Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_pilon, 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: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2087410 original size:14 final size:14
Alignment explanation
Indices: 2087393--2087447 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
2087383 GTTCGGTTAT
2087393 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
2087407 GTTCGGTTA---T-
1 GTTCGTTTATGTTC
*
2087417 GTTCGTTTATGTTT
1 GTTCGTTTATGTTC
*
2087431 GTTCGATTATGTTC
1 GTTCGTTTATGTTC
2087445 GTT
1 GTT
2087448 TATGTTCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 23 0.70
ACGTcount: A:0.09, C:0.11, G:0.24, T:0.56
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:2087448 original size:24 final size:24
Alignment explanation
Indices: 2087382--2087454 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
2087372 CGTTCGTGAA
2087382 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
2087406 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
* *
2087430 TGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
2087454 C
1 C
2087455 ATTCATTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.10, C:0.12, G:0.23, T:0.55
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:2087464 original size:24 final size:23
Alignment explanation
Indices: 2087389--2087467 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 23
2087379 GAACGTTCGG
*
2087389 TTATGTTCGTTTATGTTCGTTCGG
1 TTATGTTCGTTTATGTTCGTTC-A
*
2087413 TTATGTTCGTTTATGTTTGTTCGA
1 TTATGTTCGTTTATGTTCGTTC-A
*
2087437 TTATGTTCGTTTATGTTCATTCA
1 TTATGTTCGTTTATGTTCGTTCA
2087460 TTTATGTT
1 -TTATGTT
2087468 TAACCCAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.02
24 49 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.58
Consensus pattern (23 bp):
TTATGTTCGTTTATGTTCGTTCA
Found at i:2088565 original size:16 final size:16
Alignment explanation
Indices: 2088544--2088596 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
2088534 GTCTCCAACG
2088544 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
2088560 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
2088576 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
2088592 TTTAT
1 TTTAT
2088597 TTATTAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:2092925 original size:15 final size:14
Alignment explanation
Indices: 2092882--2092926 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
2092872 TATATATAAA
* *
2092882 TTTAAAATTTAGAG
1 TTTAAAATTAAGAT
2092896 TTTAAAATATAAGAT
1 TTTAAAAT-TAAGAT
2092911 TTTAAAATTCAAGAT
1 TTTAAAATT-AAGAT
2092926 T
1 T
2092927 AAAATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (14 bp):
TTTAAAATTAAGAT
Found at i:2092929 original size:28 final size:27
Alignment explanation
Indices: 2092866--2092932 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
2092856 CTAAAAGAAT
*
2092866 GATTAATATATATAAATTTAAAATTTAGA
1 GATTAA-A-ATATAAATTTAAAATTCAGA
*
2092895 GTTTAAAATATAAGATTTTAAAATTCA-A
1 GATTAAAATATAA-A-TTTAAAATTCAGA
2092923 GATTAAAATA
1 GATTAAAATA
2092933 AATTATACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 6 0.18
28 12 0.36
29 15 0.45
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.39
Consensus pattern (27 bp):
GATTAAAATATAAATTTAAAATTCAGA
Found at i:2093571 original size:17 final size:18
Alignment explanation
Indices: 2093542--2093575 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2093532 CCGGTTTCGG
2093542 TTTTAAAATAACCGGTTT
1 TTTTAAAATAACCGGTTT
2093560 TTTTAAAA-AACCGGTT
1 TTTTAAAATAACCGGTT
2093576 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (18 bp):
TTTTAAAATAACCGGTTT
Found at i:2093815 original size:21 final size:21
Alignment explanation
Indices: 2093763--2093803 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2093753 ACACTTAGGG
2093763 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
2093784 AACCGATTCCCTATGAGAGG
1 AACCGATTCCCTATGAGAGG
2093804 GTACTGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:2094032 original size:13 final size:13
Alignment explanation
Indices: 2094011--2094065 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2094001 AAGTTCGATA
*
2094011 AATTCAAATACTT
1 AATTGAAATACTT
2094024 AATTGAAATACTT
1 AATTGAAATACTT
* *
2094037 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
2094051 AATTGAAATACTT
1 AATTGAAATACTT
2094064 AA
1 AA
2094066 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:2096381 original size:12 final size:13
Alignment explanation
Indices: 2096363--2096401 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
2096353 TTCCGGATAA
2096363 AAACCGGTTTTTT
1 AAACCGGTTTTTT
2096376 -AACCGGTTTTTTT
1 AAACCGG-TTTTTT
2096389 CAAACCGGTTTTT
1 -AAACCGGTTTTT
2096402 ATCCGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.26
13 6 0.26
14 5 0.22
15 6 0.26
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (13 bp):
AAACCGGTTTTTT
Found at i:2096394 original size:15 final size:14
Alignment explanation
Indices: 2096363--2096401 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
2096353 TTCCGGATAA
2096363 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
2096376 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
2096389 CAAACCGGTTTTT
1 -AAACCGGTTTTT
2096402 ATCCGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.26
13 6 0.26
15 11 0.48
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:2105015 original size:22 final size:23
Alignment explanation
Indices: 2104989--2105051 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
2104979 TTAGTGTAGA
***
2104989 GGGAATCGATACCCCCTTGA-AG
1 GGGAATCGATACCCCCCCCACAG
*
2105011 GGGAATCGATTCCCCCCCCCACAG
1 GGGAATCGA-TACCCCCCCCACAG
2105035 GGGAATCGATACCCCCC
1 GGGAATCGATACCCCCC
2105052 TAAGGGTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 9 0.26
23 14 0.41
24 11 0.32
ACGTcount: A:0.24, C:0.38, G:0.24, T:0.14
Consensus pattern (23 bp):
GGGAATCGATACCCCCCCCACAG
Found at i:2106268 original size:18 final size:18
Alignment explanation
Indices: 2106247--2106286 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2106237 GAACATCACA
*
2106247 AGGAACAAGCTCCACCAG
1 AGGAACAAGCACCACCAG
*
2106265 AGGAACAAGCACGACCAG
1 AGGAACAAGCACCACCAG
2106283 AGGA
1 AGGA
2106287 TCAAATGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.28, T:0.03
Consensus pattern (18 bp):
AGGAACAAGCACCACCAG
Found at i:2111649 original size:2 final size:2
Alignment explanation
Indices: 2111642--2111667 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2111632 ATAGTTTTTC
2111642 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
2111668 CTTATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2112030 original size:2 final size:2
Alignment explanation
Indices: 2112023--2112056 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2112013 GCCAAAGGAT
2112023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2112057 ATGAGTCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2112186 original size:19 final size:20
Alignment explanation
Indices: 2112134--2112186 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
2112124 GAATATAATC
2112134 AAATTATATT-TTTTATTAA
1 AAATTATATTGTTTTATTAA
* *
2112153 AAATTATAATTGTTTTTTTTA
1 AAATTAT-ATTGTTTTATTAA
2112174 AAATTAT-TTGTTT
1 AAATTATATTGTTT
2112187 AGGATTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
AAATTATATTGTTTTATTAA
Found at i:2116436 original size:2 final size:2
Alignment explanation
Indices: 2116429--2116454 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2116419 TTTTCAAATA
2116429 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
2116455 CTAAATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2120244 original size:52 final size:52
Alignment explanation
Indices: 2120188--2120291 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
2120178 TATTGAGCTA
2120188 AATAATTTACTCACTTGAATTATTGTGCTGATTTTGCCTCATTTCTGGCTTT
1 AATAATTTACTCACTTGAATTATTGTGCTGATTTTGCCTCATTTCTGGCTTT
2120240 AATAATTTACTCACTTGAATTATTGTGCTGATTTTGCCTCATTTCTGGCTTT
1 AATAATTTACTCACTTGAATTATTGTGCTGATTTTGCCTCATTTCTGGCTTT
2120292 TTTTTTCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.48
Consensus pattern (52 bp):
AATAATTTACTCACTTGAATTATTGTGCTGATTTTGCCTCATTTCTGGCTTT
Found at i:2120999 original size:13 final size:13
Alignment explanation
Indices: 2120981--2121005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2120971 CTTACCAATA
2120981 AGAGAAAACTAGG
1 AGAGAAAACTAGG
2120994 AGAGAAAACTAG
1 AGAGAAAACTAG
2121006 CTACCATTTT
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:0.28, T:0.08
Consensus pattern (13 bp):
AGAGAAAACTAGG
Found at i:2121106 original size:2 final size:2
Alignment explanation
Indices: 2121099--2121129 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2121089 ATCTCTAGTT
2121099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2121130 TTTGGATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2127968 original size:79 final size:79
Alignment explanation
Indices: 2127837--2127983 Score: 240
Period size: 79 Copynumber: 1.9 Consensus size: 79
2127827 CTAATTTAAG
* *
2127837 ATAATACTTTCTTCTTGTATTCTTGTAACCACCACGTATGGGGTTGGGTGAATTCATATAATCAA
1 ATAATACTTTCTTCTTGTATTCTTATAACCACCACGTATGGGGTTGAGTGAATTCATATAATCAA
2127902 TTTGGAAATTCAAA
66 TTTGGAAATTCAAA
* * * *
2127916 ATAATACTTTCTTCTTGTATTCTTATAGCCACCACGTCTTGGGTTGAGTGAATTCATATAATCCA
1 ATAATACTTTCTTCTTGTATTCTTATAACCACCACGTATGGGGTTGAGTGAATTCATATAATCAA
2127981 TTT
66 TTT
2127984 AGGAGTATAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 62 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (79 bp):
ATAATACTTTCTTCTTGTATTCTTATAACCACCACGTATGGGGTTGAGTGAATTCATATAATCAA
TTTGGAAATTCAAA
Found at i:2129187 original size:2 final size:2
Alignment explanation
Indices: 2129180--2129212 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2129170 ATGTAACAAT
*
2129180 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2129213 CATCATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2129556 original size:30 final size:30
Alignment explanation
Indices: 2129520--2129592 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
2129510 CCCGAAGGAC
2129520 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
2129550 CTATCCAGATGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
2129580 CTATCCATAGGTC
1 CTATCCAGAGGTC
2129593 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:2129632 original size:31 final size:31
Alignment explanation
Indices: 2129578--2129670 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
2129568 GATCCTCGGT
* *
2129578 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
2129609 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * * *
2129640 TACTGTACATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
2129671 GTTCTTTGAC
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 1 0.02
31 48 0.98
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:2130752 original size:64 final size:64
Alignment explanation
Indices: 2130600--2130756 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
2130590 CAATGAAAGT
* * * ** *
2130600 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATCACTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
* * * *
2130664 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATAAAAG
2130727 AG
63 AG
2130729 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACCTGTGCATCGAT
2130757 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 1 0.01
64 60 0.79
65 15 0.20
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
Found at i:2133511 original size:2 final size:2
Alignment explanation
Indices: 2133504--2133538 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2133494 CGGTTGGAAT
2133504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2133539 GAAAATATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2133577 original size:17 final size:18
Alignment explanation
Indices: 2133537--2133577 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2133527 ATATATATAT
* *
2133537 ATGAAAATATGTAAGGAA
1 ATGAAAAGATGTAAGAAA
2133555 AT-AAAAGATG-AAGAAA
1 ATGAAAAGATGTAAGAAA
2133571 ATGAAAA
1 ATGAAAA
2133578 TACATAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.35
17 11 0.55
18 2 0.10
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (18 bp):
ATGAAAAGATGTAAGAAA
Found at i:2135710 original size:29 final size:29
Alignment explanation
Indices: 2135668--2135726 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2135658 ATTTTCACCT
2135668 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2135697 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2135726 A
1 A
2135727 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2140395 original size:29 final size:29
Alignment explanation
Indices: 2140353--2140411 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2140343 ATTTTCACCT
2140353 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2140382 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2140411 A
1 A
2140412 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2140920 original size:74 final size:68
Alignment explanation
Indices: 2140793--2140938 Score: 195
Period size: 68 Copynumber: 2.1 Consensus size: 68
2140783 AATTAATATG
*
2140793 TTTCCTTGTAGTTGTAGAACTAGGTTATGGTCAGCTAATTAATCATAATCTCATTATCGATAAA-
1 TTTCCCTGTAGTTGTAGAACTAGGTTATGGTCAGCTAATTAATCATAATCTCATTATCGATAAAT
2140857 CATA
66 CA-A
* *
2140861 TTTCCCTGTAGTTGTAGGACTAGGTTATGGTTAGCTAATTAATCATAATCATAATCTCATTATCG
1 TTTCCCTGTAGTTGTAGAACTAGGTTATGGTCAGC----TAAT--TAATCATAATCTCATTATCG
2140926 ATAAATCAA
60 ATAAATCAA
2140935 TTTC
1 TTTC
2140939 TTATAACATG
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
68 32 0.47
72 4 0.06
74 30 0.44
75 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (68 bp):
TTTCCCTGTAGTTGTAGAACTAGGTTATGGTCAGCTAATTAATCATAATCTCATTATCGATAAAT
CAA
Found at i:2156795 original size:52 final size:53
Alignment explanation
Indices: 2156719--2156819 Score: 168
Period size: 52 Copynumber: 1.9 Consensus size: 53
2156709 ATGAATCAAA
*
2156719 TTGAATAACAATATTTTTAATGAATAAGAGTCAAACACTATTCAACTCTCGAT
1 TTGAATAACAATATTTTTAATGAATAAGAGTAAAACACTATTCAACTCTCGAT
* *
2156772 TTGAATAACAAT-TTTTTAATGAATACGAGTAAAATACTATTCAACTCT
1 TTGAATAACAATATTTTTAATGAATAAGAGTAAAACACTATTCAACTCT
2156820 TGATCGAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 33 0.73
53 12 0.27
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.36
Consensus pattern (53 bp):
TTGAATAACAATATTTTTAATGAATAAGAGTAAAACACTATTCAACTCTCGAT
Found at i:2157379 original size:11 final size:11
Alignment explanation
Indices: 2157334--2157380 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
2157324 AAACACTATA
2157334 AAATAATTATT
1 AAATAATTATT
2157345 AAAT--TTATT
1 AAATAATTATT
* * *
2157354 GAATAACTATA
1 AAATAATTATT
2157365 AAATAATTATT
1 AAATAATTATT
2157376 AAATA
1 AAATA
2157381 TAATCTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
9 8 0.29
11 20 0.71
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
AAATAATTATT
Found at i:2162971 original size:15 final size:16
Alignment explanation
Indices: 2162943--2162974 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2162933 GTTTTCTTTA
2162943 TAATTTTCTTAAATAT
1 TAATTTTCTTAAATAT
2162959 TAATTTT-TTAAATAT
1 TAATTTTCTTAAATAT
2162974 T
1 T
2162975 TAGATGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTTCTTAAATAT
Found at i:2163262 original size:2 final size:2
Alignment explanation
Indices: 2163255--2163308 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2163245 ATCTTTAACA
2163255 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2163297 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2163309 CCTTCAACAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2170057 original size:31 final size:31
Alignment explanation
Indices: 2170019--2170203 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
2170009 GGGTCGAGGG
2170019 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2170050 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2170081 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2170112 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
2170143 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
2170174 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
2170204 GTCCTTCGGG
Statistics
Matches: 150, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 149 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:2174247 original size:31 final size:31
Alignment explanation
Indices: 2174209--2174393 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
2174199 GGGTCGAGGG
2174209 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2174240 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2174271 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2174302 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
2174333 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
2174364 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
2174394 GTCCTTCGGG
Statistics
Matches: 150, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 149 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:2194055 original size:31 final size:31
Alignment explanation
Indices: 2194017--2194096 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
2194007 AACATTTGTG
* * *
2194017 AGGGACTAAACTCGAATAGATAAAAAATGTT
1 AGGGACTAAAATCGAACAGATAAAAAACGTT
* *
2194048 AGGGACTAAAATCGAACAGATCAATAACGTT
1 AGGGACTAAAATCGAACAGATAAAAAACGTT
2194079 AGGGACTAAAATCGAACA
1 AGGGACTAAAATCGAACA
2194097 AATCGATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (31 bp):
AGGGACTAAAATCGAACAGATAAAAAACGTT
Found at i:2194119 original size:33 final size:32
Alignment explanation
Indices: 2194045--2194144 Score: 141
Period size: 31 Copynumber: 3.2 Consensus size: 32
2194035 GATAAAAAAT
* * *
2194045 GTTAGGGACTAAAATCGAACAGATCAATAA-C
1 GTTAGGGACTAAAATCGAACAAATCGATAATG
2194076 GTTAGGGACTAAAATCGAACAAATCGATAATG
1 GTTAGGGACTAAAATCGAACAAATCGATAATG
*
2194108 GCTTAGGGACTAAAATCGAATAAATCGATAAT-
1 G-TTAGGGACTAAAATCGAACAAATCGATAATG
2194140 GTTAG
1 GTTAG
2194145 AGATCACTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
31 32 0.51
32 2 0.03
33 29 0.46
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (32 bp):
GTTAGGGACTAAAATCGAACAAATCGATAATG
Found at i:2197180 original size:231 final size:231
Alignment explanation
Indices: 2196749--2197196 Score: 498
Period size: 231 Copynumber: 1.9 Consensus size: 231
2196739 AACTTCGTTT
* * *
2196749 GAAAGAGCAAGCTTTTCAGATGGAAAAAGAATCCAAAGAGAAACTTAGAGAAGTTTGTGATGCTT
1 GAAAGAGCAAGCTTTGCAGATCGAAAAAGAATCCAAAGAGAAACTTAGAGAAGTTTGCGATGCTT
* * * *
2196814 TAGAAACAACAGAATCTGAACTGGCAGAAGAACAGGAGAAAGTAGAATCTTTGTCAAGGAGGGGT
66 TAGAAACAACAAAATCTGAACTGGCAGAAGAACA-GAGAAAGTAGAAGCTTTGTCAAGAAAGGGT
* ** * * * * * *
2196879 GAGTCCTTGGATCTTATAGAAGGGCAGTGGCTCCTGCTGCAGAAAGAGCTTGAGAGGTATAAGAA
130 GAGTCCTTAGATCCAATAGAAGGACAGTGGCTCCAGCTACAGAAAGAGCTTCAGAGGCAAAAGAA
2196944 AATGCTCGAGGAAGCATCTAGGTTTCGAGCACAATTC
195 AATGCTCGAGGAAGCATCTAGGTTTCGAGCACAATTC
* *
2196981 GAAA-AGCAAGCTTTGCAGATCGACAACGAATCCAAAGAGAAA-TATAGAGAAGTTTGCGATGCT
1 GAAAGAGCAAGCTTTGCAGATCGAAAAAGAATCCAAAGAGAAACT-TAGAGAAGTTTGCGATGCT
* * *
2197044 TTAGAAACAACAAAATCTGAACTGG-ATGAAGAAC-GAGAGAG-A-ACAGCTTTGTTGATGAAAA
65 TTAGAAACAACAAAATCTGAACTGGCA-GAAGAACAGAGAAAGTAGA-AGCTTTG-TCAAG-AAA
* * * * * *
2197105 GGGTCGAGTCTTTAGATCCAATTGAAGGACGGTGGCTCCAGAC-ACAGGAGGAGCTTCAGCGGCA
126 GGGT-GAGTCCTTAGATCCAATAGAAGGACAGTGGCTCCAG-CTACAGAAAGAGCTTCAGAGGCA
* *
2197169 CAAAG-AAATGCTCGAGGATGCATGTAGG
189 -AAAGAAAATGCTCGAGGAAGCATCTAGG
2197197 CGTCAATGTC
Statistics
Matches: 179, Mismatches: 29, Indels: 17
0.80 0.13 0.08
Matches are distributed among these distances:
227 1 0.01
228 7 0.04
229 9 0.05
230 7 0.04
231 147 0.82
232 8 0.04
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (231 bp):
GAAAGAGCAAGCTTTGCAGATCGAAAAAGAATCCAAAGAGAAACTTAGAGAAGTTTGCGATGCTT
TAGAAACAACAAAATCTGAACTGGCAGAAGAACAGAGAAAGTAGAAGCTTTGTCAAGAAAGGGTG
AGTCCTTAGATCCAATAGAAGGACAGTGGCTCCAGCTACAGAAAGAGCTTCAGAGGCAAAAGAAA
ATGCTCGAGGAAGCATCTAGGTTTCGAGCACAATTC
Found at i:2200809 original size:29 final size:29
Alignment explanation
Indices: 2200765--2200939 Score: 133
Period size: 29 Copynumber: 6.0 Consensus size: 29
2200755 CCCGACCCAA
2200765 TGACATTTTAGG-AATTATTTTGAAAAAGG
1 TGACATTTT-GGAAATTATTTTGAAAAAGG
*
2200794 TGACATTTTGGAAATTATTTTGAAAAATG
1 TGACATTTTGGAAATTATTTTGAAAAAGG
**
2200823 TGACATTTTGGAAATT-TTTT-AAAAACAT
1 TGACATTTTGGAAATTATTTTGAAAAA-GG
* * * * * * *
2200851 TGAAATTCTAGTAATTATTTTTAAAATGA
1 TGACATTTTGGAAATTATTTTGAAAAAGG
* * *
2200880 TGACATTTTGGGAATTA-TTTGTAAAACGA
1 TGACATTTTGGAAATTATTTTG-AAAAAGG
* * * *
2200909 CGATATTTTGGTAATTATTTTTAATAAAGG
1 TGACATTTTGGAAATTATTTTGAA-AAAGG
2200939 T
1 T
2200940 AATATTTCTA
Statistics
Matches: 116, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
27 5 0.04
28 21 0.18
29 80 0.69
30 10 0.09
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (29 bp):
TGACATTTTGGAAATTATTTTGAAAAAGG
Found at i:2200832 original size:17 final size:17
Alignment explanation
Indices: 2200781--2200832 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
2200771 TTTAGGAATT
*
2200781 ATTTTGAAAAAGGTGAC
1 ATTTTGAAAAATGTGAC
*
2200798 ATTTTG-GAAAT-T---
1 ATTTTGAAAAATGTGAC
2200810 ATTTTGAAAAATGTGAC
1 ATTTTGAAAAATGTGAC
2200827 ATTTTG
1 ATTTTG
2200833 GAAATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
12 6 0.22
13 4 0.15
14 1 0.04
15 1 0.04
16 3 0.11
17 12 0.44
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (17 bp):
ATTTTGAAAAATGTGAC
Found at i:2200928 original size:58 final size:58
Alignment explanation
Indices: 2200764--2200932 Score: 177
Period size: 58 Copynumber: 2.9 Consensus size: 58
2200754 ACCCGACCCA
* * * * *
2200764 ATGACATTTTAGGAATTATTTTGAAAAA-GGTGACATTTTGGAAATTATTTTGAAAAATG
1 ATGACATTTTGGGAATTATTTT-AAAAACGATGAAATTTTGGTAATTATTTT-TAAAATG
* * *
2200823 -TGACATTTTGGAAATT-TTTTAAAAAC-ATTGAAATTCTAGTAATTATTTTTAAAATG
1 ATGACATTTTGGGAATTATTTTAAAAACGA-TGAAATTTTGGTAATTATTTTTAAAATG
* *
2200879 ATGACATTTTGGGAATTATTTGT-AAAACGACGATATTTTGGTAATTATTTTTAA
1 ATGACATTTTGGGAATTATTT-TAAAAACGATGAAATTTTGGTAATTATTTTTAA
2200933 TAAAGGTAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
56 11 0.12
57 36 0.40
58 42 0.46
59 2 0.02
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (58 bp):
ATGACATTTTGGGAATTATTTTAAAAACGATGAAATTTTGGTAATTATTTTTAAAATG
Found at i:2208356 original size:18 final size:18
Alignment explanation
Indices: 2208300--2208350 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
2208290 TTGACCGGTC
* *
2208300 TGACCTGACCCGACCTGT
1 TGACCCGACCCGACCCGT
*
2208318 TGA-CCGACCCAACCCGT
1 TGACCCGACCCGACCCGT
2208335 TGACCCGACCCGACCC
1 TGACCCGACCCGACCC
2208351 AGTGACATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.14
Consensus pattern (18 bp):
TGACCCGACCCGACCCGT
Found at i:2208482 original size:58 final size:58
Alignment explanation
Indices: 2208357--2208493 Score: 177
Period size: 58 Copynumber: 2.3 Consensus size: 58
2208347 ACCCAGTGAC
* * *
2208357 ATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTTTTTAAAAAAACAATAAT
1 ATTTTGGTAATTATTTT-TAAAATGTGACATTTTGGGAATTATTTAAAAAAACAATAAT
* ** * *
2208416 ATTCTGGTAATTATTTTTAAAATGATGACATTTTGGGAATTATTT-GTAAAACGATGAT
1 ATTTTGGTAATTATTTTTAAAATG-TGACATTTTGGGAATTATTTAAAAAAACAATAAT
2208474 ATTTTGGTAATTATTTTTAA
1 ATTTTGGTAATTATTTTTAA
2208494 TAAAGGGGAT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 34 0.50
59 34 0.50
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (58 bp):
ATTTTGGTAATTATTTTTAAAATGTGACATTTTGGGAATTATTTAAAAAAACAATAAT
Found at i:2208507 original size:30 final size:29
Alignment explanation
Indices: 2208357--2208515 Score: 124
Period size: 29 Copynumber: 5.4 Consensus size: 29
2208347 ACCCAGTGAC
* * *
2208357 ATTTTGGGAATTATTTTGAAAAATG-TGAC
1 ATTTTGGTAATTATTTTTAAAAA-GATGAT
* * * *
2208386 ATTTTGGGAATT-TTTTAAAAAAACAATAAT
1 ATTTTGGTAATTATTTT-TAAAAA-GATGAT
* * *
2208416 ATTCTGGTAATTATTTTTAAAATGATGAC
1 ATTTTGGTAATTATTTTTAAAAAGATGAT
* * *
2208445 ATTTTGGGAATTATTTGTAAAACGATGAT
1 ATTTTGGTAATTATTTTTAAAAAGATGAT
**
2208474 ATTTTGGTAATTATTTTTAATAAAGGGGAT
1 ATTTTGGTAATTATTTTTAA-AAAGATGAT
*
2208504 ATTTTTGTAATT
1 ATTTTGGTAATT
2208516 TTTGAATGTG
Statistics
Matches: 103, Mismatches: 23, Indels: 7
0.77 0.17 0.05
Matches are distributed among these distances:
28 4 0.04
29 62 0.60
30 33 0.32
31 4 0.04
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (29 bp):
ATTTTGGTAATTATTTTTAAAAAGATGAT
Found at i:2208508 original size:59 final size:59
Alignment explanation
Indices: 2208357--2208508 Score: 171
Period size: 59 Copynumber: 2.6 Consensus size: 59
2208347 ACCCAGTGAC
* * * *
2208357 ATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTTTTTAAAAAAACAATAAT
1 ATTTTGGTAATTATTTTTAAAAAGGTGACATTTTGGGAATTATTTAAAAAAACAATAAT
* * * ** * *
2208416 ATTCTGGTAATTATTTTTAAAATGATGACATTTTGGGAATTATTT-GTAAAACGATGAT
1 ATTTTGGTAATTATTTTTAAAAAGGTGACATTTTGGGAATTATTTAAAAAAACAATAAT
* *
2208474 ATTTTGGTAATTATTTTTAATAAAGGGGATATTTT
1 ATTTTGGTAATTATTTTTAA-AAAGGTGACATTTT
2208509 TGTAATTTTT
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
58 28 0.37
59 48 0.63
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.44
Consensus pattern (59 bp):
ATTTTGGTAATTATTTTTAAAAAGGTGACATTTTGGGAATTATTTAAAAAAACAATAAT
Found at i:2214086 original size:19 final size:19
Alignment explanation
Indices: 2214062--2214102 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2214052 TCAATTCTAC
2214062 ACTTTCTTTATAGCTTCAA
1 ACTTTCTTTATAGCTTCAA
2214081 ACTTTCTTTATAGCTTCAA
1 ACTTTCTTTATAGCTTCAA
2214100 ACT
1 ACT
2214103 CGATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (19 bp):
ACTTTCTTTATAGCTTCAA
Found at i:2218290 original size:20 final size:19
Alignment explanation
Indices: 2218267--2218312 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2218257 CGATATAACA
*
2218267 GGTAAAAATATGATAAAACT
1 GGTAAAAA-ATGATAAAACC
*
2218287 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
2218307 GGTAAA
1 GGTAAA
2218313 GCGCTACCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2220031 original size:22 final size:23
Alignment explanation
Indices: 2219987--2220037 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
2219977 TTTTGTGTTT
*
2219987 TTATATAAAATGATAGTATATTTA
1 TTATATAAAATGATAG-AAATTTA
*
2220011 TTATATAAAATTATA-AAATTTA
1 TTATATAAAATGATAGAAATTTA
2220033 TTATA
1 TTATA
2220038 AATGTAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.44
24 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
TTATATAAAATGATAGAAATTTA
Found at i:2220448 original size:21 final size:21
Alignment explanation
Indices: 2220424--2220467 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2220414 AAGACAATCA
2220424 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2220445 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2220466 AG
1 AG
2220468 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2220537 original size:33 final size:33
Alignment explanation
Indices: 2220500--2220565 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2220490 AAATAGATGG
*
2220500 AGTGGTGAAAGAAGTAGAGGTATTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTATTAAGGGGTGA
* *
2220533 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTATTAAGGGGTGA
2220566 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTATTAAGGGGTGA
Found at i:2222926 original size:201 final size:201
Alignment explanation
Indices: 2222603--2223029 Score: 712
Period size: 201 Copynumber: 2.1 Consensus size: 201
2222593 ACATATGCAT
* * *
2222603 CCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
2222668 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
** *
2222733 ATGCAAAAAAGGGTGAACGCTTAAAGTGTCGATACATTTAT-TAAAAGTGTCGATCCCAAAAACA
131 ATGCAAAAAAGGGTGAACGAATAAAGTGTCGATACATTT-TCAAAAAGTGTCGATCCCAAAAACA
2222797 TCGAAAC
195 TCGAAAC
* *
2222804 CCATAATTATAATGTAATGGGTAAATTTACAATGTAACTGGTATAAATATACCGATTTTATGAGA
1 CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
*
2222869 GAATAGGTCTACAACATGTATCGACATTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
66 GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
* * * *
2222934 ATGCCAGAAAGGGTGAACGAATAAAGTGTTGATACATTTTCAAAAAGTGTCGATCCCAGAAACAT
131 ATGCAAAAAAGGGTGAACGAATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACAT
2222999 CGAAAC
196 CGAAAC
*
2223005 TCATAATTATAATGTAATAGGTAAA
1 CCATAATTATAATGTAATAGGTAAA
2223030 ACTTTTAATT
Statistics
Matches: 210, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
200 1 0.00
201 209 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (201 bp):
CCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGA
GAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGG
ATGCAAAAAAGGGTGAACGAATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACAT
CGAAAC
Found at i:2224492 original size:51 final size:53
Alignment explanation
Indices: 2224437--2224546 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 53
2224427 AGAATAAATG
*
2224437 CCAAAAAGGG-TGAAC-CTACAAAGTGTCGATACATTT-TCATAGAGTGTCGAT-
1 CCAAAAAGGGCTGAACGC-ACAAAGTGTCGATACATTTATCA-AAAGTGTCGATC
* * *
2224488 CC-AAAAGGGCTGCACGCATAAAGTGTCGATACATTTATTAAAAGTGTCGATC
1 CCAAAAAGGGCTGAACGCACAAAGTGTCGATACATTTATCAAAAGTGTCGATC
2224540 CCAAAAA
1 CCAAAAA
2224547 TATCAAAACC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
50 7 0.14
51 34 0.68
52 5 0.10
53 4 0.08
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (53 bp):
CCAAAAAGGGCTGAACGCACAAAGTGTCGATACATTTATCAAAAGTGTCGATC
Found at i:2224701 original size:250 final size:250
Alignment explanation
Indices: 2224254--2224737 Score: 659
Period size: 250 Copynumber: 1.9 Consensus size: 250
2224244 TAAAGTTTTC
* *
2224254 CATAAAGTGTCGATCCATATATAAAAAGTAACGACCCAAAAAACATCGAAACCAATAATTATAAT
1 CATAAAGTGTCGATACATATATAAAAAGTAACGACCCAAAAAACATCAAAACCAATAATTATAAT
* ** *
2224319 GTAATGGGTAATTTTTCAATATAACCGGTATAAATATACCGGTTTTATGAAAAATATGTCTACAA
66 GTAATAGGTAATTTTTCAATATAACCGGTATAAATATACCAATTTTATGAAAAATAGGTCTACAA
* * * * *
2224384 CATTTATCGACACTTATTAGTATTGTGTCGATACTTTTTGTCCAGAATAAATGCCAAAAAGGGTG
131 CATGTATCAACACTTATTAATATTGTGTCGATAATTTTTGTCCAGAATAAATGCCAAAAAAGGTG
* *
2224449 AAC-CTACAAAGTGTCGATACATTTTCATAGAGTGTCGATCCAAAAGGGCTGCACG
196 AACGC-ACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCAAAAGGGCTGCACG
* * ** * *
2224504 CATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCC-AAAAATATCAAAACCCATAATTATAA
1 CATAAAGTGTCGATACATATATAAAAAGTAACGA-CCCAAAAAACATCAAAACCAATAATTATAA
* * * * *
2224568 TGTAATATGTAATTTTTTAATATAACCGGTATACATATACCAATTTTATGAGAGAATAGGTCTAT
65 TGTAATAGGTAATTTTTCAATATAACCGGTATAAATATACCAATTTTATGA-AAAATAGGTCTAC
* * **
2224633 AATATGTATCAACACTTATTAATATTGTGTCGATAATTTTTGTCCATAATGGATG-CAAAAAAGG
129 AACATGTATCAACACTTATTAATATTGTGTCGATAATTTTTGTCCAGAATAAATGCCAAAAAAGG
*
2224697 TGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGAT
194 TGAACGCACAAAGTGTCGATACATTTTCAAAAAGTGTCGAT
2224738 AAAACATCGA
Statistics
Matches: 202, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
250 141 0.70
251 61 0.30
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (250 bp):
CATAAAGTGTCGATACATATATAAAAAGTAACGACCCAAAAAACATCAAAACCAATAATTATAAT
GTAATAGGTAATTTTTCAATATAACCGGTATAAATATACCAATTTTATGAAAAATAGGTCTACAA
CATGTATCAACACTTATTAATATTGTGTCGATAATTTTTGTCCAGAATAAATGCCAAAAAAGGTG
AACGCACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCAAAAGGGCTGCACG
Found at i:2227724 original size:200 final size:197
Alignment explanation
Indices: 2227324--2228025 Score: 745
Period size: 200 Copynumber: 3.5 Consensus size: 197
2227314 ACCTAAATAT
* * *
2227324 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAACATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAA
* * * * * *
2227387 TAGGTAAATTAACAATGTAACCGGTATAAATATATCAG-TTAATTAGAAAACAAGTCAACATAAT
64 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAAGTC-ACATAAT
* * * *
2227451 GTATCGACACTTGTGTAATTTGTGTCGATACTTATTGTCCAGGATGAAT-GCACAAACGAGGTAC
128 GTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCAGAATGAATACCA-AAAAG-GGTGC
2227515 -ACGCATAAA
189 AAC-CATAAA
* *
2227524 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAATCGATAATTATAATGTATTA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
*** * * *
2227589 GGTAAATTTACAATGTAACAAATATAAATATACCGGTTTTATGATAAAATAGGTCAGCATAAAGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAAGTCA-CATAATGT
*
2227654 ATCGACACTTGATAAATTTGTGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGGTGCAACC
130 ATCGACACTTG-TTAATTTGTGTCGATACTTTT-GTCCAGAATGAATACCAAAAAGGGTGCAACC
2227719 ATAAA
193 ATAAA
* ** * *
2227724 GTGTCGATACATTTATAAAAAGTATCGATCCCGGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * *
2227789 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATATGTCTAAATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAAGTC-ACATAATGT
* * * ** *
2227854 ATCGACACGTTGTTAGTTTGTGTCGATATTTTTTTCCAGAATGAAATATGAATGCCCAACCA-CG
130 ATCGACAC-TTGTTAATTTGTGTCGATACTTTTGTCCAGAATG--A-AT--A---CCAAAAAGGG
*
2227918 TGCAAGCATAAA
186 TGCAACCATAAA
* ** * *
2227930 GTGTCGATACATTTA--AAATTGTATCGATCTAAAAAACATCGTAACCGATAATAATAATGTAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* *
2227993 AGGTAAATTTATAATGTTACCGGTATAAATATA
65 AGGTAAATTTACAATGTAACCGGTATAAATATA
2228026 TCGATTTACT
Statistics
Matches: 425, Mismatches: 58, Indels: 33
0.82 0.11 0.06
Matches are distributed among these distances:
199 9 0.02
200 235 0.55
201 75 0.18
202 5 0.01
204 4 0.01
205 65 0.15
206 27 0.06
207 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (197 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAAGTCACATAATGTA
TCGACACTTGTTAATTTGTGTCGATACTTTTGTCCAGAATGAATACCAAAAAGGGTGCAACCATA
AA
Found at i:2228152 original size:23 final size:23
Alignment explanation
Indices: 2228124--2228175 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2228114 TCCGGTTAAA
**
2228124 TACCTATTTTATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
*
2228147 TGCCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
2228170 TACCTA
1 TACCTA
2228176 ATATGTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGC
Found at i:2228197 original size:87 final size:87
Alignment explanation
Indices: 2228050--2228211 Score: 279
Period size: 87 Copynumber: 1.9 Consensus size: 87
2228040 AAATAAGTCA
2228050 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
*
2228115 CCGGTTAAATACCTATTTTATT
66 CCGATTAAATACCTATTTTATT
* * *
2228137 ATATAAGCGCTGCCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
*
2228202 CTGATTAAAT
66 CCGATTAAAT
2228212 GATATAACAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
CCGATTAAATACCTATTTTATT
Found at i:2228760 original size:35 final size:35
Alignment explanation
Indices: 2228714--2228780 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
2228704 CTTAACTGAA
*
2228714 GTATTTAATTCTTATTCACCTTA-AGTTTTTTCTTC
1 GTATTTAATTCTCATTCACCTTAGA-TTTTTTCTTC
2228749 GTATTTAATTCTCATTCACCTTAGATTTTTTC
1 GTATTTAATTCTCATTCACCTTAGATTTTTTC
2228781 CTCTTTACGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.55
Consensus pattern (35 bp):
GTATTTAATTCTCATTCACCTTAGATTTTTTCTTC
Found at i:2230440 original size:144 final size:144
Alignment explanation
Indices: 2230235--2231069 Score: 945
Period size: 144 Copynumber: 5.8 Consensus size: 144
2230225 ATCACCGGCA
* * * * * * *
2230235 AGAAGGACCGCATTGATGACGATGAAACAGTACTCCGAAACGGAGGATTCTGAGCATGATAAGGA
1 AGAAAGACCGCGTTGATGACGACGAAGCAGTACTCCGAAATGGAGGATTCCGAGCAAGATAAGGA
* * * *
2230300 ACATAATGATCGTGAAAAAGAAAGCGATCAACCCACTCTAAGAACGAGAAGATCACCATCACCGA
66 ACATAATGATCATGATAAAGAAAGCGAACAACCCACTCTAAGAACAAGAAGATCACCATCACCGA
2230365 TTCCGATGGTGGTG
131 TTCCGATGGTGGTG
* ** * * *
2230379 AGAAAGACCGCATTGATGACGGTGAAGCAGTACTCAGACATGGAGGATTCCGAGCAAGATAAAGA
1 AGAAAGACCGCGTTGATGACGACGAAGCAGTACTCCGAAATGGAGGATTCCGAGCAAGATAAGGA
* * * *
2230444 ACATAATGATCCTGATAAAGAAAGCGAACAACCCGCACTAAGAGCAAGAAGATCACCATCACCGA
66 ACATAATGATCATGATAAAGAAAGCGAACAACCCACTCTAAGAACAAGAAGATCACCATCACCGA
* * *
2230509 TACCAATGGTGATG
131 TTCCGATGGTGGTG
* * * * * *
2230523 AGAAAGACCGCGGT-AGTGACAATGAAGCAGTACTCCGAAATGGAAGAATCTGAGCAAGATAAGG
1 AGAAAGACCGCGTTGA-TGACGACGAAGCAGTACTCCGAAATGGAGGATTCCGAGCAAGATAAGG
* ** ** * *
2230587 AACATAATGATCAAGATAAAGAAAGCGAACAGTCCGTTCCAAGACCAAGAAGATCACCATCACCG
65 AACATAATGATCATGATAAAGAAAGCGAACAACCCACTCTAAGAACAAGAAGATCACCATCACCG
*
2230652 ATTCCGATGGTGTTG
130 ATTCCGATGGTGGTG
* * * ** *
2230667 AGAAAGACCGCGGTGGTGACAACGAAGCAGTACTCCGAAATGGAGGATTCTAAGCAAGATGAGGA
1 AGAAAGACCGCGTTGATGACGACGAAGCAGTACTCCGAAATGGAGGATTCCGAGCAAGATAAGGA
* * * *
2230732 ACATAATGATCGA-GATAAAGAAAGTGAACAACCCACACGAAGAACAAGAAGATCACCATCACCA
66 ACATAATGATC-ATGATAAAGAAAGCGAACAACCCACTCTAAGAACAAGAAGATCACCATCACCG
2230796 ATAT-CGA---TGGTG
130 AT-TCCGATGGTGGTG
* * *
2230808 AGAAAGACCGCGTTGATGACGACGAAGCAATACT-CGCAAATGGAGAATTCCGAGCAAGGTAAGG
1 AGAAAGACCGCGTTGATGACGACGAAGCAGTACTCCG-AAATGGAGGATTCCGAGCAAGATAAGG
* *
2230872 AACATAATGATCACGATAAAGAAAGCGAACAACCCA-TACTAAAAACAAGAAGATCACCATCACC
65 AACATAATGATCATGATAAAGAAAGCGAACAACCCACT-CTAAGAACAAGAAGATCACCATCACC
*
2230936 GATACC---GGTGGTG
129 GATTCCGATGGTGGTG
* * * * * *
2230949 AGAAAGAACGCGTTGATGACGACGAAGAAGCACTCGGAAATAGAGAATTCCGAGCAAGATAAGGA
1 AGAAAGACCGCGTTGATGACGACGAAGCAGTACTCCGAAATGGAGGATTCCGAGCAAGATAAGGA
* * * * * * *
2231014 AGATAATGATCATGATAAAGAAAGCGAGCAATCCGCCCCAAGACCAAGAAGATCAC
66 ACATAATGATCATGATAAAGAAAGCGAACAACCCACTCTAAGAACAAGAAGATCAC
2231070 AATCGCCGTT
Statistics
Matches: 592, Mismatches: 87, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
140 3 0.01
141 223 0.38
142 1 0.00
143 1 0.00
144 362 0.61
145 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (144 bp):
AGAAAGACCGCGTTGATGACGACGAAGCAGTACTCCGAAATGGAGGATTCCGAGCAAGATAAGGA
ACATAATGATCATGATAAAGAAAGCGAACAACCCACTCTAAGAACAAGAAGATCACCATCACCGA
TTCCGATGGTGGTG
Found at i:2232030 original size:30 final size:30
Alignment explanation
Indices: 2231994--2232074 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
2231984 CAAAATTCAA
*
2231994 TGGACTTAAGTTCAACGCATCATAAATCAG
1 TGGACTTAAGTTCAACACATCATAAATCAG
*
2232024 TGGACTTGAA-TTCAACACATCATAAATTAG
1 TGGACTT-AAGTTCAACACATCATAAATCAG
* *
2232054 TGGACTTAGGTTCAACCCATC
1 TGGACTTAAGTTCAACACATC
2232075 TTCACAAGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 1 0.02
30 42 0.93
31 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (30 bp):
TGGACTTAAGTTCAACACATCATAAATCAG
Found at i:2234106 original size:142 final size:142
Alignment explanation
Indices: 2233928--2234212 Score: 552
Period size: 142 Copynumber: 2.0 Consensus size: 142
2233918 CTTAAGTGGT
2233928 AGTAGAAGACTACAGAAAGAACAATGAAAACTAAAAATGAAGCAAACTCCAAAAGAAATAAATCA
1 AGTAGAAGACTACAGAAAGAACAATGAAAACTAAAAATGAAGCAAACTCCAAAAGAAATAAATCA
2233993 ATGGAAAGAGAAAAGGAGAAACGTGAAGGAAAGGTAAATAATTGAAGGAACTAAAGCATAACTAA
66 ATGGAAAGAGAAAAGGAGAAACGTGAAGGAAAGGTAAATAATTGAAGGAACTAAAGCATAACTAA
2234058 ATATGAATCTGC
131 ATATGAATCTGC
*
2234070 AGTAGAAGACTACAGAAAGAACAATGGAAACTAAAAATGAAGCAAACTCCAAAAGAAATAAATCA
1 AGTAGAAGACTACAGAAAGAACAATGAAAACTAAAAATGAAGCAAACTCCAAAAGAAATAAATCA
*
2234135 ATGGAAAGAGAAAAGGAGAAACGTGAAGGAAATGTAAATAATTGAAGGAACTAAAGCATAACTAA
66 ATGGAAAGAGAAAAGGAGAAACGTGAAGGAAAGGTAAATAATTGAAGGAACTAAAGCATAACTAA
2234200 ATATGAATCTGC
131 ATATGAATCTGC
2234212 A
1 A
2234213 AGCAGTTAAC
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.55, C:0.11, G:0.20, T:0.15
Consensus pattern (142 bp):
AGTAGAAGACTACAGAAAGAACAATGAAAACTAAAAATGAAGCAAACTCCAAAAGAAATAAATCA
ATGGAAAGAGAAAAGGAGAAACGTGAAGGAAAGGTAAATAATTGAAGGAACTAAAGCATAACTAA
ATATGAATCTGC
Found at i:2239115 original size:24 final size:25
Alignment explanation
Indices: 2239077--2239126 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
2239067 AAACATCTTC
2239077 ATTTATAATATTTA-TAACTATGTTT
1 ATTTATAATATTTATTAACTAT-TTT
2239102 ATTTAT-ATATTTATTAACTATTTT
1 ATTTATAATATTTATTAACTATTTT
2239126 A
1 A
2239127 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTATAATATTTATTAACTATTTT
Found at i:2240426 original size:37 final size:36
Alignment explanation
Indices: 2240327--2240428 Score: 161
Period size: 35 Copynumber: 2.8 Consensus size: 36
2240317 TGGCAACCAA
* *
2240327 CTTTGAAAAAACGGTTTTCAAAGTTTGATAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
2240364 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
2240399 CTTTGAAAAATGGTTTTTCAAAGTTTGGTA
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTA
2240429 GATACTTGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
35 33 0.54
36 7 0.11
37 21 0.34
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2240441 original size:36 final size:36
Alignment explanation
Indices: 2240333--2240445 Score: 122
Period size: 35 Copynumber: 3.2 Consensus size: 36
2240323 CCAACTTTGA
* * ** *
2240333 AAAAACGGTTTTCAAAGTTTGATAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATACTTCGTTG
** *
2240369 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATACTTCGTTG
*
2240404 AAAAATGGTTTTTCAAAGTTTGGTAGATACTT-GTTG
1 AAAAATGG-TTTTCAAAGTTTGGTAAATACTTCGTTG
2240440 AAAAAT
1 AAAAAT
2240446 TGTAATGGGG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 33 0.48
36 16 0.23
37 20 0.29
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.42
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATACTTCGTTG
Found at i:2245028 original size:37 final size:36
Alignment explanation
Indices: 2244929--2245047 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
2244919 TGGCAACCAA
2244929 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
2244966 CTTTG-AATATGGTTTTCAAAGTTTGGTAAGTGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
2245001 CTTTGAAAAATGATTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATG-GTTTTCAAAGTTTGGTAAATGTTT
*
2245038 -GTTGAAAAAT
1 CTTTGAAAAAT
2245048 TGTAATGGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 33 0.45
36 14 0.19
37 27 0.36
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2247817 original size:6 final size:6
Alignment explanation
Indices: 2247808--2247859 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
2247798 TATCGATATA
* *
2247808 GTGGTC GTGGTC G-GGTC GGGGTC GTAGTC GTGGTC GTGGTC GTGGTC
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
2247855 GTGGT
1 GTGGT
2247860 AATACGTGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
5 5 0.12
6 37 0.88
ACGTcount: A:0.02, C:0.15, G:0.52, T:0.31
Consensus pattern (6 bp):
GTGGTC
Found at i:2247965 original size:20 final size:20
Alignment explanation
Indices: 2247940--2247991 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2247930 TTTTTAAACT
*
2247940 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
2247960 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
2247980 ATCGCAACGCGA
1 ATCGCAACGCGA
2247992 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:2248006 original size:21 final size:21
Alignment explanation
Indices: 2247980--2248033 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
2247970 GAAATGGAAA
2247980 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
2248001 ATCGCAACGCAATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
2248022 ATCGCAACGCGA
1 ATCGCAACGCGA
2248034 AATGCAACGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:2249057 original size:12 final size:12
Alignment explanation
Indices: 2249040--2249071 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2249030 AATACATATG
2249040 GTGTGTGTGTTT
1 GTGTGTGTGTTT
2249052 GTGTGTGTGTTT
1 GTGTGTGTGTTT
2249064 GTGTGTGT
1 GTGTGTGT
2249072 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.44, T:0.56
Consensus pattern (12 bp):
GTGTGTGTGTTT
Found at i:2249076 original size:2 final size:2
Alignment explanation
Indices: 2249071--2249140 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
2249061 TTTGTGTGTG
2249071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2249113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2249141 CTAATAGAAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2251398 original size:30 final size:30
Alignment explanation
Indices: 2251288--2251613 Score: 256
Period size: 30 Copynumber: 10.8 Consensus size: 30
2251278 TTAAAATCAC
*
2251288 ATCTTAACATTAAAAAATATATTTTATT-TT
1 ATCTTAAC-TTATAAAATATATTTTATTCTT
* * *
2251318 -TTTTAACTTATTAAATTTATTTTATTCTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
*
2251347 ATCTTAAC-TAAAAAATATATTTTAATT-TT
1 ATCTTAACTTATAAAATATATTTT-ATTCTT
* *
2251376 ATCTTAACTTATAAAGTATATTTTATTCCT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* *
2251406 ATTTTAACTTA-AAAATATATTTTTATTTTT
1 ATCTTAACTTATAAAATATA-TTTTATTCTT
* * ** *
2251436 ATCTTAACTTGTTACGTATATTATATTCTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* * *
2251466 ACCTTAAATTATTAAATAT-TATTTATTCTT
1 ATCTTAACTTATAAAATATAT-TTTATTCTT
2251496 ATCTTAACTTGA-AAATATATATTTTATT-TT
1 ATCTTAACTT-ATAAA-ATATATTTTATTCTT
* * *
2251526 AATTTTAAAACATATATTAATATATTTTATTCTT
1 -ATCTT--AACTTATA-AAATATATTTTATTCTT
* * * * *
2251560 ATTTTAATTTA-AAAATAGATTCTATTTTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
*
2251589 ATCTTAACTATAAAAAATATATTTT
1 ATCTTAACT-TATAAAATATATTTT
2251614 TATCTTAATT
Statistics
Matches: 233, Mismatches: 44, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
28 16 0.07
29 61 0.26
30 95 0.41
31 34 0.15
32 2 0.01
33 22 0.09
34 3 0.01
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (30 bp):
ATCTTAACTTATAAAATATATTTTATTCTT
Found at i:2251522 original size:25 final size:26
Alignment explanation
Indices: 2251489--2251543 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
2251479 AAATATTATT
*
2251489 TATTCTTATCTTAACTTGAAAATATA
1 TATTCTTATCTTAACTTGAAAACATA
* * *
2251515 TATT-TTATTTTAATTTTAAAACATA
1 TATTCTTATCTTAACTTGAAAACATA
2251540 TATT
1 TATT
2251544 AATATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTCTTATCTTAACTTGAAAACATA
Found at i:2251610 original size:149 final size:148
Alignment explanation
Indices: 2251320--2251635 Score: 353
Period size: 149 Copynumber: 2.1 Consensus size: 148
2251310 TTTATTTTTT
*
2251320 TTAACTTATTAAAT-TTATTTTATTCTTATCTTAACTAAAAAATATATTTTAATTTTATCTTAAC
1 TTAAATTATTAAATATTA-TTTATTCTTATCTTAACTAAAAAATATATTTTAATTTTATCTTAAC
* * *
2251384 TTATAAAGTATATTTTATTCCTATTTTAACTTAAAAATATATTTTTATTTTTATCTTAACTTGTT
65 TTATAAAGTATATTTTATTCCTATTTTAACTTAAAAATAGATTTCTATTTTTATCTTAACTTGAT
* * *
2251449 ACGTATATTATATTCTTACC
130 AC-AAAAATATATTCTTACC
* *
2251469 TTAAATTATTAAATATTATTTATTCTTATCTTAACTTGAAAATATATATTTT-ATTTTAATTTTA
1 TTAAATTATTAAATATTATTTATTCTTATCTTAAC-T-AAAAAATATATTTTAATTTT-ATCTT-
* * *
2251533 AAACATATATTAA-TATATTTTATTCTTATTTTAATTTAAAAATAGA-TTCTATTTTTATCTTAA
62 -AAC-T-TATAAAGTATATTTTATTCCTATTTTAACTTAAAAATAGATTTCTATTTTTATCTTAA
* *
2251596 C-T-ATA-AAAAATATATTTTTATC
124 CTTGATACAAAAATATATTCTTACC
2251618 TT-AATT-TTAAAATATTAT
1 TTAAATTATT-AAATATTAT
2251636 AAAAATAAAT
Statistics
Matches: 144, Mismatches: 14, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
147 2 0.01
148 13 0.09
149 44 0.31
150 9 0.06
151 19 0.13
152 1 0.01
153 20 0.14
154 31 0.22
155 5 0.03
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (148 bp):
TTAAATTATTAAATATTATTTATTCTTATCTTAACTAAAAAATATATTTTAATTTTATCTTAACT
TATAAAGTATATTTTATTCCTATTTTAACTTAAAAATAGATTTCTATTTTTATCTTAACTTGATA
CAAAAATATATTCTTACC
Found at i:2256553 original size:13 final size:13
Alignment explanation
Indices: 2256535--2256572 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2256525 TTTAGTTGTA
2256535 ATTTTATAATTTT
1 ATTTTATAATTTT
*
2256548 ATTTTAT-TTTTT
1 ATTTTATAATTTT
*
2256560 ATTTTGTAATTTT
1 ATTTTATAATTTT
2256573 TTTAGATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
ATTTTATAATTTT
Found at i:2258729 original size:15 final size:16
Alignment explanation
Indices: 2258693--2258729 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2258683 GAAGGTAAAT
2258693 TCTTTTTCTTATCAAG
1 TCTTTTTCTTATCAAG
*
2258709 TCTTTTTCTTATTAAG
1 TCTTTTTCTTATCAAG
2258725 T-TTTT
1 TCTTTT
2258730 CCCCCCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.16, C:0.14, G:0.05, T:0.65
Consensus pattern (16 bp):
TCTTTTTCTTATCAAG
Found at i:2262353 original size:2 final size:2
Alignment explanation
Indices: 2262346--2262398 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2262336 CACAATATTC
2262346 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2262388 AT AT AT AT AT A
1 AT AT AT AT AT A
2262399 AAAACAGTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2263151 original size:29 final size:29
Alignment explanation
Indices: 2263062--2263200 Score: 123
Period size: 30 Copynumber: 5.0 Consensus size: 29
2263052 ACACAATTAT
* * *
2263062 CACCCTTTTAAGAAATATTTACGAAAATAA
1 CACCATTTTAA-AAATAATTACGAAAATAG
* * *
2263092 CACCATTCTAAAATTTAATTACGAAACTAG
1 CACCATTTTAAAA-ATAATTACGAAAATAG
*
2263122 CACCTTTTTAAAAATAATTACGAAAATAG
1 CACCATTTTAAAAATAATTACGAAAATAG
*
2263151 CA-C------AAAA-AATTACTAAAATAG
1 CACCATTTTAAAAATAATTACGAAAATAG
*
2263172 CACAATTTTAAAAATAATTACGAAAATAG
1 CACCATTTTAAAAATAATTACGAAAATAG
2263201 GTCAACGGTC
Statistics
Matches: 87, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
21 15 0.17
22 4 0.05
28 5 0.06
29 31 0.36
30 32 0.37
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.28
Consensus pattern (29 bp):
CACCATTTTAAAAATAATTACGAAAATAG
Found at i:2263163 original size:21 final size:22
Alignment explanation
Indices: 2263132--2263176 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
2263122 CACCTTTTTA
2263132 AAAATAATTACGAAAATAGCAC
1 AAAATAATTACGAAAATAGCAC
*
2263154 AAAA-AATTACTAAAATAGCAC
1 AAAATAATTACGAAAATAGCAC
2263175 AA
1 AA
2263177 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.62, C:0.13, G:0.07, T:0.18
Consensus pattern (22 bp):
AAAATAATTACGAAAATAGCAC
Found at i:2270098 original size:6 final size:6
Alignment explanation
Indices: 2270089--2270113 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2270079 TAAATTCTTG
2270089 GTCAAA GTCAAA GTCAAA GTCAAA G
1 GTCAAA GTCAAA GTCAAA GTCAAA G
2270114 GGTTTGACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (6 bp):
GTCAAA
Found at i:2270360 original size:29 final size:29
Alignment explanation
Indices: 2270306--2270454 Score: 183
Period size: 29 Copynumber: 5.1 Consensus size: 29
2270296 ACACAATTAT
* * *
2270306 CACCATTTTAATAAATATTTAAGAAAATAA
1 CACCATTTTAA-AAATAATTACGAAAATAG
* *
2270336 CACCATTTTAAAAATAATTACGAAACTGG
1 CACCATTTTAAAAATAATTACGAAAATAG
*
2270365 CACC-TTTTTAAAATAATTACGAAAATAG
1 CACCATTTTAAAAATAATTACGAAAATAG
* * *
2270393 CACCTTTTTAAAAATAATTACTAATATAG
1 CACCATTTTAAAAATAATTACGAAAATAG
* *
2270422 CACCATTTTAAAAATAATTATGAAAATAT
1 CACCATTTTAAAAATAATTACGAAAATAG
2270451 CACC
1 CACC
2270455 CGATCAACGG
Statistics
Matches: 102, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
28 25 0.25
29 66 0.65
30 11 0.11
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (29 bp):
CACCATTTTAAAAATAATTACGAAAATAG
Found at i:2270402 original size:57 final size:58
Alignment explanation
Indices: 2270306--2270454 Score: 185
Period size: 57 Copynumber: 2.6 Consensus size: 58
2270296 ACACAATTAT
* *
2270306 CACCATTTTAATAAATATTTAAGAAAATAACACCATTTTAAAAATAATTACGAA-ACTGG
1 CACCATTTTAA-AAATAATTAAGAAAATAACACCATTTTAAAAATAATTACGAATA-TAG
* * * * *
2270365 CACC-TTTTTAAAATAATTACGAAAATAGCACCTTTTTAAAAATAATTACTAATATAG
1 CACCATTTTAAAAATAATTAAGAAAATAACACCATTTTAAAAATAATTACGAATATAG
* *
2270422 CACCATTTTAAAAATAATTATGAAAATATCACC
1 CACCATTTTAAAAATAATTAAGAAAATAACACC
2270455 CGATCAACGG
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 43 0.55
58 31 0.40
59 4 0.05
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (58 bp):
CACCATTTTAAAAATAATTAAGAAAATAACACCATTTTAAAAATAATTACGAATATAG
Found at i:2277049 original size:16 final size:16
Alignment explanation
Indices: 2277028--2277059 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2277018 ATGTTCAAAT
*
2277028 TCAAAATACACTGCTG
1 TCAAAATACACGGCTG
2277044 TCAAAATACACGGCTG
1 TCAAAATACACGGCTG
2277060 CTAGTGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.22
Consensus pattern (16 bp):
TCAAAATACACGGCTG
Found at i:2277833 original size:25 final size:24
Alignment explanation
Indices: 2277805--2277854 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2277795 TTAATGTGAT
2277805 TAAACATCTTCATTTATAATATTTA
1 TAAACATCTTCATTTAT-ATATTTA
* * *
2277830 TAAATATGTTTATTTATATATTTA
1 TAAACATCTTCATTTATATATTTA
2277854 T
1 T
2277855 TAACTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (24 bp):
TAAACATCTTCATTTATATATTTA
Found at i:2279524 original size:29 final size:29
Alignment explanation
Indices: 2279482--2279540 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2279472 ATTTTCACCT
2279482 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2279511 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2279540 A
1 A
2279541 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2284119 original size:29 final size:29
Alignment explanation
Indices: 2284077--2284135 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2284067 ATTTTCACCT
*
2284077 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
2284106 AACTAAATTGATGTAAGCAATAACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
2284135 A
1 A
2284136 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATAACATCAA
Found at i:2285265 original size:24 final size:24
Alignment explanation
Indices: 2285233--2285284 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
2285223 TGAATCTGCA
2285233 GAAACCTGAAAGAAATAAGAAAGG
1 GAAACCTGAAAGAAATAAGAAAGG
2285257 GAAACCTGAAAGAAATAAGAAAGG
1 GAAACCTGAAAGAAATAAGAAAGG
2285281 GAAA
1 GAAA
2285285 GAGAGCTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.60, C:0.08, G:0.25, T:0.08
Consensus pattern (24 bp):
GAAACCTGAAAGAAATAAGAAAGG
Found at i:2285991 original size:30 final size:30
Alignment explanation
Indices: 2285888--2286239 Score: 269
Period size: 30 Copynumber: 11.8 Consensus size: 30
2285878 TTAAAATCAC
*
2285888 ATCTTAACATTAAAAAATATATTTTA-T-TT
1 ATCTTAAC-TTATAAAATATATTTTATTCTT
** *
2285917 -T-TTAACTTATTGAATTTATTTTATTCTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
*
2285945 ATATTAAC-TA-AAAATATATTTTAATT-TT
1 ATCTTAACTTATAAAATATATTTT-ATTCTT
*
2285973 ATCTTAACTTATAAAATATATTTTATTCCT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* * *
2286003 ATTTTAACTTA-AACATATATTTTATTTTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* * * *
2286032 ATCTTAACTTGTTACATATATTATATTCTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* * * *
2286062 AGCTTAAATTATTAAATATATTATATTCTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* * *
2286092 ACCTTAAATTATTAAATAT-TATTTATTCTT
1 ATCTTAACTTATAAAATATAT-TTTATTCTT
2286122 ATCTTAACTT-TAAAATATATATTTTATT-TT
1 ATCTTAACTTAT-AAA-ATATATTTTATTCTT
* * *
2286152 AATTTTAAAACATATATTAATATATTTTATTCTT
1 -ATCTT--AACTTATA-AAATATATTTTATTCTT
* * * * *
2286186 ATTTTCATTTA-AAAATATATTCTATTTTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
*
2286215 ATCTTAACTATAAAAAATATATTTT
1 ATCTTAACT-TATAAAATATATTTT
2286240 TATCTTAATT
Statistics
Matches: 262, Mismatches: 40, Indels: 40
0.77 0.12 0.12
Matches are distributed among these distances:
26 13 0.05
27 6 0.02
28 21 0.08
29 57 0.22
30 110 0.42
31 28 0.11
32 1 0.00
33 22 0.08
34 4 0.02
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (30 bp):
ATCTTAACTTATAAAATATATTTTATTCTT
Found at i:2286153 original size:25 final size:26
Alignment explanation
Indices: 2286115--2286169 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
2286105 AAATATTATT
*
2286115 TATTCTTATCTTAACTTTAAAATATA
1 TATTCTTATCTTAACTTTAAAACATA
* *
2286141 TATT-TTATTTTAATTTTAAAACATA
1 TATTCTTATCTTAACTTTAAAACATA
2286166 TATT
1 TATT
2286170 AATATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTCTTATCTTAACTTTAAAACATA
Found at i:2286243 original size:119 final size:114
Alignment explanation
Indices: 2285888--2286258 Score: 313
Period size: 119 Copynumber: 3.2 Consensus size: 114
2285878 TTAAAATCAC
* * *
2285888 ATCTTAACATTAAAAAATATATTTTA-TTT--T-TTAACTTATTGAATTTATTTTATTCTTATAT
1 ATCTTAACTTTAAAATATATATTTTATTTTAATCTTAACTTATT-AATATATTTTATTCTTATAT
* * * *
2285949 TAACTAAAAATATATTTTAATTTTATCTTAACTTATAAAATATATTTTATTCCT
65 TAATTAAAAATATATTATATTTTTATCTTAAC-TATAAAATATATATT-TT--T
* * * * * **
2286003 ATTTTAAC-TT-AAACATATATTTTATTTTTATCTTAACTTGTTACATATATTATATTCTTAGCT
1 ATCTTAACTTTAAAATATATATTTTATTTTAATCTTAACTTATTA-ATATATTTTATTCTTATAT
* * * * * *
2286066 TAAATTATTAAATATATTATATTCTTACCTTAAATTATTAAATATTATTTATTCTT
65 T-AATTA-AAAATATATTATATTTTTATCTT-AACTA-TAAA-A-TATATATTTTT
*
2286122 ATCTTAACTTTAAAATATATATTTTATTTTAATTTTAAAACATATATTAATATATTTTATTCTTA
1 ATCTTAACTTTAAAATATATATTTTATTTTAATCTT--AAC-T-TATTAATATATTTTATTCTTA
* * * *
2286187 TTTTCATTTAAAAATATATTCTATTTTTATCTTAACTATAAAAAATATATTTTT
62 TATT-AATTAAAAATATATTATATTTTTATCTTAACTATAAAATATATATTTTT
*
2286241 ATCTTAATTTTAAAATAT
1 ATCTTAACTTTAAAATAT
2286259 TATAAAAATA
Statistics
Matches: 203, Mismatches: 36, Indels: 30
0.75 0.13 0.11
Matches are distributed among these distances:
113 13 0.06
114 5 0.02
115 7 0.03
116 2 0.01
117 25 0.12
118 4 0.02
119 53 0.26
120 9 0.04
121 27 0.13
122 10 0.05
123 22 0.11
124 22 0.11
125 4 0.02
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (114 bp):
ATCTTAACTTTAAAATATATATTTTATTTTAATCTTAACTTATTAATATATTTTATTCTTATATT
AATTAAAAATATATTATATTTTTATCTTAACTATAAAATATATATTTTT
Found at i:2286282 original size:93 final size:92
Alignment explanation
Indices: 2286105--2286282 Score: 207
Period size: 93 Copynumber: 1.9 Consensus size: 92
2286095 TTAAATTATT
* * * **
2286105 AAATATTATTTATTCTTATCTTAACTTTAAAATATATATTTTATTTTAATTTTAAAACATATATT
1 AAATATTATTTATTCTTATCTTAACTATAAAAAATATATTTTATCTTAATTTTAAAACATATAAA
* * **
2286170 AATATATTTTATTCTTATTTTCATTTAA
66 AATAAAATTTA-TAATATTTTCATTTAA
* *
2286198 AAATA-TATTCTATTTTTATCTTAACTATAAAAAATATATTTTTATCTTAATTTTAAAATATTAT
1 AAATATTATT-TATTCTTATCTTAACTATAAAAAATATA-TTTTATCTTAATTTTAAAACA-TAT
2286262 AAAAATAAAATTTA-AATATTT
63 AAAAATAAAATTTATAATATTT
2286283 AAGTTAAGGT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
92 4 0.06
93 35 0.49
94 19 0.27
95 13 0.18
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (92 bp):
AAATATTATTTATTCTTATCTTAACTATAAAAAATATATTTTATCTTAATTTTAAAACATATAAA
AATAAAATTTATAATATTTTCATTTAA
Found at i:2294319 original size:2 final size:2
Alignment explanation
Indices: 2294312--2294348 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2294302 ATTAAAGTAA
*
2294312 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2294349 AGGTTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2296654 original size:73 final size:73
Alignment explanation
Indices: 2296533--2296864 Score: 544
Period size: 73 Copynumber: 4.6 Consensus size: 73
2296523 TTTCTAGAAA
* * * * * *
2296533 TGTTTTAATAAAAATAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAATTTTCTCAAGCAAT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
2296598 AAACAGTT
66 AAACAGTT
*
2296606 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
2296671 AAACAGTT
66 AAACAGTT
* *
2296679 TGTTTTAAGAAAAACAATCTCAACTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
2296744 AAACAGTT
66 AAACAGTT
*
2296752 TGTTTTAAGAAAAACAATCTCAAGTTAGATAAATTGCTATTTCAAGTGAAA-TATTCTCAA--GA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACT-TTCTCAAGCGA
2296814 GAAACAGTT
65 GAAACAGTT
2296823 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
2296865 GAAAACATCC
Statistics
Matches: 244, Mismatches: 14, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
71 52 0.21
72 1 0.00
73 191 0.78
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
AAACAGTT
Found at i:2296665 original size:37 final size:37
Alignment explanation
Indices: 2296550--2296812 Score: 144
Period size: 37 Copynumber: 7.2 Consensus size: 37
2296540 ATAAAAATAA
* * *
2296550 TCTCAAGTGAGATAAATTGCTATTTCGAGTGAAATTT
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
* ** * * ** **
2296587 TCTCAAG-CA-ATAAACAGTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATTG-TTATTTCAAGTGAAACTT
2296623 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
* * * * ** **
2296660 TCTCAAGCGAGA-AACAGT-TTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAA-ATTGTTATTTCAAGTGAAACTT
* *
2296696 TCTCAACTGAGATAAATTGCTATTTCAAGTGAAACTT
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
* * * * * ** **
2296733 TCTCCAGCGAGA-AACAGT-TTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAA-ATTGTTATTTCAAGTGAAACTT
* *
2296769 TCTCAAGTTAGATAAATTGCTATTTCAAGTGAAA-TAT
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACT-T
2296806 TCTCAAG
1 TCTCAAG
2296813 AGAAACAGTT
Statistics
Matches: 155, Mismatches: 61, Indels: 20
0.66 0.26 0.08
Matches are distributed among these distances:
35 6 0.04
36 67 0.43
37 76 0.49
38 6 0.04
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (37 bp):
TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
Found at i:2299871 original size:7 final size:7
Alignment explanation
Indices: 2299859--2299928 Score: 69
Period size: 7 Copynumber: 10.7 Consensus size: 7
2299849 CTTGATTCAA
2299859 TTTCTTT
1 TTTCTTT
*
2299866 TTTCTTC
1 TTTCTTT
*
2299873 TTTC-AT
1 TTTCTTT
2299879 TTTCTTT
1 TTTCTTT
2299886 TTT-TTT
1 TTTCTTT
*
2299892 TTTTTTT
1 TTTCTTT
*
2299899 TTTTTTT
1 TTTCTTT
2299906 TTTC-TT
1 TTTCTTT
2299912 TTTC--T
1 TTTCTTT
2299917 TTTCTTT
1 TTTCTTT
2299924 TTTCT
1 TTTCT
2299929 GATGAATGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
5 5 0.09
6 16 0.30
7 33 0.61
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTCTTT
Found at i:2299877 original size:20 final size:19
Alignment explanation
Indices: 2299854--2299928 Score: 80
Period size: 20 Copynumber: 3.9 Consensus size: 19
2299844 TCCATCTTGA
*
2299854 TTCAATTTCTTTTTTCTTCT
1 TTCATTTTCTTTTTTCTT-T
*
2299874 TTCATTTTCTTTTTTTTTTT
1 TTCATTTTC-TTTTTTCTTT
** *
2299894 TTTTTTTTTTTTTTTCTTT
1 TTCATTTTCTTTTTTCTTT
2299913 TTC-TTTTCTTTTTTCT
1 TTCATTTTCTTTTTTCT
2299929 GATGAATGAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 12 0.26
19 11 0.24
20 15 0.33
21 8 0.17
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (19 bp):
TTCATTTTCTTTTTTCTTT
Found at i:2299887 original size:1 final size:1
Alignment explanation
Indices: 2299878--2299926 Score: 62
Period size: 1 Copynumber: 49.0 Consensus size: 1
2299868 TCTTCTTTCA
* * * *
2299878 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTCTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2299927 CTGATGAATG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:2299887 original size:6 final size:6
Alignment explanation
Indices: 2299859--2299925 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
2299849 CTTGATTCAA
* *
2299859 TTTCTTT TTTCTT CTTTCAT TTTCTT TTT-TT TTT-TT TTT-TT TTTTTT
1 TTTC-TT TTTCTT -TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
2299906 TTTCTT TTTC-T TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTT
2299926 TCTGATGAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
5 20 0.37
6 25 0.46
7 9 0.17
ACGTcount: A:0.01, C:0.12, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTCTT
Found at i:2299901 original size:33 final size:33
Alignment explanation
Indices: 2299863--2299926 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2299853 ATTCAATTTC
*
2299863 TTTTTTCTTCTTTCATTTTCTTTTTTTTTTTTT
1 TTTTTTCTTCTTTCATTTTCTTTTCTTTTTTTT
* * *
2299896 TTTTTTTTTTTTTCTTTTTCTTTTCTTTTTT
1 TTTTTTCTTCTTTCATTTTCTTTTCTTTTTT
2299927 CTGATGAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.88
Consensus pattern (33 bp):
TTTTTTCTTCTTTCATTTTCTTTTCTTTTTTTT
Found at i:2302463 original size:17 final size:16
Alignment explanation
Indices: 2302441--2302474 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2302431 TAAAAACAGT
2302441 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2302458 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2302474 A
1 A
2302475 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2302993 original size:24 final size:24
Alignment explanation
Indices: 2302949--2302995 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2302939 ATAAAGAACC
*
2302949 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
2302973 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
2302996 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:2306217 original size:25 final size:25
Alignment explanation
Indices: 2306167--2306219 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
2306157 CTCTATGCCT
*
2306167 GACATGGAGAATAAATCCTCACGAA
1 GACATGGAGAATAAATCATCACGAA
* *
2306192 GACATGGAGAATAAATTATCAGGAA
1 GACATGGAGAATAAATCATCACGAA
2306217 GAC
1 GAC
2306220 GTCACTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (25 bp):
GACATGGAGAATAAATCATCACGAA
Found at i:2306921 original size:2 final size:2
Alignment explanation
Indices: 2306914--2306950 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2306904 AAAATTAAAG
2306914 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2306951 TTAAGGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2307277 original size:4 final size:4
Alignment explanation
Indices: 2307268--2307294 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2307258 TGACTAAACC
2307268 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
2307295 CAGTACTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:2307360 original size:14 final size:14
Alignment explanation
Indices: 2307341--2307376 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2307331 AAAATAAAAA
2307341 AAATTAAAGTAAC-G
1 AAATTAAAG-AACTG
2307355 AAATTAAAGAACTG
1 AAATTAAAGAACTG
2307369 AAATTAAA
1 AAATTAAA
2307377 TAAATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 3 0.14
14 18 0.86
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.22
Consensus pattern (14 bp):
AAATTAAAGAACTG
Found at i:2307425 original size:25 final size:26
Alignment explanation
Indices: 2307374--2307435 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
2307364 AACTGAAATT
* *
2307374 AAAT-AAATAAAAAGTAAATGGCATA
1 AAATAAAATATAAAGTAAATGACATA
*
2307399 AATTAAAATATAAAGTAAATGAC-TA
1 AAATAAAATATAAAGTAAATGACATA
2307424 AAATAAAATATA
1 AAATAAAATATA
2307436 TCAGAAGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (26 bp):
AAATAAAATATAAAGTAAATGACATA
Found at i:2313851 original size:22 final size:22
Alignment explanation
Indices: 2313820--2313862 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2313810 GTTTAAAAAT
2313820 ACTAACATTTATATAGCTATTA
1 ACTAACATTTATATAGCTATTA
*
2313842 ACTAATATTTATATAGCTATT
1 ACTAACATTTATATAGCTATT
2313863 TAATAAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (22 bp):
ACTAACATTTATATAGCTATTA
Found at i:2317266 original size:20 final size:20
Alignment explanation
Indices: 2317237--2317283 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2317227 GCAGCGTATG
*
2317237 GTTTCGTGGATGATGATGAT
1 GTTTCATGGATGATGATGAT
*
2317257 TTTTCATGGATGATGATGAT
1 GTTTCATGGATGATGATGAT
2317277 GTTTCAT
1 GTTTCAT
2317284 TTGCATCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.06, G:0.28, T:0.45
Consensus pattern (20 bp):
GTTTCATGGATGATGATGAT
Found at i:2321035 original size:31 final size:31
Alignment explanation
Indices: 2320993--2321144 Score: 77
Period size: 29 Copynumber: 5.1 Consensus size: 31
2320983 TGTAGATTAA
*
2320993 ATATATCTTATTCTTATCTTAATTTTAAAAT
1 ATATATTTTATTCTTATCTTAATTTTAAAAT
* *** ***
2321024 ATATATTTTATT-TTAATTTTAAAACATATTTT
1 ATATATTTTATTCTT-ATCTT-AATTTTAAAAT
* * *
2321056 AATATATTTTATTCCTATTTTAA-TTTAGAA-
1 -ATATATTTTATTCTTATCTTAATTTTAAAAT
* * * *
2321086 ATATATTCTATTTTTATCTTAACTATAAAA-
1 ATATATTTTATTCTTATCTTAATTTTAAAAT
*
2321116 A-ATA---TATTTTTATCTTAATTTTAAAAT
1 ATATATTTTATTCTTATCTTAATTTTAAAAT
2321143 AT
1 AT
2321145 TATAAGAATA
Statistics
Matches: 92, Mismatches: 22, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
26 20 0.22
27 1 0.01
29 21 0.23
30 8 0.09
31 17 0.18
32 7 0.08
33 17 0.18
34 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.55
Consensus pattern (31 bp):
ATATATTTTATTCTTATCTTAATTTTAAAAT
Found at i:2321039 original size:25 final size:26
Alignment explanation
Indices: 2321001--2321052 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
2320991 AAATATATCT
*
2321001 TATTCTTATCTTAATTTTAAAATATA
1 TATTCTTATCTTAATTTTAAAACATA
*
2321027 TATT-TTATTTTAATTTTAAAACATA
1 TATTCTTATCTTAATTTTAAAACATA
2321052 T
1 T
2321053 TTTAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTCTTATCTTAATTTTAAAACATA
Found at i:2321107 original size:29 final size:29
Alignment explanation
Indices: 2321056--2321144 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
2321046 AACATATTTT
* ** *
2321056 AATATATTTTATTCCTATTTTAA-TTTAGA
1 AATATATTATATTTTTATCTTAACTTTA-A
* *
2321085 AATATATTCTATTTTTATCTTAACTATAA
1 AATATATTATATTTTTATCTTAACTTTAA
*
2321114 AA-A-A-TATATTTTTATCTTAATTTTAA
1 AATATATTATATTTTTATCTTAACTTTAA
2321140 AATAT
1 AATAT
2321145 TATAAGAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
26 21 0.43
27 2 0.04
28 1 0.02
29 22 0.45
30 3 0.06
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (29 bp):
AATATATTATATTTTTATCTTAACTTTAA
Found at i:2325193 original size:24 final size:28
Alignment explanation
Indices: 2325164--2325221 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
2325154 ATAATACATA
*
2325164 ATTTTACTA-A-ATTTTA-AT-TATTTT
1 ATTTTACTATATATTTTATATCTAATTT
*
2325188 ATTTTATTATATATTTTATATCTAATTT
1 ATTTTACTATATATTTTATATCTAATTT
2325216 ATTTTA
1 ATTTTA
2325222 TTTTAATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 8 0.29
25 1 0.04
26 6 0.21
27 2 0.07
28 11 0.39
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTTTACTATATATTTTATATCTAATTT
Found at i:2325265 original size:19 final size:20
Alignment explanation
Indices: 2325224--2325267 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2325214 TTATTTTATT
* *
2325224 TTAATAACTTAAAGTTATCA
1 TTAATAACTTAAAATAATCA
*
2325244 TTAATAA-TTAAAATAATTA
1 TTAATAACTTAAAATAATCA
2325263 TTAAT
1 TTAAT
2325268 GATAACTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAATAACTTAAAATAATCA
Found at i:2335387 original size:145 final size:145
Alignment explanation
Indices: 2335205--2335481 Score: 536
Period size: 145 Copynumber: 1.9 Consensus size: 145
2335195 TTATTCAGCG
*
2335205 ATTTCTTGTTCTTGTTCGTGTTTATTGAATTGAATCTCAACATAAATTTGAAAGAACAATTTATT
1 ATTTCTTGTTCTTGTTAGTGTTTATTGAATTGAATCTCAACATAAATTTGAAAGAACAATTTATT
2335270 GTCATAAGAAGCTGACACTATAATATGTTACAACAAGGATTGTAGGACAAATTAGCAGATCGAAC
66 GTCATAAGAAGCTGACACTATAATATGTTACAACAAGGATTGTAGGACAAATTAGCAGATCGAAC
2335335 AAGGATTGTAGGACA
131 AAGGATTGTAGGACA
*
2335350 ATTTTTTGTTCTTGTTAGTGTTTATTGAATTGAATCTCAACATAAATTTGAAAGAACAATTTATT
1 ATTTCTTGTTCTTGTTAGTGTTTATTGAATTGAATCTCAACATAAATTTGAAAGAACAATTTATT
2335415 GTCATAAGAAGCTGACACTATAATATGTTACAACAAGGATTGTAGGACAAATTAGCAGATCGAAC
66 GTCATAAGAAGCTGACACTATAATATGTTACAACAAGGATTGTAGGACAAATTAGCAGATCGAAC
2335480 AA
131 AA
2335482 AACATTTATG
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 130 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (145 bp):
ATTTCTTGTTCTTGTTAGTGTTTATTGAATTGAATCTCAACATAAATTTGAAAGAACAATTTATT
GTCATAAGAAGCTGACACTATAATATGTTACAACAAGGATTGTAGGACAAATTAGCAGATCGAAC
AAGGATTGTAGGACA
Found at i:2338058 original size:2 final size:2
Alignment explanation
Indices: 2338051--2338112 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
2338041 GTGGTTAACC
2338051 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2338093 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
2338113 CTAACATTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2351698 original size:2 final size:2
Alignment explanation
Indices: 2351691--2351720 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2351681 ACATTACTCC
2351691 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
2351721 TTCAATTCTC
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:2352973 original size:18 final size:18
Alignment explanation
Indices: 2352950--2352995 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2352940 AAATTGTCCT
*
2352950 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
2352968 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
2352985 TATATATATAT
1 TAT-TATATAT
2352996 ATTTTCTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 11 0.48
18 11 0.48
19 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:2353015 original size:38 final size:38
Alignment explanation
Indices: 2352981--2353052 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
2352971 TATAAATTGT
2352981 AAAATATATATAT-ATATTTTCTTTA-AAAATTAAATTC
1 AAAATATATATATAAT-TTTTCTTTACAAAATTAAATTC
* * *
2353018 ATAATATTTATATAATTTTTTTTTACAAAATTAAA
1 AAAATATATATATAATTTTTCTTTACAAAATTAAA
2353053 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 19 0.63
38 11 0.37
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (38 bp):
AAAATATATATATAATTTTTCTTTACAAAATTAAATTC
Found at i:2371553 original size:23 final size:23
Alignment explanation
Indices: 2371523--2371569 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2371513 TTTTTGACTT
2371523 ATTTACTTTTTAAAATACGTACA
1 ATTTACTTTTTAAAATACGTACA
2371546 ATTTACTTTTTAAAATACGTACA
1 ATTTACTTTTTAAAATACGTACA
2371569 A
1 A
2371570 CGTTTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (23 bp):
ATTTACTTTTTAAAATACGTACA
Found at i:2379594 original size:2 final size:2
Alignment explanation
Indices: 2379587--2379613 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2379577 CTAAACTTGA
2379587 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2379614 ATTACCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2386871 original size:19 final size:20
Alignment explanation
Indices: 2386832--2386871 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2386822 TCCTTTTTTC
*
2386832 ACTTTTATAATTTTAATGTT
1 ACTTTTATAATTCTAATGTT
*
2386852 ACTTTTCTAATTCT-ATGTT
1 ACTTTTATAATTCTAATGTT
2386871 A
1 A
2386872 GTTGAATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (20 bp):
ACTTTTATAATTCTAATGTT
Done.