATCA
1 AAAATGGTAATTTTTG-GAAGTTTGAGGGT-A
*
29493 AAAATGG-AATTTTTTGAAGTTTGAGGGT-
1 AAAATGGTAATTTTTGGAAGTTTGAGGGTA
*
29521 AAAATGGTAATTTTTGGGAAGTTTGGGGGTA
1 AAAATGGTAATTTTT-GGAAGTTTGAGGGTA
* * *
29552 AAAATAG-AGTTTTTGGAAGTTCGAGGGT-
1 AAAATGGTAATTTTTGGAAGTTTGAGGGTA
* * *
29580 TAAATGGTAATTTTTGGAGAATTTGAGGTTA
1 AAAATGGTAATTTTTGGA-AGTTTGAGGGTA
* *
29611 AAAATAG-AATTTTTGGAAGTTCGAGGGGTA
1 AAAATGGTAATTTTTGGAAGTTTGA-GGGTA
*
29641 AAAAT-GTAATTTTTGTAAAGTTT-AGGGGTA
1 AAAATGGTAATTTTTG-GAAGTTTGA-GGGTA
29671 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
29685 ATAAAATTTT
Statistics
Matches: 284, Mismatches: 54, Indels: 57
0.72 0.14 0.14
Matches are distributed among these distances:
27 13 0.05
28 26 0.09
29 112 0.39
30 109 0.38
31 24 0.08
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGTTTGAGGGTA
Found at i:29546 original size:59 final size:59
Alignment explanation
Indices: 29289--29684 Score: 312
Period size: 59 Copynumber: 6.8 Consensus size: 59
29279 ATTGAGCGGC
* * * * *
29289 AAAATGGTAA-TTTT-GGACACTTTGGGGGC-AAAATAGTAATTTTCGGAGGTTCGAGGGT
1 AAAATGGTAATTTTTGGGA-AGTTTGGGGTCAAAAAT-GGAATTTTTGGAAGTTCGAGGGT
** * * *
29347 AAAACAGTAATTTTT-GGACA-TTCGAGGGTCAAAAATGGGA-TTTTGGAAATTCGAGGGT
1 AAAATGGTAATTTTTGGGA-AGTTTG-GGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
* * *** * * * *
29405 AAAATGGTACTTTTTGGGAAGATCAAGATCAAAAAT-GAAATTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGGAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
* * ** * * *
29463 AAAAT-GTGATTTTCGAAAAGTTTGGGATCAAAAATGGAATTTTTTGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGGAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
* *
29521 AAAATGGTAATTTTTGGGAAGTTTGGGGGT-AAAAATAGAGTTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGGAAGTTT-GGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
* * * *
29580 TAAATGGTAATTTTTGGAGAA-TTTGAGGTTAAAAATAGAATTTTTGGAAGTTCGAGGGGT
1 AAAATGGTAATTTTTGG-GAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGA-GGGT
** *
29640 AAAAAT-GTAATTTTTGTAAAGTTTAGGGGT-AAAAATGTAATTTTT
1 -AAAATGGTAATTTTTGGGAAGTTT-GGGGTCAAAAATGGAATTTTT
29685 ATAAAATTTT
Statistics
Matches: 273, Mismatches: 50, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
57 23 0.08
58 96 0.35
59 104 0.38
60 42 0.15
61 8 0.03
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGGAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
Found at i:29653 original size:29 final size:28
Alignment explanation
Indices: 29318--29683 Score: 160
Period size: 30 Copynumber: 12.5 Consensus size: 28
29308 CTTTGGGGGC
*
29318 AAAATAGTAATTTTCGGAGGTTCGAGGGTA
1 AAAAT-GTAATTTT-GGAAGTTCGAGGGTA
29348 AAACA-GTAATTTTTGGACA-TTCGAGGGTCA
1 AAA-ATGTAA-TTTTGGA-AGTTCGAGGGT-A
** *
29378 AAAATGGGATTTTGGAAATTCGAGGGT-
1 AAAATGTAATTTTGGAAGTTCGAGGGTA
* * * *
29405 AAAATGGTACTTTTTGGGAAGATC-AAGATCA
1 AAAAT-GTA-ATTTT-GGAAGTTCGAGGGT-A
* * *
29436 AAAATGAAATTTTGGAAGTTTGGGGGT-
1 AAAATGTAATTTTGGAAGTTCGAGGGTA
* * * *
29463 AAAATGTGATTTTCGAAAAGTTTG-GGATCA
1 AAAATGTAATTTT-G-GAAGTTCGAGGGT-A
* * *
29493 AAAATGGAATTTTTTGAAGTTTGAGGGT-
1 AAAATGTAA-TTTTGGAAGTTCGAGGGTA
* *
29521 AAAATGGTAATTTTTGGGAAGTTTGGGGGTA
1 AAAAT-GTAA-TTTT-GGAAGTTCGAGGGTA
*
29552 AAAATAG-AGTTTTTGGAAGTTCGAGGGT-
1 AAAAT-GTA-ATTTTGGAAGTTCGAGGGTA
* * * *
29580 TAAATGGTAATTTTTGGAGAATTTGAGGTTA
1 AAAAT-GTAA-TTTTGGA-AGTTCGAGGGTA
29611 AAAATAG-AATTTTTGGAAGTTCGAGGGGTA
1 AAAAT-GTAA-TTTTGGAAGTTCGA-GGGTA
* *
29641 AAAATGTAATTTTTGTAAAGTT-TAGGGGTA
1 AAAATGTAA-TTTTG-GAAGTTCGA-GGGTA
29671 AAAATGTAATTTT
1 AAAATGTAATTTT
29684 TATAAAATTT
Statistics
Matches: 261, Mismatches: 46, Indels: 59
0.71 0.13 0.16
Matches are distributed among these distances:
27 16 0.06
28 22 0.08
29 98 0.38
30 99 0.38
31 26 0.10
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAGTTCGAGGGTA
Found at i:29737 original size:30 final size:30
Alignment explanation
Indices: 29634--29747 Score: 131
Period size: 30 Copynumber: 3.7 Consensus size: 30
29624 TGGAAGTTCG
** *
29634 AGGGGTAAAAATGTAATTTTTGTAAAGTTT
1 AGGGGTAAAAATGTAATTTTTAAAAACTTT
*
29664 AGGGGTAAAAATGTAATTTTTATAAAATTTT
1 AGGGGTAAAAATGTAATTTTTA-AAAACTTT
*
29695 AGGGGGTTAAAATGTAATTTTTAAAAACTTT
1 A-GGGGTAAAAATGTAATTTTTAAAAACTTT
* *
29726 -GGGGTTAAAAATATGATTTTTA
1 AGGGG-TAAAAATGTAATTTTTA
29748 TACAGTTCAG
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
29 4 0.05
30 35 0.48
31 14 0.19
32 20 0.27
ACGTcount: A:0.39, C:0.01, G:0.20, T:0.40
Consensus pattern (30 bp):
AGGGGTAAAAATGTAATTTTTAAAAACTTT
Found at i:30856 original size:3 final size:3
Alignment explanation
Indices: 30848--30895 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
30838 CCTTTTTGTT
30848 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30896 GTGCTATAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31702 original size:17 final size:17
Alignment explanation
Indices: 31629--31719 Score: 60
Period size: 17 Copynumber: 5.4 Consensus size: 17
31619 TTAATTTAAT
* * *
31629 TTTAAGTTTAAAACCAT
1 TTTAAATTTAAAACAAA
31646 TTTAAATTT--AACTAAA
1 TTTAAATTTAAAAC-AAA
*
31662 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAACAAA
** *
31680 AATAAATTTAAAACCAA
1 TTTAAATTTAAAACAAA
* * *
31697 TTTAAACTTAATATAAA
1 TTTAAATTTAAAACAAA
31714 TTTAAA
1 TTTAAA
31720 ATCAAAAGTT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
15 3 0.05
16 10 0.18
17 31 0.55
18 10 0.18
19 2 0.04
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (17 bp):
TTTAAATTTAAAACAAA
Found at i:34104 original size:6 final size:7
Alignment explanation
Indices: 34084--34109 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
34074 TATCTAGATT
34084 ATTAAAA
1 ATTAAAA
34091 ATTAAAA
1 ATTAAAA
34098 ATTAAAA
1 ATTAAAA
34105 ATTAA
1 ATTAA
34110 TTTCGACCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
ATTAAAA
Found at i:35075 original size:30 final size:30
Alignment explanation
Indices: 35036--35358 Score: 263
Period size: 30 Copynumber: 10.8 Consensus size: 30
35026 ATTTGGGAAC
*
35036 AAATGTAATTTTGGAAAAATTTAGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTAGGGGTCA
* *
35066 AAATATAATTTTAGG-AAAGTTTA-GGGTTA
1 AAATGTAATTTT-GGAAAAGTTTAGGGGTCA
** * * *
35095 AAATGTGCTTTTAGAAAGGTTTGGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTAGGGGTCA
*
35125 AAATGT-GTTTTAAGG-AAAGTTTAGGGGTCA
1 AAATGTAATTTT--GGAAAAGTTTAGGGGTCA
* * *
35155 AAATGTGATTTT--AAGAATGTTTAAGGGTTA
1 AAATGTAATTTTGGAA-AA-GTTTAGGGGTCA
*
35185 AAATGTAATTTTGTAAAAGTTT-GAGGGTCA
1 AAATGTAATTTTGGAAAAGTTTAG-GGGTCA
* * *
35215 AAATGTAATTTGGGAAAA-ATTAGGTGTCA
1 AAATGTAATTTTGGAAAAGTTTAGGGGTCA
* *
35244 AAATGTAATTTTGGGAAAA-TTT-GAAGGTTA
1 AAATGTAATTTT-GGAAAAGTTTAG-GGGTCA
* * *
35274 AAATGTGATTTTAGAAAAGTTTAGGGGTTA
1 AAATGTAATTTTGGAAAAGTTTAGGGGTCA
* * * *
35304 AAATTTAATTTTGGAAAAGTTCAGAGATCA
1 AAATGTAATTTTGGAAAAGTTTAGGGGTCA
35334 AAAT-TCAATTTTGGAAAAGTTTAGG
1 AAATGT-AATTTTGGAAAAGTTTAGG
35359 ATTAAAATAT
Statistics
Matches: 234, Mismatches: 41, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.01
29 51 0.22
30 169 0.72
31 10 0.04
32 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
AAATGTAATTTTGGAAAAGTTTAGGGGTCA
Found at i:35156 original size:89 final size:88
Alignment explanation
Indices: 35036--35383 Score: 321
Period size: 89 Copynumber: 3.9 Consensus size: 88
35026 ATTTGGGAAC
* *
35036 AAATGTAATTTTGGAAAAATTTAGGGGTCAAAATATAATTTTAGGAAAGTTT-AGGGTTAAAATG
1 AAATGT-ATTTTGG-AAAGTTTAGGGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATG
* *
35100 TGCTTTTAGAAAGGTTTGGGGGTCA
64 TGATTTTAGAAAAGTTTGGGGGTCA
* * * *
35125 AAATGTGTTTTAAGGAAAGTTTAGGGGTCAAAATGTGATTTTAAGAATGTTTAAGGGTTAAAATG
1 AAATGTATTTT--GGAAAGTTTAGGGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATG
* *
35190 TAATTTT-GTAAAAGTTTGAGGGTCA
64 TGATTTTAG-AAAAGTTTGGGGGTCA
* ** * * *
35215 AAATGTAATTTGGGAAAAATTAGGTGTCAAAATGTAATTTTGGGAAAATTTGAA-GGTTAAAATG
1 AAATGT-ATTTTGGAAAGTTTAGGGGTCAAAATGTAATTTTAGGAAAGTTT-AAGGGTTAAAATG
* *
35279 TGATTTTAGAAAAGTTTAGGGGTTA
64 TGATTTTAGAAAAGTTTGGGGGTCA
* * * * *
35304 AAATTTAATTTTGGAAAAGTTCAGAGATCAAAAT-TCAATTTT-GGAAAAGTTT-AGGATTAAAA
1 AAATGT-ATTTTGG-AAAGTTTAGGGGTCAAAATGT-AATTTTAGG-AAAGTTTAAGGGTTAAAA
* * *
35366 TATGATTTTTGGAAAGTT
62 TGTGATTTTAGAAAAGTT
35384 CAGTTCTAAG
Statistics
Matches: 211, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
88 5 0.02
89 136 0.64
90 67 0.32
91 3 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (88 bp):
AAATGTATTTTGGAAAGTTTAGGGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGTG
ATTTTAGAAAAGTTTGGGGGTCA
Found at i:35188 original size:60 final size:58
Alignment explanation
Indices: 35036--35307 Score: 174
Period size: 59 Copynumber: 4.6 Consensus size: 58
35026 ATTTGGGAAC
* * ** * * * *
35036 AAATGTAATTTTGGAAAAATTTAGGGGTCAAAATATAATTTTAGGAAAGTTTAGGGTTA
1 AAATGTGATTTTAGAAAGGTTTAAGGGTCAAAATGT-GTTTTAGGAAAGTTTAGGGTCA
* **
35095 AAATGTGCTTTTAGAAAGGTTTGGGGGTCAAAATGTGTTTTAAGGAAAGTTTAGGGGTCA
1 AAATGTGATTTTAGAAAGGTTTAAGGGTCAAAATGTGTTTT-AGGAAAGTTTA-GGGTCA
* * * *
35155 AAATGTGATTTTA-AGAATGTTTAAGGGTTAAAATGTAATTTT-GTAAAAGTTTGAGGGTCA
1 AAATGTGATTTTAGA-AAGGTTTAAGGGTCAAAATGT-GTTTTAG-GAAAGTTT-AGGGTCA
* ** ** * * * * *
35215 AAATGTAATTTGGGAAA-AATT-AGGTGTCAAAATGTAATTTTGGGAAAATTTGAAGGTTA
1 AAATGTGATTTTAGAAAGGTTTAAGG-GTCAAAATGT-GTTTTAGGAAAGTTT-AGGGTCA
* * *
35274 AAATGTGATTTTAGAAAAGTTTAGGGGTTAAAAT
1 AAATGTGATTTTAGAAAGGTTTAAGGGTCAAAAT
35308 TTAATTTTGG
Statistics
Matches: 169, Mismatches: 33, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
58 7 0.04
59 85 0.50
60 69 0.41
61 8 0.05
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (58 bp):
AAATGTGATTTTAGAAAGGTTTAAGGGTCAAAATGTGTTTTAGGAAAGTTTAGGGTCA
Found at i:35383 original size:29 final size:29
Alignment explanation
Indices: 35173--35380 Score: 117
Period size: 30 Copynumber: 7.0 Consensus size: 29
35163 TTTTAAGAAT
* *
35173 GTTTAAGGGTTAAAA-TGTAATTTTGTAAAA
1 GTTT-AGGATTAAAATTG-AATTTTGGAAAA
* * *
35203 GTTTGAGGGTCAAAA-TGTAATTTGGGAAAA
1 GTTT-AGGATTAAAATTG-AATTTTGGAAAA
*
35233 -ATTAGG-TGTCAAAA-TGTAATTTTGGGAAAA
1 GTTTAGGAT-T-AAAATTG-AATTTT-GGAAAA
*
35263 -TTTGAAGG-TTAAAATGTG-ATTTTAGAAAA
1 GTTT--AGGATTAAAAT-TGAATTTTGGAAAA
* *
35292 GTTTAGGGGTTAAAATTTAATTTTGGAAAA
1 GTTTA-GGATTAAAATTGAATTTTGGAAAA
* * *
35322 GTTCAGAGATCAAAATTCAATTTTGGAAAA
1 GTTTAG-GATTAAAATTGAATTTTGGAAAA
*
35352 GTTTAGGATTAAAATATGATTTTTGGAAA
1 GTTTAGGATTAAAAT-TGAATTTTGGAAA
35381 GTTCAGTTCT
Statistics
Matches: 146, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.01
28 4 0.03
29 31 0.21
30 103 0.71
31 1 0.01
32 6 0.04
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (29 bp):
GTTTAGGATTAAAATTGAATTTTGGAAAA
Found at i:37387 original size:85 final size:85
Alignment explanation
Indices: 37244--37408 Score: 276
Period size: 85 Copynumber: 1.9 Consensus size: 85
37234 CGTTTCATTG
* * *
37244 ATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTTATTGATTTAATCCACTTCTTT
1 ATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCTTTATTGATTTAATCCACTTATTT
37309 GTATCTCATCAGGAAGACGA
66 GTATCTCATCAGGAAGACGA
* * *
37329 ATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCTCTTTATTGCTTTGATCCACTTATTT
1 ATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCTTTATTGATTTAATCCACTTATTT
37394 GTATCTCATCAGGAA
66 GTATCTCATCAGGAA
37409 CATGACTCAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
85 74 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (85 bp):
ATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCTTTATTGATTTAATCCACTTATTT
GTATCTCATCAGGAAGACGA
Found at i:37712 original size:48 final size:48
Alignment explanation
Indices: 37639--37818 Score: 175
Period size: 48 Copynumber: 4.0 Consensus size: 48
37629 TATTGAGCTT
* ** *
37639 CGCTTCATTGATTTGGTTTAATTCTCTGTATCTCATCAGGAAGATGAC
1 CGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
* *
37687 CGCTTCATTGATTTAATCCACTTCTCTATATCTCATCAGG-A-A-G--
1 CGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
*
37730 -G--TC---GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAC
1 CGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
* * * * *
37772 CACTTTATTGCTTTGACCCACTTCTCTGTATCTCATTAGGAAGATGA
1 CGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGA
37819 GGTTTGAAGT
Statistics
Matches: 106, Mismatches: 15, Indels: 22
0.74 0.10 0.15
Matches are distributed among these distances:
37 28 0.26
38 1 0.01
39 1 0.01
40 3 0.03
42 1 0.01
45 2 0.02
46 1 0.01
47 1 0.01
48 68 0.64
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (48 bp):
CGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
Found at i:37905 original size:48 final size:48
Alignment explanation
Indices: 37847--37939 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
37837 TATTGAGCTT
* *
37847 CGCTTTATTGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATAAC
1 CGCTTTATTGATTTGATCCACTTCTTTGTATCTCATCAAGAAGATAAC
* * * *
37895 CGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGAT
1 CGCTTTATTGATTTGATCCACTTCTTTGTATCTCATCAAGAAGAT
37940 GGATTTGGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (48 bp):
CGCTTTATTGATTTGATCCACTTCTTTGTATCTCATCAAGAAGATAAC
Found at i:37935 original size:208 final size:208
Alignment explanation
Indices: 37178--38391 Score: 1713
Period size: 208 Copynumber: 5.9 Consensus size: 208
37168 AATTTGGTCT
* * * * *
37178 ACTTCTCTGTTTCTCATAAGGAAGATGGGGTTTGAAGTCTTATTCGTATTGAGCTTCGTTTCATT
1 ACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
* * *
37243 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTTATTGATTTAATCCACTTCTT
66 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
* * * * *
37308 TGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCTCTTT
131 TGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTT
*
37373 ATTGCTTTGATCC
196 ATTGCTTTGACCC
* * *
37386 ACTTATTTGTATCTCATCAGG-A-A-CA----TG-A--CTCATTCGTATTGAGCTTCAGC-TCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTC-GCTTCAT
* * *
37440 TGATTTGGTCTACTTCTCTGTATCTTATCAGGAAGATGACCGCTTAATTGATTTAATCCACTTCT
65 TGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCT
* * * * * *
37505 TTGTATCTCATCAGGAACGCAGATTTGGTCCACTTCTTTATATCTCAAT-AAGAAGATGACCGTT
130 CTGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTC-ATCAAGAAGATGACCGCT
*
37569 TTATTGTTTTGACCC
194 TTATTGCTTTGACCC
* * * * * * *
37584 ACTTTTCTATATATTATCAAGAAGATGGGGTTTGAAGTCTTATT-GTATTGAGCTTCGCTTCATT
1 ACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
* * *
37648 GATTTGGTTTAATTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
66 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
* * *
37713 TATATCTCATCAGGAAGGTC-GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTT
131 TGTATCTCATCAGGAAGG-CGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTT
37777 TATTGCTTTGACCC
195 TATTGCTTTGACCC
* *
37791 ACTTCTCTGTATCTCATTAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTTATT
1 ACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
* *
37856 GATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATAACCGCTTCATTGATTTAATCCACTTCTC
66 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
** * * *
37921 TGTATCTCATCAGGAAGATGGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGACCTCTTT
131 TGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTT
37986 ATTGCTTTGACCC
196 ATTGCTTTGACCC
* * **
37999 ACTTCTTTGTATCTCATCAGGAAGATGAGATTCAAAGTCTCATTCGTATTGAGCTTCGCTTCATT
1 ACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
* * *
38064 TATTTGGTCTACTTCTTTGTATCTCATTAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
66 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
* * *
38129 TGTATCTCATCAAGAAGGCGGATTTGATCCACTTCTCTGTATCTCAAT-AAGAAGATGACCGTTT
131 TGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTC-ATCAAGAAGATGACCGCTT
38193 TATTGCTTTGACCC
195 TATTGCTTTGACCC
38207 ACTTCTCTGTATCTCATCAGGAAGAT-AGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGA-GGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCAT
38271 TGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCT
65 TGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCT
* * *
38336 CTGTATCTCATCAAGAAGGCGGAGTTGGTCTACTTCTCTGTATCTCATCAAGAAGA
130 CTGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGA
38392 CGGAGTTGGT
Statistics
Matches: 894, Mismatches: 92, Indels: 40
0.87 0.09 0.04
Matches are distributed among these distances:
198 164 0.18
199 4 0.00
200 2 0.00
201 2 0.00
205 2 0.00
206 6 0.01
207 182 0.20
208 530 0.59
209 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (208 bp):
ACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
TGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTT
ATTGCTTTGACCC
Found at i:38001 original size:85 final size:86
Alignment explanation
Indices: 37856--38030 Score: 280
Period size: 85 Copynumber: 2.0 Consensus size: 86
37846 TCGCTTTATT
*
37856 GATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATAACCGCTTCATTGATTTAATCCACTTCTC
1 GATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATAACCGCTTCATTGATTTAACCCACTTCTC
37921 TGTATCTCATCAGGAAGATG-
66 TGTATCTCATCAGGAAGATGA
* * * * * *
37941 GATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGACCTCTTTATTGCTTTGACCCACTTCTT
1 GATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATAACCGCTTCATTGATTTAACCCACTTCTC
38006 TGTATCTCATCAGGAAGATGA
66 TGTATCTCATCAGGAAGATGA
38027 GATT
1 GATT
38031 CAAAGTCTCA
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 78 0.95
86 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (86 bp):
GATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATAACCGCTTCATTGATTTAACCCACTTCTC
TGTATCTCATCAGGAAGATGA
Found at i:38162 original size:37 final size:37
Alignment explanation
Indices: 38112--38182 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
38102 CCGCTTCATT
38112 GATTTAATCCACTTCTCTGTATCTC-ATCAAGAAGGCG
1 GATTTAATCCACTTCTCTGTATCTCAAT-AAGAAGGCG
*
38149 GATTTGATCCACTTCTCTGTATCTCAATAAGAAG
1 GATTTAATCCACTTCTCTGTATCTCAATAAGAAG
38183 ATGACCGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
37 30 0.94
38 2 0.06
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (37 bp):
GATTTAATCCACTTCTCTGTATCTCAATAAGAAGGCG
Found at i:38209 original size:85 final size:85
Alignment explanation
Indices: 38065--38230 Score: 242
Period size: 85 Copynumber: 2.0 Consensus size: 85
38055 CGCTTCATTT
* * * * *
38065 ATTTGGTCTACTTCTTTGTATCTCATTAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
1 ATTTGATCCACTTCTCTGTATCTCAATAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
38130 GTATCTCATCAAGAAGGCGG
66 GTATCTCATCAAGAAGGCGG
* * * *
38150 ATTTGATCCACTTCTCTGTATCTCAATAAGAAGATGACCGTTTTATTGCTTTGACCCACTTCTCT
1 ATTTGATCCACTTCTCTGTATCTCAATAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
*
38215 GTATCTCATCAGGAAG
66 GTATCTCATCAAGAAG
38231 ATAGGGTTTG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (85 bp):
ATTTGATCCACTTCTCTGTATCTCAATAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
GTATCTCATCAAGAAGGCGG
Found at i:38380 original size:37 final size:37
Alignment explanation
Indices: 38330--38428 Score: 180
Period size: 37 Copynumber: 2.7 Consensus size: 37
38320 GATTTAATCC
*
38330 ACTTCTCTGTATCTCATCAAGAAGGCGGAGTTGGTCT
1 ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGGTCT
38367 ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGGTCT
1 ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGGTCT
*
38404 ACTTCTCTGTATCTCATCAGGAAGA
1 ACTTCTCTGTATCTCATCAAGAAGA
38429 TGGTTGCTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (37 bp):
ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGGTCT
Found at i:38387 original size:245 final size:245
Alignment explanation
Indices: 38122--38636 Score: 773
Period size: 245 Copynumber: 2.1 Consensus size: 245
38112 GATTTAATCC
* *
38122 ACTTCTCTGTATCTCATCAAGAAGGCGGATTTGATCCACTTCTCTGTATCTCAAT-AAGAAGATG
1 ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGATCCACTTCTCTGTATCTC-ATCAAGAAGATG
*
38186 ACCGTTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAGT-CTCAT
65 ACCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAGTCCT-AT
*
38250 TCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCT
129 TCGTATTAAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCT
* *
38315 TCATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGGCGGAGTTGGTCT
194 TCATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGAGTTGATCT
* * * *
38367 ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGG
1 ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGATCCACTTCTCTGTATCTCATCAAGAAGATGA
** * * *
38432 TTGCTTTATTGCTTTGACCCATTTTTTTGTATCTCATCAGGAAGATAGGGTTTGAAGTCCTATTC
66 CCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAGTCCTATTC
* * * *
38497 GTATTAAGTTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGATGATGACTGCTTC
131 GTATTAAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTC
* * * * *
38562 ATTGATTTAATCCACTTTTTTGTATCTTATCAAGAATACGGATTTGATCT
196 ATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGAGTTGATCT
*
38612 ACTTCTTTGTATCTCATCAAGAAGA
1 ACTTCTCTGTATCTCATCAAGAAGA
38637 TGACTACTTT
Statistics
Matches: 243, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
244 2 0.01
245 239 0.98
246 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (245 bp):
ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGATCCACTTCTCTGTATCTCATCAAGAAGATGA
CCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAGTCCTATTC
GTATTAAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTC
ATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGAGTTGATCT
Found at i:38499 original size:453 final size:452
Alignment explanation
Indices: 37914--38763 Score: 1276
Period size: 453 Copynumber: 1.9 Consensus size: 452
37904 GATTTAATCC
* * * *
37914 ACTTCTCTGTATCTCATCAGGAAGATGGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGA
1 ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGA
37979 CCTCTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGGAAGATGAGATTCAAAGTCTCATTC
66 CCTCTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGGAAGATGAGATTCAAAGTCTCATTC
* * * *
38044 GTATTGAGCTTCGCTTCATTTATTTGGTCTACTTCTTTGTATCTCATTAAGAAGATGACCGCTTC
131 GTATTAAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTC
*
38109 ATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGGCGGATTTGATCCACTTCTCTGTATCTC
196 ATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGATCCACTTCTCTGTATCTC
** *
38174 AAT-AAGAAGATGACCGTTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGT
261 -ATCAAGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGT
* *
38238 TTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAG
325 TTGAAGTCTCATT-GTATTGAACTTCGCTTCATTGATTTAGTCTACTTCTCTGTATCTCATCAAG
38303 AAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGGCGGAGTTGGTCT
389 AAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGGCGGAGTTGGTCT
*
38367 ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGGTCTACTTCTCTGTATCTCATCAGGAAGATG-
1 ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGA
** * * * **
38431 GTTGCTTTATTGCTTTGACCCATTTTTTTGTATCTCATCAGGAAGAT-AGGGTTTGAAGTC-CTA
66 CCT-CTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGGAAGATGA-GATTCAAAGTCTC-A
* * * *
38494 TTCGTATTAAGTTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGATGATGACTGC
128 TTCGTATTAAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGC
* * * * * *
38559 TTCATTGATTTAATCCACTTTTTTGTATCTTATCAAGAATACGGATTTGATCTACTTCTTTGTAT
193 TTCATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGATCCACTTCTCTGTAT
* * *
38624 CTCATCAAGAAGATGACTACTTTATTACTTTGACCCACTTCTTTGTATCTCATCAGGAAGATGGG
258 CTCATCAAGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGG
* * * *
38689 GTTTGAAGTCTCATTGTATTGAACTTTGCTTTATTTATTTAGTCTACTTCTCTGTATCTCATCAG
323 GTTTGAAGTCTCATTGTATTGAACTTCGCTTCATTGATTTAGTCTACTTCTCTGTATCTCATCAA
38754 GAAGATGACC
388 GAAGATGACC
38764 TTTTGAAGTT
Statistics
Matches: 354, Mismatches: 39, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
452 59 0.17
453 295 0.83
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (452 bp):
ACTTCTCTGTATCTCATCAAGAAGACGGAGTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGA
CCTCTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGGAAGATGAGATTCAAAGTCTCATTC
GTATTAAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTC
ATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGATCCACTTCTCTGTATCTC
ATCAAGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTT
TGAAGTCTCATTGTATTGAACTTCGCTTCATTGATTTAGTCTACTTCTCTGTATCTCATCAAGAA
GATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGGCGGAGTTGGTCT
Found at i:38560 original size:123 final size:122
Alignment explanation
Indices: 38149--38593 Score: 409
Period size: 123 Copynumber: 3.6 Consensus size: 122
38139 CAAGAAGGCG
* * * * * *
38149 GATTTGATCCACTTCTCTGTATCTCAAT-AAGAAGATGACCGTTTTATTGCTTTGACCCACTTCT
1 GATTTGGTCTACTTCTCTGTATCTC-ATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCT
* *
38213 CTGTATCTCATCAGGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
65 CTGTATCTCATCAGGAAGATAGGGTTTGAAGTCT-ATTCGTATTAAGTTTCGCTTCATT
*
38272 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
* ** * *** *** **
38337 TGTATCTCATCAAGAAG-GCGGAG-TTG--GTCTACTTCTCTGTATCTCA-TCAAG-AAGACG
66 TGTATCTCATCAGGAAGATAGG-GTTTGAAGTCTA--T-TC-GTAT-TAAGTTTCGCTTCATT
* * *** * * * * * *
38394 GAGTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGGTTGCTTTATTGCTTTGACCCATTTTTT
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
38459 TGTATCTCATCAGGAAGATAGGGTTTGAAGTCCTATTCGTATTAAGTTTCGCTTCATT
66 TGTATCTCATCAGGAAGATAGGGTTTGAAGT-CTATTCGTATTAAGTTTCGCTTCATT
* * * * * *
38517 GATTTGGTCTACTTCTCTGTATCTCATCAGGATGATGACTGCTTCATTGATTTAATCCACTTTTT
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
*
38582 TGTATCTTATCA
66 TGTATCTCATCA
38594 AGAATACGGA
Statistics
Matches: 254, Mismatches: 54, Indels: 28
0.76 0.16 0.08
Matches are distributed among these distances:
119 1 0.00
120 4 0.02
121 3 0.01
122 86 0.34
123 152 0.60
124 3 0.01
125 2 0.01
126 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (122 bp):
GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
TGTATCTCATCAGGAAGATAGGGTTTGAAGTCTATTCGTATTAAGTTTCGCTTCATT
Found at i:38662 original size:85 final size:85
Alignment explanation
Indices: 38517--38678 Score: 218
Period size: 85 Copynumber: 1.9 Consensus size: 85
38507 TCGCTTCATT
* * * * * *
38517 GATTTGGTCTACTTCTCTGTATCTCATCAGGATGATGACTGCTTCATTGATTTAATCCACTTTTT
1 GATTTGATCTACTTCTCTGTATCTCATCAAGAAGATGACTACTTCATTGATTTAACCCACTTCTT
*
38582 TGTATCTTATCAAGAATACG
66 TGTATCTCATCAAGAATACG
* * *
38602 GATTTGATCTACTTCTTTGTATCTCATCAAGAAGATGACTACTTTATT-ACTTTGACCCACTTCT
1 GATTTGATCTACTTCTCTGTATCTCATCAAGAAGATGACTACTTCATTGA-TTTAACCCACTTCT
38666 TTGTATCTCATCA
65 TTGTATCTCATCA
38679 GGAAGATGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
84 1 0.02
85 65 0.98
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (85 bp):
GATTTGATCTACTTCTCTGTATCTCATCAAGAAGATGACTACTTCATTGATTTAACCCACTTCTT
TGTATCTCATCAAGAATACG
Found at i:41331 original size:30 final size:30
Alignment explanation
Indices: 41297--41650 Score: 269
Period size: 30 Copynumber: 11.8 Consensus size: 30
41287 AATTTGGGGA
*
41297 TAAAATATAATTTTGGAAAAATTCAAGGGT
1 TAAAATATAATTTTGGAAAAATTTAAGGGT
*
41327 TAAAATATAATTTTAGG-AAAGTTT-AGGGT
1 TAAAATATAATTTT-GGAAAAATTTAAGGGT
* * * ** *
41356 TAAAATGTGATTTTAGAAAGGTTT-GGGGT
1 TAAAATATAATTTTGGAAAAATTTAAGGGT
* * *
41385 CAAAAATATAATTTTGG-GAAGTTTAAGGGT
1 -TAAAATATAATTTTGGAAAAATTTAAGGGT
* *
41415 TAAAATGTAAATTTTGG--AAATTTGAGGGT
1 TAAAATAT-AATTTTGGAAAAATTTAAGGGT
** *
41444 TAAAATGTGATTTTTTTGGAAAAGTTTAAGGGT
1 TAAAA--T-ATAATTTTGGAAAAATTTAAGGGT
* *
41477 CAAAATGTAATTTTAGG-AAAATTTAAGGGT
1 TAAAATATAATTTT-GGAAAAATTTAAGGGT
* * * *
41507 TAAAATGTAATTTTAG-AAAATTTTAGTTGT
1 TAAAATATAATTTTGGAAAAATTTAAG-GGT
*
41537 TAAAATATAATTTTGGAAAAATTT-AGGGG
1 TAAAATATAATTTTGGAAAAATTTAAGGGT
* * *
41566 TCAAATGTAATTTTGGAAAAATTT-AGATGT
1 TAAAATATAATTTTGGAAAAATTTAAG-GGT
* * *
41596 TAAAATGTAGTTTTGGAAAAGTTTAAGGGT
1 TAAAATATAATTTTGGAAAAATTTAAGGGT
* * *
41626 TAAAATATGATTTTTGAAAAGTTTA
1 TAAAATATAATTTTGGAAAAATTTA
41651 GGGACCTTTT
Statistics
Matches: 261, Mismatches: 48, Indels: 30
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.00
29 88 0.34
30 136 0.52
31 21 0.08
32 1 0.00
33 14 0.05
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.38
Consensus pattern (30 bp):
TAAAATATAATTTTGGAAAAATTTAAGGGT
Found at i:41369 original size:59 final size:58
Alignment explanation
Indices: 41297--41653 Score: 301
Period size: 59 Copynumber: 6.0 Consensus size: 58
41287 AATTTGGGGA
* *
41297 TAAAATATAATTTTGGAAAAATTCAAGGGTTAAAATATAATTTTAGGAAAGTTTAGGGT
1 TAAAATGTAATTTTGGAAAAATTTAAGGGTTAAAATATAATTTT-GGAAAGTTTAGGGT
* * ** * * *
41356 TAAAATGTGATTTTAGAAAGGTTT-GGGGTCAAAAATATAATTTTGGGAAGTTTAAGGGT
1 TAAAATGTAATTTTGGAAAAATTTAAGGGT-TAAAATATAATTTTGGAAAGTTT-AGGGT
* **
41415 TAAAATGTAAATTTTGG--AAATTTGAGGGTTAAAATGTGATTTTTTTGGAAAAGTTTAAGGGT
1 TAAAATGT-AATTTTGGAAAAATTTAAGGGTTAAAA--T-ATAATTTTGG-AAAGTTT-AGGGT
* * * * *
41477 CAAAATGTAATTTTAGG-AAAATTTAAGGGTTAAAATGTAATTTTAGAAAATTTTAGTTGT
1 TAAAATGTAATTTT-GGAAAAATTTAAGGGTTAAAATATAATTTT-GGAAAGTTTAG-GGT
* * * * * *
41537 TAAAATATAATTTTGGAAAAATTT-AGGGGTCAAATGTAATTTTGGAAAAATTTAGATGT
1 TAAAATGTAATTTTGGAAAAATTTAAGGGTTAAAATATAATTTTGG-AAAGTTTAG-GGT
* * * *
41596 TAAAATGTAGTTTTGGAAAAGTTTAAGGGTTAAAATATGATTTTTGAAAAGTTTAGGG
1 TAAAATGTAATTTTGGAAAAATTTAAGGGTTAAAATAT-AATTTTGGAAAGTTTAGGG
41654 ACCTTTTAAG
Statistics
Matches: 239, Mismatches: 43, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
58 21 0.09
59 102 0.43
60 57 0.24
61 22 0.09
62 21 0.09
63 16 0.07
ACGTcount: A:0.39, C:0.01, G:0.22, T:0.38
Consensus pattern (58 bp):
TAAAATGTAATTTTGGAAAAATTTAAGGGTTAAAATATAATTTTGGAAAGTTTAGGGT
Found at i:42630 original size:3 final size:3
Alignment explanation
Indices: 42617--42646 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
42607 AACTTCCTTT
42617 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
42647 TAAAAGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:43725 original size:71 final size:73
Alignment explanation
Indices: 43628--43844 Score: 287
Period size: 75 Copynumber: 3.0 Consensus size: 73
43618 AAAGACATAT
* * *
43628 TTTAAA-GAATAGATTTTAATT-GAAAAAA-ATATTGAGGGACTTAAAAGAAAAAATAATTAAAG
1 TTTAAATGAATAGATTTTAATTAAAAAAAAGACATTGAGGGACTTAAAAGAAGAAATAATTAAAG
43690 GATAAATA
66 GATAAATA
* * * *
43698 TTTAAATGAATAGATATTAATTAAAAAAAAAAGACATTGATGGCCTTGAAAGAAGAAATAATTAA
1 TTTAAATGAATAGATTTTAATT--AAAAAAAAGACATTGAGGGACTTAAAAGAAGAAATAATTAA
*
43763 ATGATAAATA
64 AGGATAAATA
* *
43773 TTTAAATGAATAAATTTTAATTAAAAAAAAGACATTGATGGGACTTAGAAAGAAGAAACAATTAA
1 TTTAAATGAATAGATTTTAATTAAAAAAAAGACATTGA-GGGACTTA-AAAGAAGAAATAATTAA
43838 AGGATAA
64 AGGATAA
43845 TTTTTTTGTG
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
70 6 0.05
71 14 0.11
73 16 0.13
74 11 0.09
75 78 0.62
ACGTcount: A:0.55, C:0.03, G:0.14, T:0.28
Consensus pattern (73 bp):
TTTAAATGAATAGATTTTAATTAAAAAAAAGACATTGAGGGACTTAAAAGAAGAAATAATTAAAG
GATAAATA
Found at i:43777 original size:15 final size:16
Alignment explanation
Indices: 43753--43792 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
43743 TTGAAAGAAG
*
43753 AAATAATTAAATG-AT
1 AAATATTTAAATGAAT
43768 AAATATTTAAATGAAT
1 AAATATTTAAATGAAT
43784 AAAT-TTTAA
1 AAATATTTAA
43793 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (16 bp):
AAATATTTAAATGAAT
Found at i:48521 original size:17 final size:18
Alignment explanation
Indices: 48499--48532 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48489 TAAATGAGTT
48499 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
48516 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
48533 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:48805 original size:17 final size:18
Alignment explanation
Indices: 48775--48808 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48765 GAGATGAATG
*
48775 ATAGTTTATATTGAATTA
1 ATAGTATATATTGAATTA
48793 ATAGTATAT-TTGAATT
1 ATAGTATATATTGAATT
48809 GAATTTGAAT
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:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (18 bp):
ATAGTATATATTGAATTA
Done.