Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 72 of 325
Found at i:25315232 original size:43 final size:43
Alignment explanation
Indices: 25315184--25315269 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
25315174 GAAAGTTTTA
25315184 CCAGTGAACAAATTCAGATATTGACTTCTCATGGTTTCTTTCG
1 CCAGTGAACAAATTCAGATATTGACTTCTCATGGTTTCTTTCG
25315227 CCAGTGAACAAATTCAGATATTGACTTCTCATGGTTTCTTTCG
1 CCAGTGAACAAATTCAGATATTGACTTCTCATGGTTTCTTTCG
25315270 GCTCCCATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (43 bp):
CCAGTGAACAAATTCAGATATTGACTTCTCATGGTTTCTTTCG
Found at i:25322454 original size:12 final size:12
Alignment explanation
Indices: 25322424--25322448 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25322414 AGAAAATGGC
25322424 TGATTTTTTCCT
1 TGATTTTTTCCT
25322436 TGATTTTTTCCT
1 TGATTTTTTCCT
25322448 T
1 T
25322449 TCTTTTCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (12 bp):
TGATTTTTTCCT
Found at i:25327191 original size:49 final size:48
Alignment explanation
Indices: 25327098--25327191 Score: 107
Period size: 49 Copynumber: 1.9 Consensus size: 48
25327088 AGGTGTCTTG
* * * *
25327098 CTTTTTTAATTATAAAATAATGGTTCAATTTTAATTATGATCTTTCAC
1 CTTTTTTAATTATAAAATAATGGCTAAATCTCAATTATGATCTTTCAC
* * * *
25327146 CTTTTTTAATTTATATAATAATTGCTAAATCTCAATTTTGGTCTTT
1 CTTTTTTAA-TTATAAAATAATGGCTAAATCTCAATTATGATCTTT
25327192 ATTGTACACC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
48 9 0.24
49 28 0.76
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (48 bp):
CTTTTTTAATTATAAAATAATGGCTAAATCTCAATTATGATCTTTCAC
Found at i:25332513 original size:29 final size:30
Alignment explanation
Indices: 25332458--25332515 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
25332448 TAATTAATTC
*
25332458 TTAAATTTTTAAAAATAATTTATAATATTT
1 TTAAATTTTAAAAAATAATTTATAATATTT
25332488 TTAAATTTTAAAAAATTAA-TTA-AATATT
1 TTAAATTTTAAAAAA-TAATTTATAATATT
25332516 GACATGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.23
30 17 0.65
31 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TTAAATTTTAAAAAATAATTTATAATATTT
Found at i:25340612 original size:53 final size:53
Alignment explanation
Indices: 25340535--25340642 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
25340525 TGGTAAAATA
25340535 AAATAAAAGAAGAATCCATATAGAATTACACTTCTTTTATTTTATTTTAGAAT
1 AAATAAAAGAAGAATCCATATAGAATTACACTTCTTTTATTTTATTTTAGAAT
25340588 AAATAAAAGAAGAATCCATATAGAATTACACTTCTTTTATTTTATTTTAGAAT
1 AAATAAAAGAAGAATCCATATAGAATTACACTTCTTTTATTTTATTTTAGAAT
25340641 AA
1 AA
25340643 GGTTTTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.39
Consensus pattern (53 bp):
AAATAAAAGAAGAATCCATATAGAATTACACTTCTTTTATTTTATTTTAGAAT
Found at i:25345237 original size:13 final size:13
Alignment explanation
Indices: 25345219--25345247 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
25345209 CTTGTGAAAT
25345219 AATTTAAAATAAA
1 AATTTAAAATAAA
25345232 AATTTAAAATAAA
1 AATTTAAAATAAA
25345245 AAT
1 AAT
25345248 AAAATGTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTTAAAATAAA
Found at i:25345816 original size:24 final size:26
Alignment explanation
Indices: 25345761--25345817 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
25345751 TATTTTAATA
25345761 TTTATTT-TTATGTTTTTAAATGTAT
1 TTTATTTATTATGTTTTTAAATGTAT
* * *
25345786 TTGATTTATTAT-TTTTTTAAT-TTT
1 TTTATTTATTATGTTTTTAAATGTAT
25345810 TTTATTTA
1 TTTATTTA
25345818 ATGAAATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 9 0.33
25 14 0.52
26 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTATTTATTATGTTTTTAAATGTAT
Found at i:25354983 original size:14 final size:14
Alignment explanation
Indices: 25354966--25354997 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25354956 AATTTAAAGA
25354966 AAAATGAATATTGT
1 AAAATGAATATTGT
*
25354980 AAAATGAATGTTGT
1 AAAATGAATATTGT
25354994 AAAA
1 AAAA
25354998 ATCATGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (14 bp):
AAAATGAATATTGT
Found at i:25355366 original size:23 final size:23
Alignment explanation
Indices: 25355319--25355366 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
25355309 CTCATTTATA
*
25355319 AAATATATTTTTACATAATAGTT
1 AAATATATTTTTACATAATAATT
25355342 AAATATATTTTTATCATAA-AATT
1 AAATATATTTTTA-CATAATAATT
25355365 AA
1 AA
25355367 TATGACTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATATATTTTTACATAATAATT
Found at i:25361114 original size:21 final size:21
Alignment explanation
Indices: 25361090--25361129 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25361080 CTATGTGGCT
*
25361090 AAGGGACACGACCGTGTGACC
1 AAGGGAAACGACCGTGTGACC
* *
25361111 AAGGTAAACGCCCGTGTGA
1 AAGGGAAACGACCGTGTGA
25361130 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.25, G:0.33, T:0.12
Consensus pattern (21 bp):
AAGGGAAACGACCGTGTGACC
Found at i:25364782 original size:13 final size:14
Alignment explanation
Indices: 25364754--25364787 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
25364744 ATTTTTCCAA
25364754 AAATAAAATGAAAT
1 AAATAAAATGAAAT
*
25364768 AAATAACAT-AAAT
1 AAATAAAATGAAAT
25364781 AAATAAA
1 AAATAAA
25364788 TGTATATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAAAATGAAAT
Found at i:25378116 original size:13 final size:14
Alignment explanation
Indices: 25378082--25378113 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25378072 AGGGCATGTT
*
25378082 ATTTTAGTTAATGG
1 ATTTTAATTAATGG
25378096 ATTTTAATTAATGG
1 ATTTTAATTAATGG
25378110 ATTT
1 ATTT
25378114 AATGGCTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (14 bp):
ATTTTAATTAATGG
Found at i:25385967 original size:6 final size:6
Alignment explanation
Indices: 25385956--25386012 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
25385946 TCACCGATAA
*
25385956 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATGGAT
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT
*
25386004 ATGGAT ATA
1 ATAGAT ATA
25386013 AATCCATGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (6 bp):
ATAGAT
Found at i:25392698 original size:42 final size:42
Alignment explanation
Indices: 25392640--25392723 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
25392630 CTTTAGTAGG
* *
25392640 CGGTTCCTGGCTACCATCTGCCCCAAAATTCTCAACTTTACC
1 CGGTTCCTGACCACCATCTGCCCCAAAATTCTCAACTTTACC
* * *
25392682 CGGTTCCTGACCACCATCTGCCTCAAATTTCTCATCTTTACC
1 CGGTTCCTGACCACCATCTGCCCCAAAATTCTCAACTTTACC
25392724 TAACTCAGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.38, G:0.11, T:0.31
Consensus pattern (42 bp):
CGGTTCCTGACCACCATCTGCCCCAAAATTCTCAACTTTACC
Found at i:25400543 original size:189 final size:189
Alignment explanation
Indices: 25400223--25400603 Score: 744
Period size: 189 Copynumber: 2.0 Consensus size: 189
25400213 TGAACACTGT
25400223 TGGCCAAAATATAATATTAAGTCTAACTTTTCTTTGTTTAGTTTAATCTCTGGGAAGAGAATTGA
1 TGGCCAAAATATAATATTAAGTCTAACTTTTCTTTGTTTAGTTTAATCTCTGGGAAGAGAATTGA
25400288 ATTTTCCCTGCTATTTCTGGAGGGATAAAGAGTTTCGCTGTTCTGTCATGGATCATTAAGGTCAT
66 ATTTTCCCTGCTATTTCTGGAGGGATAAAGAGTTTCGCTGTTCTGTCATGGATCATTAAGGTCAT
25400353 GGTTAGATGGAGCAGTGCTTCAGGGTTCTATTGATGATGCAATAACGCACTAAAGTGAA
131 GGTTAGATGGAGCAGTGCTTCAGGGTTCTATTGATGATGCAATAACGCACTAAAGTGAA
*
25400412 TGGCCAAAATATAATATTAAGTCTAACTTTTCTTTGTTTAGTTTAATCTCTTGGAAGAGAATTGA
1 TGGCCAAAATATAATATTAAGTCTAACTTTTCTTTGTTTAGTTTAATCTCTGGGAAGAGAATTGA
*
25400477 ATTTTCCCTGCTATTTCTGGAGGGATAAAGAGTTTTGCTGTTCTGTCATGGATCATTAAGGTCAT
66 ATTTTCCCTGCTATTTCTGGAGGGATAAAGAGTTTCGCTGTTCTGTCATGGATCATTAAGGTCAT
25400542 GGTTAGATGGAGCAGTGCTTCAGGGTTCTATTGATGATGCAATAACGCACTAAAGTGAA
131 GGTTAGATGGAGCAGTGCTTCAGGGTTCTATTGATGATGCAATAACGCACTAAAGTGAA
25400601 TGG
1 TGG
25400604 TATAGCTGTT
Statistics
Matches: 190, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 190 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (189 bp):
TGGCCAAAATATAATATTAAGTCTAACTTTTCTTTGTTTAGTTTAATCTCTGGGAAGAGAATTGA
ATTTTCCCTGCTATTTCTGGAGGGATAAAGAGTTTCGCTGTTCTGTCATGGATCATTAAGGTCAT
GGTTAGATGGAGCAGTGCTTCAGGGTTCTATTGATGATGCAATAACGCACTAAAGTGAA
Found at i:25402629 original size:33 final size:33
Alignment explanation
Indices: 25402580--25402677 Score: 108
Period size: 33 Copynumber: 3.0 Consensus size: 33
25402570 TGGAATGTTG
25402580 TTTGCATCTGTATGGTATACTTTTTAAGTTACC
1 TTTGCATCTGTATGGTATACTTTTTAAGTTACC
* * * *
25402613 TTTGGATCTGTCTGGTATGCTTTTTAAGTTATC
1 TTTGCATCTGTATGGTATACTTTTTAAGTTACC
* * * *
25402646 TTT-TATTTTGTATGATATGCTTTTTAAGTTAC
1 TTTGCA-TCTGTATGGTATACTTTTTAAGTTAC
25402678 ATTGTCACAT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 1 0.02
33 54 0.98
ACGTcount: A:0.19, C:0.11, G:0.16, T:0.53
Consensus pattern (33 bp):
TTTGCATCTGTATGGTATACTTTTTAAGTTACC
Found at i:25404687 original size:22 final size:22
Alignment explanation
Indices: 25404662--25404704 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25404652 TAATAAAAAG
25404662 AATATCTACAAAATATTCCTAA
1 AATATCTACAAAATATTCCTAA
* *
25404684 AATATTTACAGAATATTCCTA
1 AATATCTACAAAATATTCCTA
25404705 CACTCCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATCTACAAAATATTCCTAA
Found at i:25408376 original size:22 final size:22
Alignment explanation
Indices: 25408325--25408367 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25408315 TAATAAAAGG
*
25408325 AATATCTACAAAATATTCCTAA
1 AATATTTACAAAATATTCCTAA
*
25408347 AATATTTACAGAATATTCCTA
1 AATATTTACAAAATATTCCTA
25408368 CATTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATTTACAAAATATTCCTAA
Found at i:25421732 original size:18 final size:19
Alignment explanation
Indices: 25421696--25421733 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
25421686 CTAAACCTCT
*
25421696 TAAACTTTTATATTTTTTA
1 TAAACTTTTATATTATTTA
*
25421715 TAAATTTTTA-ATTATTTA
1 TAAACTTTTATATTATTTA
25421733 T
1 T
25421734 TAACATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TAAACTTTTATATTATTTA
Found at i:25424516 original size:46 final size:46
Alignment explanation
Indices: 25424451--25424770 Score: 403
Period size: 46 Copynumber: 7.0 Consensus size: 46
25424441 TTATCTTTAA
* * * *
25424451 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
* * *
25424497 CATGTTGCCATGGTATCTTTCTACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
25424543 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * * *
25424589 CATGCTGCCATAGTATTTTTTAACCATGGTCTTATTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
* * *
25424635 CATGTTGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * *
25424681 CATGTTCCCATGATATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
25424727 CATGTTGCCATAGTATCTTTCAACCATGGTCTTACAT-ATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTCAT
25424771 TTCAGAGAGC
Statistics
Matches: 242, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
45 8 0.03
46 230 0.95
47 4 0.02
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.43
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:25424704 original size:138 final size:138
Alignment explanation
Indices: 25424451--25424761 Score: 460
Period size: 138 Copynumber: 2.3 Consensus size: 138
25424441 TTATCTTTAA
* *
25424451 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT
* ** * * * * **
25424516 TCTACCATGGTCTTATTCTTTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA
66 TCAACCATGGTCTTACACATTTCATATCATGTTCCCATGATATCTTTCAACCATGGTCTTACACA
*
25424581 TTTCATGT
131 TTTCATAT
* * * *
25424589 CATGCTGCCATAGTATTTTTTAACCATGGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT
*
25424654 TCAACTATGGTCTTACACATTTCATATCATGTTCCCATGATATCTTTCAACCATGGTCTTACACA
66 TCAACCATGGTCTTACACATTTCATATCATGTTCCCATGATATCTTTCAACCATGGTCTTACACA
25424719 TTTCATAT
131 TTTCATAT
*
25424727 CATGTTGCCATAGTATCTTTCAACCATGGTCTTAC
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTAC
25424762 ATATTTCATT
Statistics
Matches: 152, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 152 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.43
Consensus pattern (138 bp):
CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTCATATCATGTTCCCATGATATCTTTCAACCATGGTCTTACACA
TTTCATAT
Found at i:25424768 original size:21 final size:21
Alignment explanation
Indices: 25424698--25424769 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
25424688 CCATGATATC
*
25424698 TTTCAACCATGGTCTTACACA
1 TTTCAACCATGGTCTTACATA
* * * * *
25424719 TTTCATATCATGTTGCCATAGTATC
1 TTTCA-ACCATG--GTCTTA-CATA
25424744 TTTCAACCATGGTCTTACATA
1 TTTCAACCATGGTCTTACATA
25424765 TTTCA
1 TTTCA
25424770 TTTCAGAGAG
Statistics
Matches: 36, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 12 0.33
22 9 0.25
24 9 0.25
25 6 0.17
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (21 bp):
TTTCAACCATGGTCTTACATA
Found at i:25426609 original size:11 final size:11
Alignment explanation
Indices: 25426593--25426640 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
25426583 CTTTATATAC
25426593 TAATAAAATAA
1 TAATAAAATAA
*
25426604 TAATAAAATATCT
1 TAATAAAATA--A
* *
25426617 TATTAAAATAT
1 TAATAAAATAA
25426628 TAATAAAATAA
1 TAATAAAATAA
25426639 TA
1 TA
25426641 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:25427301 original size:22 final size:25
Alignment explanation
Indices: 25427245--25427305 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 25
25427235 TACATTAAAC
25427245 ATTCAATTCACATTCATGTCACATAA
1 ATTCAATTCA-ATTCATGTCACATAA
25427271 ATATACAATTCAATTCAT-TCA-AT-A
1 AT-T-CAATTCAATTCATGTCACATAA
25427295 ATTCAATTCAA
1 ATTCAATTCAA
25427306 GCTGCACGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 8 0.24
23 1 0.03
24 3 0.09
25 2 0.06
26 5 0.15
27 7 0.21
28 7 0.21
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.36
Consensus pattern (25 bp):
ATTCAATTCAATTCATGTCACATAA
Found at i:25433598 original size:30 final size:31
Alignment explanation
Indices: 25433543--25433601 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
25433533 CACCCTTAAA
* * *
25433543 ATATTTGCACTATTAGTCCTTCAAATTTTTC
1 ATATTTACACTATTAGCCCCTCAAATTTTTC
25433574 ATATTTACACT-TTAGCCCCTCAAATTTT
1 ATATTTACACTATTAGCCCCTCAAATTTT
25433602 GAGTATATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (31 bp):
ATATTTACACTATTAGCCCCTCAAATTTTTC
Found at i:25433931 original size:33 final size:33
Alignment explanation
Indices: 25433883--25433945 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
25433873 GATCAGAAGA
*
25433883 CAAAAACACTGGTAAAGGGTTTAGATTTGATGG
1 CAAAAACACTAGTAAAGGGTTTAGATTTGATGG
*
25433916 CAAAGACACTAGTAAAGGGTTTAGATTTGA
1 CAAAAACACTAGTAAAGGGTTTAGATTTGA
25433946 AGATGAAGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (33 bp):
CAAAAACACTAGTAAAGGGTTTAGATTTGATGG
Found at i:25433956 original size:33 final size:33
Alignment explanation
Indices: 25433878--25433948 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
25433868 ACTTGGATCA
* *
25433878 GAAGACAAAAACACTGGTAAAGGGTTTAGATTT
1 GAAGACAAAGACACTAGTAAAGGGTTTAGATTT
* *
25433911 GATGGCAAAGACACTAGTAAAGGGTTTAGATTT
1 GAAGACAAAGACACTAGTAAAGGGTTTAGATTT
25433944 GAAGA
1 GAAGA
25433949 TGAAGACATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (33 bp):
GAAGACAAAGACACTAGTAAAGGGTTTAGATTT
Found at i:25439785 original size:87 final size:87
Alignment explanation
Indices: 25439639--25439820 Score: 319
Period size: 87 Copynumber: 2.1 Consensus size: 87
25439629 CTTCATTACA
* *
25439639 ACTTCGTCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
1 ACTTCATCGACAGTGGAACCATTCTCCCCAACGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
*
25439704 GTCATGGCTTGGCGTATCTTCG
66 GCCATGGCTTGGCGTATCTTCG
*
25439726 ACTTCATCGACAGTGGAACCATTCTCCCCAACGAACTCGACCTCAGTAGCCTTTCTTTTGGCAAT
1 ACTTCATCGACAGTGGAACCATTCTCCCCAACGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
*
25439791 GCCATGGCTTGGCGTCTCTTCG
66 GCCATGGCTTGGCGTATCTTCG
25439813 ACTTCATC
1 ACTTCATC
25439821 TTCCGAACTG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 90 1.00
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.30
Consensus pattern (87 bp):
ACTTCATCGACAGTGGAACCATTCTCCCCAACGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
GCCATGGCTTGGCGTATCTTCG
Found at i:25442298 original size:4 final size:4
Alignment explanation
Indices: 25442289--25442313 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25442279 ATTAGGTATT
25442289 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
25442314 GGTTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:25452544 original size:31 final size:31
Alignment explanation
Indices: 25452478--25452550 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
25452468 TTCAAAATGG
* * * * *
25452478 TCAAATAAAGGCCAAATCTTTTTTTAAAGTGC
1 TCAAAT-AAGGACAAAACTTTTTTAAAAATAC
25452510 TCAAATAAGGACAAAACTTTTTTAAAAATAC
1 TCAAATAAGGACAAAACTTTTTTAAAAATAC
*
25452541 TCAAGTAAGG
1 TCAAATAAGG
25452551 GCTTTTCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 29 0.83
32 6 0.17
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (31 bp):
TCAAATAAGGACAAAACTTTTTTAAAAATAC
Found at i:25459940 original size:18 final size:18
Alignment explanation
Indices: 25459913--25459947 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25459903 ACTTTGAAAT
* *
25459913 TCACTTCACTTCAATATA
1 TCACTACACTTAAATATA
25459931 TCACTACACTTAAATAT
1 TCACTACACTTAAATAT
25459948 GTTATTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (18 bp):
TCACTACACTTAAATATA
Found at i:25460856 original size:11 final size:11
Alignment explanation
Indices: 25460840--25460870 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
25460830 AATATCTTAA
*
25460840 TAAAATATTAT
1 TAAAATAATAT
25460851 TAAAATAATAT
1 TAAAATAATAT
25460862 TAAAATAAT
1 TAAAATAAT
25460871 TCCACCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:25477961 original size:23 final size:23
Alignment explanation
Indices: 25477904--25478054 Score: 62
Period size: 23 Copynumber: 6.5 Consensus size: 23
25477894 GAGCCATATT
* *
25477904 GGTAAGCTCCTCTTGAGCTGATGAAC
1 GGTAAGCTCC-ATTAAGCTGA--AAC
*
25477930 AGTAAGCTCCATTAAGCTGAAAC
1 GGTAAGCTCCATTAAGCTGAAAC
* ** *
25477953 GGTAAGCTCTATCGAGCTG-ACC
1 GGTAAGCTCCATTAAGCTGAAAC
*
25477975 AGTAAGCT-CA-TACGAGCTGAAAC
1 GGTAAGCTCCATTA--AGCTGAAAC
* * * * *
25477998 GATAAGGTCTAATGAA-CTGAAAA
1 GGTAAGCTC-CATTAAGCTGAAAC
*
25478021 AGTAAGCT-CA-TACGAGCTGAAAC
1 GGTAAGCTCCATTA--AGCTGAAAC
25478044 GGTAAGCTCCA
1 GGTAAGCTCCA
25478055 ATGAGTTGAA
Statistics
Matches: 89, Mismatches: 26, Indels: 22
0.65 0.19 0.16
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 15 0.17
23 49 0.55
24 3 0.03
25 9 0.10
26 10 0.11
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (23 bp):
GGTAAGCTCCATTAAGCTGAAAC
Found at i:25477982 original size:45 final size:45
Alignment explanation
Indices: 25477927--25478058 Score: 144
Period size: 46 Copynumber: 2.9 Consensus size: 45
25477917 TGAGCTGATG
*
25477927 AACAGTAAGCTCCATTA-AGCTGAAACGGTAAGCTCT-ATCGAGCTG-
1 AACAGTAAGCT-CA-TACAGCTGAAACGGTAAGCTCTAAT-GAACTGA
* * *
25477972 ACCAGTAAGCTCATACGAGCTGAAACGATAAGGTCTAATGAACTGA
1 AACAGTAAGCTCATAC-AGCTGAAACGGTAAGCTCTAATGAACTGA
* *
25478018 AAAAGTAAGCTCATACGAGCTGAAACGGTAAGCTCCAATGA
1 AACAGTAAGCTCATAC-AGCTGAAACGGTAAGCTCTAATGA
25478059 GTTGAAAACA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
43 2 0.03
44 2 0.03
45 32 0.43
46 38 0.51
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (45 bp):
AACAGTAAGCTCATACAGCTGAAACGGTAAGCTCTAATGAACTGA
Found at i:25478030 original size:46 final size:47
Alignment explanation
Indices: 25477974--25478089 Score: 153
Period size: 46 Copynumber: 2.5 Consensus size: 47
25477964 TCGAGCTGAC
* *
25477974 CAGTAAGCTCATACGAGCTGAAACGATAAGGTCTAATGAACTGAAAA
1 CAGTAAGCTCATACGAGCTGAAACGATAAGCTCCAATGAACTGAAAA
* **
25478021 -AGTAAGCTCATACGAGCTGAAACGGTAAGCTCCAATGAGTTGAAAA
1 CAGTAAGCTCATACGAGCTGAAACGATAAGCTCCAATGAACTGAAAA
* * *
25478067 CAATAATCTCATACGAGTTGAAA
1 CAGTAAGCTCATACGAGCTGAAA
25478090 TATCGGTAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 41 0.68
47 19 0.32
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (47 bp):
CAGTAAGCTCATACGAGCTGAAACGATAAGCTCCAATGAACTGAAAA
Found at i:25478804 original size:17 final size:18
Alignment explanation
Indices: 25478784--25478817 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25478774 AAGTGAATTG
25478784 AAATTGC-GAAATTAAAT
1 AAATTGCAGAAATTAAAT
25478801 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
25478818 ATGAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:25479553 original size:10 final size:10
Alignment explanation
Indices: 25479546--25479583 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
25479536 AGATAAATAC
25479546 AAATAAAT-A
1 AAATAAATGA
25479555 AAGATAAATGA
1 AA-ATAAATGA
25479566 AAATAAATGA
1 AAATAAATGA
25479576 AAATAAAT
1 AAATAAAT
25479584 CCTAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 2 0.07
10 22 0.81
11 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (10 bp):
AAATAAATGA
Found at i:25479557 original size:20 final size:21
Alignment explanation
Indices: 25479534--25479583 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
25479524 TGAAATTCTA
25479534 AAAGATAAAT-ACAAATAAAT-
1 AAAGATAAATGA-AAATAAATG
25479554 AAAGATAAATGAAAATAAATG
1 AAAGATAAATGAAAATAAATG
25479575 AAA-ATAAAT
1 AAAGATAAAT
25479584 CCTAAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (21 bp):
AAAGATAAATGAAAATAAATG
Found at i:25480418 original size:96 final size:97
Alignment explanation
Indices: 25480248--25480429 Score: 267
Period size: 96 Copynumber: 1.9 Consensus size: 97
25480238 TTTTATTTTA
* * * * *
25480248 TTTATTTTTATTTAGGAATATATTGAACCTTTTGACGCCAAGAGAGATGACAGCCAAGGACCCCA
1 TTTATTTTTATTTAAGAACATATCGAACCTTTTGACGCCAAGAGAGATGACAGCAAAGCACCCCA
*
25480313 CCCCGGTTACTCAACCCAACATACTCCTAATT
66 ACCCGGTTACTCAACCCAACATACTCCTAATT
* *
25480345 TTTATTTTT-TTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCAAAGCACCTCA
1 TTTATTTTTATTTAAGAACATATCGAACCTTTTGACGCCAAGAGAGATGACAGCAAAGCACCCCA
* *
25480409 ACCCTGTTACTCAGCCCAACA
66 ACCCGGTTACTCAACCCAACA
25480430 CATTCTTAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
96 66 0.88
97 9 0.12
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (97 bp):
TTTATTTTTATTTAAGAACATATCGAACCTTTTGACGCCAAGAGAGATGACAGCAAAGCACCCCA
ACCCGGTTACTCAACCCAACATACTCCTAATT
Found at i:25481116 original size:15 final size:14
Alignment explanation
Indices: 25481096--25481160 Score: 71
Period size: 15 Copynumber: 4.5 Consensus size: 14
25481086 TTAATATCTG
25481096 AAAATAATAAATAAT
1 AAAATAATAAA-AAT
*
25481111 AAAATAATAAGAA-
1 AAAATAATAAAAAT
25481124 AAAATAAATAAAAAT
1 AAAAT-AATAAAAAT
25481139 AAAATAA-ACTAAAAT
1 AAAATAATA--AAAAT
25481154 AAAATAA
1 AAAATAA
25481161 AAATAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
13 6 0.14
14 11 0.25
15 27 0.61
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (14 bp):
AAAATAATAAAAAT
Found at i:25481143 original size:11 final size:11
Alignment explanation
Indices: 25481101--25481168 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
25481091 ATCTGAAAAT
25481101 AATAAATAATAA
1 AATAAA-AATAA
* *
25481113 AATAATAAGAA
1 AATAAAAATAA
25481124 AA-AATAAATAA
1 AATAA-AAATAA
25481135 AA-ATAAAATAA
1 AATA-AAAATAA
*
25481146 ACT-AAAATAA
1 AATAAAAATAA
25481156 AATAAAAATAA
1 AATAAAAATAA
25481167 AA
1 AA
25481169 ATTGGGTCGC
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
10 11 0.24
11 29 0.63
12 6 0.13
ACGTcount: A:0.78, C:0.01, G:0.01, T:0.19
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:25481144 original size:5 final size:5
Alignment explanation
Indices: 25481108--25481168 Score: 59
Period size: 5 Copynumber: 11.4 Consensus size: 5
25481098 AATAATAAAT
* * *
25481108 AATAA AATAA TAAGAA AAAATA AATAAA AATAA AATAA ACTAA AATAA
1 AATAA AATAA -AATAA AATA-A AAT-AA AATAA AATAA AATAA AATAA
25481156 AATAAA AATAA AA
1 AAT-AA AATAA AA
25481169 ATTGGGTCGC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
5 30 0.64
6 16 0.34
7 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:25481144 original size:25 final size:25
Alignment explanation
Indices: 25481095--25481168 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
25481085 ATTAATATCT
*
25481095 GAAAATAATAAATAATAAA-ATAATAA
1 GAAAA-AATAAATAA-AAATAAAATAA
25481121 GAAAAAATAAATAAAAATAAAATAA
1 GAAAAAATAAATAAAAATAAAATAA
*
25481146 -ACTAAAATAAAATAAAAATAAAA
1 GA-AAAAAT-AAATAAAAATAAAA
25481169 ATTGGGTCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.09
25 20 0.47
26 19 0.44
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (25 bp):
GAAAAAATAAATAAAAATAAAATAA
Found at i:25484159 original size:17 final size:18
Alignment explanation
Indices: 25484139--25484172 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25484129 AAGTTAATTG
25484139 AAATTGCA-AAATTAAAT
1 AAATTGCAGAAATTAAAT
*
25484156 AAATTGTAGAAATTAAA
1 AAATTGCAGAAATTAAA
25484173 ATGAGGAAAA
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:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:25484910 original size:10 final size:10
Alignment explanation
Indices: 25484897--25484930 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
25484887 AAGATAAAAA
25484897 AAATAAAGAT
1 AAATAAAGAT
25484907 AAATAAAGAT
1 AAATAAAGAT
25484917 AAATGAAA-AT
1 AAAT-AAAGAT
25484927 AAAT
1 AAAT
25484931 CCTAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 20 0.87
11 3 0.13
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (10 bp):
AAATAAAGAT
Found at i:25484918 original size:16 final size:16
Alignment explanation
Indices: 25484886--25484929 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
25484876 TGAAATTCTA
25484886 AAAGATAAA-AAAAAT
1 AAAGATAAATAAAAAT
*
25484901 AAAGATAAATAAAGAT
1 AAAGATAAATAAAAAT
25484917 AAATGA-AAATAAA
1 AAA-GATAAATAAA
25484930 TCCTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.35
16 15 0.58
17 2 0.08
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (16 bp):
AAAGATAAATAAAAAT
Found at i:25488695 original size:34 final size:34
Alignment explanation
Indices: 25488651--25488727 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
25488641 TTTCGTTATT
* *
25488651 TTTACCAAATTAAGCATTTAAACGGTGAAATTTC
1 TTTACGAAATTAAGCATTTAAACGGTAAAATTTC
25488685 TTTACGAAATTAAGCATTTAAACGGTAAAATTTC
1 TTTACGAAATTAAGCATTTAAACGGTAAAATTTC
25488719 TTTACGAAA
1 TTTACGAAA
25488728 CTTTCACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (34 bp):
TTTACGAAATTAAGCATTTAAACGGTAAAATTTC
Found at i:25491731 original size:16 final size:18
Alignment explanation
Indices: 25491706--25491747 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
25491696 AGCCAATTTC
*
25491706 AACCACTCAA-CA-ATTA
1 AACCATTCAATCACATTA
25491722 AACCATTCAATCACATTA
1 AACCATTCAATCACATTA
*
25491740 AATCATTC
1 AACCATTC
25491748 TCCAAGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 2 0.09
18 11 0.50
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (18 bp):
AACCATTCAATCACATTA
Found at i:25495661 original size:12 final size:12
Alignment explanation
Indices: 25495644--25495668 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25495634 GTTTATGCCA
25495644 AGTTTAAGTTTG
1 AGTTTAAGTTTG
25495656 AGTTTAAGTTTG
1 AGTTTAAGTTTG
25495668 A
1 A
25495669 ATTTTAGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (12 bp):
AGTTTAAGTTTG
Found at i:25496858 original size:13 final size:13
Alignment explanation
Indices: 25496840--25496868 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
25496830 CTCTCTAAAC
25496840 GTACAAGATATTA
1 GTACAAGATATTA
25496853 GTACAAGATATTA
1 GTACAAGATATTA
25496866 GTA
1 GTA
25496869 ACTAAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (13 bp):
GTACAAGATATTA
Found at i:25504558 original size:5 final size:5
Alignment explanation
Indices: 25504548--25504583 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
25504538 CTGTGTGTTC
25504548 TTTAT TTTA- TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
25504584 CATAAATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:25504562 original size:9 final size:9
Alignment explanation
Indices: 25504548--25504583 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
25504538 CTGTGTGTTC
25504548 TTTATTTTA
1 TTTATTTTA
25504557 TTTATTTTA
1 TTTATTTTA
25504566 TTTATTTTA
1 TTTATTTTA
25504575 TTTTATTTT
1 -TTTATTTT
25504584 CATAAATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:25504567 original size:14 final size:15
Alignment explanation
Indices: 25504548--25504583 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
25504538 CTGTGTGTTC
25504548 TTTATTTTA-TTTAT
1 TTTATTTTATTTTAT
25504562 TTTA-TTTATTTTAT
1 TTTATTTTATTTTAT
25504576 TTTATTTT
1 TTTATTTT
25504584 CATAAATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 13 0.65
15 3 0.15
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:25508828 original size:50 final size:50
Alignment explanation
Indices: 25508753--25508928 Score: 253
Period size: 50 Copynumber: 3.5 Consensus size: 50
25508743 TATGGCAACC
25508753 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGAA
1 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGAA
** * *
25508803 AGTGATAAGCAATAGCTTCAGCTACACTTATCTGATCAAAGATAAGTGAA
1 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGAA
* * * *
25508853 AGTGATAAGTGATAGCTTCGGCTACGCTTATCAGATCAAGGACAAATGACA
1 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGA-A
* *
25508904 AGTGAAAAGTGGTAGCTTCGGCTAC
1 AGTGATAAGTGATAGCTTCGGCTAC
25508929 CTGATCAGTG
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 87 0.78
51 24 0.22
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (50 bp):
AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGAA
Found at i:25508942 original size:31 final size:31
Alignment explanation
Indices: 25508904--25509052 Score: 228
Period size: 31 Copynumber: 4.8 Consensus size: 31
25508894 ACAAATGACA
25508904 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
25508935 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
25508966 AGTGAAAAGTGGTAGCTTCGACTACCTGATT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
25508997 AGTGAAAAATGGTAG-TTCTGGGTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTGATC
* *
25509028 AGTGAATAGTGGTAGCTTCGACTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
25509053 AAGTGACAAG
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
30 3 0.03
31 100 0.94
32 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:25509268 original size:49 final size:48
Alignment explanation
Indices: 25509193--25509324 Score: 168
Period size: 49 Copynumber: 2.9 Consensus size: 48
25509183 CTATGGCATC
* *
25509193 GATATGTGATCCGTGTAAGACCATAGCTGGGCTATGACATCGATATGT
1 GATATGTGATACGTGTAAGACCATAGCTGGGCTATGACATCGATATAT
* *
25509241 GATATGTGATTACGTGTAAGACTATAGCTGGGCTATGGCATCGATATAT
1 GATATGTGA-TACGTGTAAGACCATAGCTGGGCTATGACATCGATATAT
*
25509290 GA-A--T-AT--GTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGATACGTGTAAGACCATAGCTGGGCTATGACATC
25509325 ATTATGTGAA
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
42 28 0.36
44 1 0.01
45 1 0.01
46 1 0.01
48 10 0.13
49 37 0.47
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (48 bp):
GATATGTGATACGTGTAAGACCATAGCTGGGCTATGACATCGATATAT
Found at i:25509300 original size:42 final size:43
Alignment explanation
Indices: 25509166--25509368 Score: 191
Period size: 42 Copynumber: 4.7 Consensus size: 43
25509156 GGTAATTCGA
* * ***
25509166 GTAAGACCATAGTTGGGCTATGGCATCGA-TATGTG-ATCCGT
1 GTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGATGT
* *
25509207 GTAAGACCATAGCTGGGCTATGACATCGATATGTGATATG-TGATTACGT
1 GTAAGACCATAGCTGGGCTATGGCATCG--AT-T-ATATGAAGA-T--GT
* *
25509256 GTAAGACTATAGCTGGGCTATGGCATCGA-TATATGAATATGT
1 GTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGATGT
*
25509298 GTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGATGT
1 GTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGATGT
* **
25509340 GTAAGACCATAGTTGAACTATGGCATCGA
1 GTAAGACCATAGCTGGGCTATGGCATCGA
25509369 GAAAACGAAG
Statistics
Matches: 134, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
41 27 0.20
42 63 0.47
43 2 0.01
44 6 0.04
45 3 0.02
46 4 0.03
47 1 0.01
49 28 0.21
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (43 bp):
GTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGATGT
Found at i:25509331 original size:91 final size:88
Alignment explanation
Indices: 25509121--25509333 Score: 266
Period size: 91 Copynumber: 2.4 Consensus size: 88
25509111 TGCTACTATA
* * * * *
25509121 TAAGACCATATCTGGGATATGGCATCA-GTGAGATAGGTAATTCGAGTAAGACCATAGTTGGGCT
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATAGGTAATTCGAGTAAGACCATAGCTGGGCT
* *
25509185 ATGGCATCGATATGTGATCCGTG
66 ATGGCATCGATATATGATACGTG
* * * * *
25509208 TAAGACCATAGCTGGGCTATGACATCGATATGTGATATGTGATTACGTGTAAGACTATAGCTGGG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATAGGTAATT-CGAGTAAGACCATAGCTGGG
*
25509273 CTATGGCATCGATATATGAATATGTG
64 CTATGGCATCGATATATG-ATACGTG
25509299 TAAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
25509334 AGATGTGTAA
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
87 23 0.21
88 1 0.01
89 11 0.10
90 35 0.33
91 37 0.35
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (88 bp):
TAAGACCATAGCTGGGCTATGGCATCATATGTGATAGGTAATTCGAGTAAGACCATAGCTGGGCT
ATGGCATCGATATATGATACGTG
Found at i:25512201 original size:19 final size:20
Alignment explanation
Indices: 25512155--25512195 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
25512145 AAAAGCAGGG
25512155 AAAGAAAGAAAGAAAGGAGA
1 AAAGAAAGAAAGAAAGGAGA
25512175 AAAGAAAG-AAGAAAGG-GA
1 AAAGAAAGAAAGAAAGGAGA
25512193 AAA
1 AAA
25512196 TTAAAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAGGAGA
Found at i:25512899 original size:53 final size:53
Alignment explanation
Indices: 25512836--25512956 Score: 197
Period size: 53 Copynumber: 2.3 Consensus size: 53
25512826 TACTGTTACC
*
25512836 GTTACTGTTACTGTTTCAGATTTGTTCTGATGAGGTACTCTGTGTACCGTAAT
1 GTTACTGTTACTGTTTCAGATTTGTTCCGATGAGGTACTCTGTGTACCGTAAT
* * *
25512889 GTTAATGTTACTGTTTCGGATTTGTTCCGATGAGGTACTCTGTGTACCGTACT
1 GTTACTGTTACTGTTTCAGATTTGTTCCGATGAGGTACTCTGTGTACCGTAAT
*
25512942 GCTACTGTTACTGTT
1 GTTACTGTTACTGTT
25512957 ACTGTTCCGG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (53 bp):
GTTACTGTTACTGTTTCAGATTTGTTCCGATGAGGTACTCTGTGTACCGTAAT
Found at i:25513340 original size:18 final size:18
Alignment explanation
Indices: 25513067--25513344 Score: 159
Period size: 18 Copynumber: 15.1 Consensus size: 18
25513057 AAAGGTATAA
*
25513067 AATAACTGATTATTACTG
1 AATAACTGATTGTTACTG
* * *
25513085 AATAATTGACTGTTACCG
1 AATAACTGATTGTTACTG
* * *
25513103 GATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* * *
25513121 GAT-ATTAGACTGTTACTG
1 AATAACT-GATTGTTACTG
* *
25513139 AATAACTGAATATTACTG
1 AATAACTGATTGTTACTG
*
25513157 AATAACTGATTGTCACTG
1 AATAACTGATTGTTACTG
* * *
25513175 AATGAA-TAACTATTACTG
1 AAT-AACTGATTGTTACTG
*
25513193 AATAACCTAATTGTTACTG
1 AATAA-CTGATTGTTACTG
*
25513212 AATATCTGATT-TTACTG
1 AATAACTGATTGTTACTG
* *
25513229 AATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
25513247 GATAACCAATCAATTGATCGATACTG
1 AATAA-C--T-GATTG-T---TACTG
* * *
25513273 AATAACTGGTTATTATTG
1 AATAACTGATTGTTACTG
* *
25513291 AATAATTGATTGTTACCG
1 AATAACTGATTGTTACTG
*
25513309 AATAACTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
25513327 AATAAATAATTGTT-CTG
1 AATAACTGATTGTTACTG
25513344 A
1 A
25513345 GTGTTAATGA
Statistics
Matches: 202, Mismatches: 44, Indels: 29
0.73 0.16 0.11
Matches are distributed among these distances:
17 23 0.11
18 142 0.70
19 18 0.09
21 2 0.01
22 5 0.02
23 2 0.01
25 1 0.00
26 9 0.04
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:25516153 original size:63 final size:63
Alignment explanation
Indices: 25516054--25516179 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
25516044 CGAAAGTTGT
25516054 GTTCTATTAGCTAAAGGTGCTAAATAGTTATAGAACTTTAATGTAGAGGTCCTTATTGAGTAA
1 GTTCTATTAGCTAAAGGTGCTAAATAGTTATAGAACTTTAATGTAGAGGTCCTTATTGAGTAA
25516117 GTTCTATTAGCTAAAGGTGCTAAATAGTTATAGAACTTTAATGTAGAGGTCCTTATTGAGTAA
1 GTTCTATTAGCTAAAGGTGCTAAATAGTTATAGAACTTTAATGTAGAGGTCCTTATTGAGTAA
25516180 TTAGACCACT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37
Consensus pattern (63 bp):
GTTCTATTAGCTAAAGGTGCTAAATAGTTATAGAACTTTAATGTAGAGGTCCTTATTGAGTAA
Found at i:25517970 original size:208 final size:208
Alignment explanation
Indices: 25517612--25518038 Score: 759
Period size: 208 Copynumber: 2.1 Consensus size: 208
25517602 GGTAAGATGT
*
25517612 ATTTAATAGTCATACGAACTTACTAAGCTTAATTACTTACTTTGTTTATGTTTTCTGTGTTTTAT
1 ATTTAATAGTCATACGAACTGACTAAGCTTAATTACTTACTTTGTTTATGTTTTCTGTGTTTTAT
* *
25517677 AGTATTTTGGAAGCACTCGTTTCGGAAGCCGTCAGAGATCGTGCCACACTATCAAACTCTTATTT
66 AGTATTTTGGAAGCACTCGGTTCGGAAGCCGTCAGAGATCATGCCACACTATCAAACTCTTATTT
*
25517742 TGGCATTTTAGACTTTACATTTTGGGTTAAATGGCATGTATAGGTATTTTGGCTAATATGGCGTA
131 TGGCATTTTAGACTTTACATTTTGGGTTAAATGGCATGTATAGGTATTTTGGCTAATATGGCCTA
25517807 TATGTCTTGTTGA
196 TATGTCTTGTTGA
*
25517820 ATTTAATAGTCATACGAACTGACTAAGCTTAATTGCTTACTTTGTTTATGTTTTCTGTGTTTTAT
1 ATTTAATAGTCATACGAACTGACTAAGCTTAATTACTTACTTTGTTTATGTTTTCTGTGTTTTAT
*
25517885 AGTATTTTGGAAGCGCTCGGTTCGGAAGCCGTCAGAGATCATGCCACACTATCAAACTCTTATTT
66 AGTATTTTGGAAGCACTCGGTTCGGAAGCCGTCAGAGATCATGCCACACTATCAAACTCTTATTT
* * *
25517950 TGGTATTTTGGACTTTACATTTTGGGTTAAATGGCATGTATTGGTATTTTGGCTAATATGGCCTA
131 TGGCATTTTAGACTTTACATTTTGGGTTAAATGGCATGTATAGGTATTTTGGCTAATATGGCCTA
25518015 TATGTCTTGTTGA
196 TATGTCTTGTTGA
25518028 ATTT--TAGTCAT
1 ATTTAATAGTCAT
25518039 TTGTTTTGGC
Statistics
Matches: 210, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
206 7 0.03
208 203 0.97
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.42
Consensus pattern (208 bp):
ATTTAATAGTCATACGAACTGACTAAGCTTAATTACTTACTTTGTTTATGTTTTCTGTGTTTTAT
AGTATTTTGGAAGCACTCGGTTCGGAAGCCGTCAGAGATCATGCCACACTATCAAACTCTTATTT
TGGCATTTTAGACTTTACATTTTGGGTTAAATGGCATGTATAGGTATTTTGGCTAATATGGCCTA
TATGTCTTGTTGA
Found at i:25520678 original size:34 final size:32
Alignment explanation
Indices: 25520594--25520678 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 32
25520584 CCATGACAAT
* *
25520594 ATTTATAA-GTAAGACCATAGCTGGGCTATGCC
1 ATTT-TAACGTAAGACCATAACTGGGCTATGAC
* * *
25520626 ATTTTAATGAAAAGACCATAACTGGGTTATGAC
1 ATTTTAACG-TAAGACCATAACTGGGCTATGAC
25520659 ACTTTTGAACGTAAGACCAT
1 A-TTTT-AACGTAAGACCAT
25520679 GGTTGGACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
31 3 0.07
32 5 0.12
33 20 0.47
34 12 0.28
35 3 0.07
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (32 bp):
ATTTTAACGTAAGACCATAACTGGGCTATGAC
Found at i:25520743 original size:102 final size:101
Alignment explanation
Indices: 25520567--25520797 Score: 293
Period size: 102 Copynumber: 2.3 Consensus size: 101
25520557 GAATTGACGG
* * *
25520567 GTAAGACTATGGTTGGACCATGACAATATTTATAAGTAAGACCATAGCTGGGCTATGCCATTTTA
1 GTAAGACTATGGTTGGACCATGACAATATTTATAAGTAAGAACATAGCTGAGCTATGCCATTCTA
*
25520632 ATGAAAAGACCATAACTGGGTTATGACACTTTTGAAC
66 ATGAAAAGACCATAACTGGGTTATGACAC-TATGAAC
* * * * *
25520669 GTAAGACCATGGTTGGACCAT-AGTAGTATTTATAAGTAAGAACATAGTTGAGCTATGGCATTCT
1 GTAAGACTATGGTTGGACCATGA-CAATATTTATAAGTAAGAACATAGCTGAGCTATGCCATTCT
* * * *
25520733 GATGATAAGACCATAACTGGGTTATGGCACTATGAAT
65 AATGAAAAGACCATAACTGGGTTATGACACTATGAAC
* * *
25520770 GTAAAACTATGGTTGGGCCATGGCAATA
1 GTAAGACTATGGTTGGACCATGACAATA
25520798 CATGTGTAAG
Statistics
Matches: 108, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
101 27 0.25
102 81 0.75
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (101 bp):
GTAAGACTATGGTTGGACCATGACAATATTTATAAGTAAGAACATAGCTGAGCTATGCCATTCTA
ATGAAAAGACCATAACTGGGTTATGACACTATGAAC
Found at i:25531736 original size:53 final size:53
Alignment explanation
Indices: 25531671--25531775 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
25531661 TGTTTGAGTT
* *
25531671 TATTTATTTGCATAATGCAATATTGGTAGTTGTACTTGTAGTTATTCTAAGTC
1 TATTTATTTGCATAATGCAATATTGGCAGTTATACTTGTAGTTATTCTAAGTC
*
25531724 TATTTATTTGCATATTGCAATATTGGCAGTTATACTTGTAGTTATTCTAAGT
1 TATTTATTTGCATAATGCAATATTGGCAGTTATACTTGTAGTTATTCTAAGT
25531776 AAAGCAATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.48
Consensus pattern (53 bp):
TATTTATTTGCATAATGCAATATTGGCAGTTATACTTGTAGTTATTCTAAGTC
Found at i:25534099 original size:19 final size:20
Alignment explanation
Indices: 25534075--25534149 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 20
25534065 TATTTACTTA
25534075 ATATTTAA-AAATTAAAAAT
1 ATATTTAACAAATTAAAAAT
* *
25534094 ATATTTAACAAATATACTTAATT
1 ATATTTAACAAAT-TA--AAAAT
25534117 AATATTTAA-AAATTAAAAAT
1 -ATATTTAACAAATTAAAAAT
*
25534137 ATATTTAAGAAAT
1 ATATTTAACAAAT
25534150 CTGCGGATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 16 0.35
20 11 0.24
21 2 0.04
22 2 0.04
23 7 0.15
24 8 0.17
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (20 bp):
ATATTTAACAAATTAAAAAT
Found at i:25535034 original size:24 final size:24
Alignment explanation
Indices: 25535002--25535057 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
25534992 CAGAGAACAG
25535002 GAAGGTGGCAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
25535026 GAAGGTGGCAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
25535050 GAAGGTGG
1 GAAGGTGG
25535058 AAACAAGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.43, C:0.11, G:0.38, T:0.09
Consensus pattern (24 bp):
GAAGGTGGCAAGAGTAAGACACAA
Found at i:25552126 original size:2 final size:2
Alignment explanation
Indices: 25552119--25552159 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
25552109 ATGAATGCTC
* * *
25552119 AG AG AG AG AG AG AG AG AG AG AG GG AA AG GG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
25552160 ACCAGAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25556635 original size:20 final size:20
Alignment explanation
Indices: 25556595--25556634 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25556585 TTATGTATTA
*
25556595 TGTTCTTTTGAAATTCATTT
1 TGTTATTTTGAAATTCATTT
*
25556615 TGTTATTTTTAAATTC-TTT
1 TGTTATTTTGAAATTCATTT
25556634 T
1 T
25556635 TCAATGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.65
Consensus pattern (20 bp):
TGTTATTTTGAAATTCATTT
Found at i:25560545 original size:42 final size:42
Alignment explanation
Indices: 25560486--25560569 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
25560476 CAAGAAGATG
25560486 ATAGAAAAAAGGATGGAGGGATAAATGAAAGCTTGCTTCTAT
1 ATAGAAAAAAGGATGGAGGGATAAATGAAAGCTTGCTTCTAT
*
25560528 ATAGAAAAAAGGATGGAGGGGTAAATGAAAGCTTGCTTCTAT
1 ATAGAAAAAAGGATGGAGGGATAAATGAAAGCTTGCTTCTAT
25560570 CACGTGTAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.42, C:0.07, G:0.27, T:0.24
Consensus pattern (42 bp):
ATAGAAAAAAGGATGGAGGGATAAATGAAAGCTTGCTTCTAT
Found at i:25562616 original size:19 final size:19
Alignment explanation
Indices: 25562592--25562631 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
25562582 TTACTGAGTT
25562592 ATATTGGTGTGGTGGAAGG
1 ATATTGGTGTGGTGGAAGG
25562611 ATATTGGTGTGGTGGAAGG
1 ATATTGGTGTGGTGGAAGG
25562630 AT
1 AT
25562632 GTATTGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.45, T:0.33
Consensus pattern (19 bp):
ATATTGGTGTGGTGGAAGG
Found at i:25563451 original size:28 final size:28
Alignment explanation
Indices: 25563420--25563481 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
25563410 TTAGTTAACT
25563420 ATGTAAAATAAGTGGATGTTGGTATATG
1 ATGTAAAATAAGTGGATGTTGGTATATG
25563448 ATGTAAAATAAGTGGATGTTGGTATATG
1 ATGTAAAATAAGTGGATGTTGGTATATG
25563476 ATGTAA
1 ATGTAA
25563482 GCTTGTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.35
Consensus pattern (28 bp):
ATGTAAAATAAGTGGATGTTGGTATATG
Found at i:25563577 original size:48 final size:48
Alignment explanation
Indices: 25563520--25563615 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
25563510 AATATGGAGT
25563520 AAACAGTAAAATTGTCATGTTGATGTTATTTGGTTTGAATGTGTTTTG
1 AAACAGTAAAATTGTCATGTTGATGTTATTTGGTTTGAATGTGTTTTG
25563568 AAACAGTAAAATTGTCATGTTGATGTTATTTGGTTTGAATGTGTTTTG
1 AAACAGTAAAATTGTCATGTTGATGTTATTTGGTTTGAATGTGTTTTG
25563616 TGTCATTTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (48 bp):
AAACAGTAAAATTGTCATGTTGATGTTATTTGGTTTGAATGTGTTTTG
Found at i:25567448 original size:14 final size:14
Alignment explanation
Indices: 25567425--25567454 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25567415 TTGAAAATAT
25567425 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
25567439 GTTGATTTGGATTG
1 GTTGAATTGGATTG
25567453 GT
1 GT
25567455 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:25568358 original size:25 final size:25
Alignment explanation
Indices: 25568299--25568411 Score: 88
Period size: 25 Copynumber: 4.5 Consensus size: 25
25568289 GTACATGTAT
* * * *
25568299 GCTCATACGAACTATAAATCGGTAT
1 GCTCATACGAGCTATGAATCAGTAA
* *
25568324 GC-CCTCACGAGCTGTGAATC-GATAA
1 GCTCAT-ACGAGCTATGAATCAG-TAA
*
25568349 GCTCATACGAGCTAAGAATCAGTAA
1 GCTCATACGAGCTATGAATCAGTAA
* **
25568374 GCTC-TCACAAGCTACAAATCAGTAA
1 GCTCAT-ACGAGCTATGAATCAGTAA
25568399 GCTCATACGAGCT
1 GCTCATACGAGCT
25568412 GTGGTGTGTC
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
24 4 0.06
25 62 0.89
26 4 0.06
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCAGTAA
Found at i:25568381 original size:50 final size:50
Alignment explanation
Indices: 25568299--25568411 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 50
25568289 GTACATGTAT
* * * * ***
25568299 GCTCATACGAACTATAAATCGGTATGCCCTCACGAGCTGTGAATC-GATAA
1 GCTCATACGAGCTATAAATCAGTAAGCCCTCACAAGCTACAAATCAG-TAA
*
25568349 GCTCATACGAGCTA-AGAATCAGTAAGCTCTCACAAGCTACAAATCAGTAA
1 GCTCATACGAGCTATA-AATCAGTAAGCCCTCACAAGCTACAAATCAGTAA
25568399 GCTCATACGAGCT
1 GCTCATACGAGCT
25568412 GTGGTGTGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
49 1 0.02
50 51 0.96
51 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (50 bp):
GCTCATACGAGCTATAAATCAGTAAGCCCTCACAAGCTACAAATCAGTAA
Found at i:25568748 original size:16 final size:17
Alignment explanation
Indices: 25568722--25568755 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
25568712 ATAAATTTAA
25568722 CTCATTTCAATATAATT
1 CTCATTTCAATATAATT
*
25568739 CTCA-TTCAATTTAATT
1 CTCATTTCAATATAATT
25568755 C
1 C
25568756 AACATGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (17 bp):
CTCATTTCAATATAATT
Found at i:25569285 original size:5 final size:5
Alignment explanation
Indices: 25569275--25569299 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25569265 TGAATGATAA
25569275 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
25569300 ATCATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:25570139 original size:36 final size:35
Alignment explanation
Indices: 25570098--25570171 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 35
25570088 TCTTATTTTT
25570098 ATTTTTTTAATAATTAATATGTGTTTTTATATGATC
1 ATTTTTTTAATAATTAATATGTG-TTTTATATGATC
*
25570134 ATTTTTTTAATGATTAATATGTGTTTTATATGATC
1 ATTTTTTTAATAATTAATATGTGTTTTATATGATC
25570169 ATT
1 ATT
25570172 CAATGTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 15 0.41
36 22 0.59
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (35 bp):
ATTTTTTTAATAATTAATATGTGTTTTATATGATC
Found at i:25574563 original size:16 final size:16
Alignment explanation
Indices: 25574542--25574587 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
25574532 TGAATAAGGT
* *
25574542 AATAAAATAAAGAATG
1 AATAAAAAAAAGAAAG
*
25574558 AATAAAAGAAAGAAAG
1 AATAAAAAAAAGAAAG
25574574 AA-AAAAAAAAGAAA
1 AATAAAAAAAAGAAA
25574588 TAGTGACAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (16 bp):
AATAAAAAAAAGAAAG
Found at i:25575973 original size:23 final size:23
Alignment explanation
Indices: 25575942--25575987 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
25575932 TCAAAGGTTC
* *
25575942 ATGAGTTATTTTATGTCTCATTG
1 ATGAGTTATTTTATCTATCATTG
*
25575965 ATGATTTATTTTATCTATCATTG
1 ATGAGTTATTTTATCTATCATTG
25575988 GAAATGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (23 bp):
ATGAGTTATTTTATCTATCATTG
Found at i:25576602 original size:20 final size:20
Alignment explanation
Indices: 25576577--25576634 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
25576567 TACCCATGGG
*
25576577 CAGGCCACACGGCCATGTTC
1 CAGGCCACACGGCCATGTCC
*
25576597 CAGGCCACACGACCATGTCC
1 CAGGCCACACGGCCATGTCC
* *
25576617 CAGGCCATACGGGCATGT
1 CAGGCCACACGGCCATGT
25576635 GTAACACCCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.38, G:0.26, T:0.14
Consensus pattern (20 bp):
CAGGCCACACGGCCATGTCC
Found at i:25577540 original size:38 final size:38
Alignment explanation
Indices: 25577464--25577638 Score: 179
Period size: 38 Copynumber: 4.5 Consensus size: 38
25577454 GAATCCAGTC
* * *
25577464 ACCAGCACAAAACCTGCGGGACTTTTAAGCTCGAATATAAT
1 ACCAGCACAAAGCCTGCGGGA--TTTAA-CCCGGATATAAT
* * * *
25577505 ACCAGTACTATGCCTGTGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
* * * *
25577543 ACCAACACGAAGCCTGCGGGATTTAACCCAGATATATT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
* * *
25577581 ACCAGCACAAAGCCTGCGAGATTTATCCTGGATATAAT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
* *
25577619 ACCAGCATATAGCCTGCGGG
1 ACCAGCACAAAGCCTGCGGG
25577639 TCTTTAAGCC
Statistics
Matches: 110, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
38 89 0.81
39 5 0.05
41 16 0.15
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (38 bp):
ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
Found at i:25577792 original size:37 final size:31
Alignment explanation
Indices: 25577721--25577783 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
25577711 TCATTAGTAG
25577721 TCATTTGCTACATTCGGATACAAGCTCCATA
1 TCATTTGCTACATTCGGATACAAGCTCCATA
*
25577752 TCATTTGCTACATTCGGATACAAGCTCAATA
1 TCATTTGCTACATTCGGATACAAGCTCCATA
25577783 T
1 T
25577784 AAACATCATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (31 bp):
TCATTTGCTACATTCGGATACAAGCTCCATA
Found at i:25582516 original size:15 final size:15
Alignment explanation
Indices: 25582491--25582548 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
25582481 TCAAATTTAT
25582491 TATACAATTCAATCAA
1 TATA-AATTCAATCAA
25582507 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
25582522 AATAATTTCAATCAA
1 TATAAATTCAATCAA
25582537 TATAAATTCAAT
1 TATAAATTCAAT
25582549 AAAACAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:25582702 original size:2 final size:2
Alignment explanation
Indices: 25582697--25582725 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25582687 TCTCATTCAT
25582697 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
25582726 TATATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25588686 original size:21 final size:21
Alignment explanation
Indices: 25588660--25588720 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
25588650 ATCAGTATAA
25588660 GACACATAAAGTGCCTGATAC
1 GACACATAAAGTGCCTGATAC
** *
25588681 GACACACGAGGTGCCTGATAC
1 GACACATAAAGTGCCTGATAC
*
25588702 GACACATAAAGTGTCTGAT
1 GACACATAAAGTGCCTGAT
25588721 CGATAAAGCC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
GACACATAAAGTGCCTGATAC
Found at i:25589115 original size:15 final size:15
Alignment explanation
Indices: 25589090--25589147 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
25589080 TCATGTATAT
25589090 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
25589106 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
25589121 AATAATTTCAATCAA
1 TATAAATTCAATCAA
25589136 TATAAATTCAAT
1 TATAAATTCAAT
25589148 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:25590433 original size:5 final size:5
Alignment explanation
Indices: 25590418--25590449 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
25590408 TTGTATAGTT
25590418 TATATA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA T
25590450 TAAAACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:25590443 original size:15 final size:16
Alignment explanation
Indices: 25590418--25590500 Score: 63
Period size: 16 Copynumber: 5.5 Consensus size: 16
25590408 TTGTATAGTT
25590418 TATATATATAATATAA
1 TATATATATAATATAA
25590434 TATA-ATATAATATAA
1 TATATATATAATATAA
*
25590449 T-TA-A-A-ACATAAAA
1 TATATATATA-ATATAA
* * *
25590462 TATCTTTATTATATAA
1 TATATATATAATATAA
25590478 TA-ATATAATAATATAA
1 TATATAT-ATAATATAA
25590494 TA-ATATA
1 TATATATA
25590501 CTAAACATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
12 1 0.02
13 7 0.13
14 4 0.08
15 15 0.28
16 26 0.49
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATATATAATATAA
Found at i:25590485 original size:8 final size:8
Alignment explanation
Indices: 25590472--25590500 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
25590462 TATCTTTATT
25590472 ATATAATA
1 ATATAATA
25590480 ATATAATA
1 ATATAATA
25590488 ATATAATA
1 ATATAATA
25590496 ATATA
1 ATATA
25590501 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:25593576 original size:38 final size:38
Alignment explanation
Indices: 25593533--25593688 Score: 233
Period size: 38 Copynumber: 4.1 Consensus size: 38
25593523 TAAGCTCGAT
25593533 TATAATACCAGCACTAAGCCTGCGGGATTTAACCCGGA
1 TATAATACCAGCACTAAGCCTGCGGGATTTAACCCGGA
* *
25593571 TATAATACCAGCACGAAGCCTGCGGAATTTAACCCGGA
1 TATAATACCAGCACTAAGCCTGCGGGATTTAACCCGGA
* *
25593609 TATATTACCAGCACAAAGCCTGCGGGATTTAACCCGGA
1 TATAATACCAGCACTAAGCCTGCGGGATTTAACCCGGA
*
25593647 TATAATACCAGCA-TATAGCCTGCGGGTCTTTAAGCCCGGA
1 TATAATACCAGCACTA-AGCCTGCGGG-ATTTAA-CCCGGA
25593687 TA
1 TA
25593689 CACATAAAAT
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
37 1 0.01
38 93 0.87
39 5 0.05
40 8 0.07
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (38 bp):
TATAATACCAGCACTAAGCCTGCGGGATTTAACCCGGA
Found at i:25596752 original size:16 final size:16
Alignment explanation
Indices: 25596728--25596758 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25596718 TGTAAAACTA
25596728 ATGTATGATATTTTTT
1 ATGTATGATATTTTTT
*
25596744 ATGTTTGATATTTTT
1 ATGTATGATATTTTT
25596759 ATACTATGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (16 bp):
ATGTATGATATTTTTT
Found at i:25600571 original size:21 final size:21
Alignment explanation
Indices: 25600545--25600597 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
25600535 CATTATTTCT
* *
25600545 AATCTCACCGCTATAGTATCC
1 AATCTCACCACTATAGTAACC
*
25600566 AATCTCACCACTATAGTAACT
1 AATCTCACCACTATAGTAACC
25600587 AATCTCACCAC
1 AATCTCACCAC
25600598 CACCGCTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.26
Consensus pattern (21 bp):
AATCTCACCACTATAGTAACC
Found at i:25600792 original size:39 final size:40
Alignment explanation
Indices: 25600738--25600819 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 40
25600728 TTTCTTTCTT
25600738 TTTGCATTTTATAATAAAAGGTTAAATTTTAGTTTTA-TA
1 TTTGCATTTTATAATAAAAGGTTAAATTTTAGTTTTAGTA
25600777 TTTGCATTTTATAATAAAAGGTTAAATTTTAGTTTTAGTA
1 TTTGCATTTTATAATAAAAGGTTAAATTTTAGTTTTAGTA
25600817 TTT
1 TTT
25600820 TAATATGCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 37 0.88
40 5 0.12
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (40 bp):
TTTGCATTTTATAATAAAAGGTTAAATTTTAGTTTTAGTA
Found at i:25603745 original size:43 final size:43
Alignment explanation
Indices: 25603697--25603783 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
25603687 TAGTTCTTAG
25603697 TTACTTAATATTATGCATCATAAGTGTAATTACAATTGTAAAC
1 TTACTTAATATTATGCATCATAAGTGTAATTACAATTGTAAAC
25603740 TTACTTAATATTATGCATCATAAGTGTAATTACAATTGTAAAC
1 TTACTTAATATTATGCATCATAAGTGTAATTACAATTGTAAAC
25603783 T
1 T
25603784 AGTAGTTGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (43 bp):
TTACTTAATATTATGCATCATAAGTGTAATTACAATTGTAAAC
Found at i:25605758 original size:70 final size:70
Alignment explanation
Indices: 25605676--25605816 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
25605666 TCTTTCTGTT
25605676 ATATGGTTTGAAAGGCATAGTTTAAGTTGCAGTGGTTTTCATGAAGAAAAAGTATTATATATTTA
1 ATATGGTTTGAAAGGCATAGTTTAAGTTGCAGTGGTTTTCATGAAGAAAAAGTATTATATATTTA
25605741 CTCCA
66 CTCCA
25605746 ATATGGTTTGAAAGGCATAGTTTAAGTTGCAGTGGTTTTCATGAAGAAAAAGTATTATATATTTA
1 ATATGGTTTGAAAGGCATAGTTTAAGTTGCAGTGGTTTTCATGAAGAAAAAGTATTATATATTTA
25605811 CTCCA
66 CTCCA
25605816 A
1 A
25605817 ATAGATTCCA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (70 bp):
ATATGGTTTGAAAGGCATAGTTTAAGTTGCAGTGGTTTTCATGAAGAAAAAGTATTATATATTTA
CTCCA
Found at i:25623097 original size:15 final size:15
Alignment explanation
Indices: 25623077--25623108 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
25623067 CCAATAGCCA
25623077 TAGCCTCAACATAAG
1 TAGCCTCAACATAAG
25623092 TAGCCTCAACATAAG
1 TAGCCTCAACATAAG
25623107 TA
1 TA
25623109 ATGAACTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (15 bp):
TAGCCTCAACATAAG
Found at i:25630097 original size:15 final size:14
Alignment explanation
Indices: 25630077--25630117 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
25630067 ACTTTTAACT
25630077 AAAATTATATATTTA
1 AAAATTAT-TATTTA
*
25630092 AAAATTATTAATTA
1 AAAATTATTATTTA
*
25630106 AAATTTATTATT
1 AAAATTATTATT
25630118 AAATATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAAATTATTATTTA
Found at i:25630125 original size:14 final size:14
Alignment explanation
Indices: 25630071--25630130 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
25630061 AATTTTACTT
*
25630071 TTAACTAAAA-TTA
1 TTAATTAAAATTTA
* *
25630084 TATATTTAAAAATTA
1 T-TAATTAAAATTTA
25630099 TTAATTAAAATTTA
1 TTAATTAAAATTTA
*
25630113 TT-ATTAAATATTTG
1 TTAATTAAA-ATTTA
25630127 TTAA
1 TTAA
25630131 GAATAAAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 7 0.18
14 26 0.68
15 5 0.13
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (14 bp):
TTAATTAAAATTTA
Found at i:25636764 original size:17 final size:18
Alignment explanation
Indices: 25636731--25636764 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25636721 TTCATAGCAA
*
25636731 CTTTCTTTCTCCTCTTGT
1 CTTTCTTTCTACTCTTGT
25636749 CTTTCTTT-TACTCTTG
1 CTTTCTTTCTACTCTTG
25636765 GCCAGTTTAA
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:0.03, C:0.29, G:0.06, T:0.62
Consensus pattern (18 bp):
CTTTCTTTCTACTCTTGT
Found at i:25645529 original size:41 final size:41
Alignment explanation
Indices: 25645476--25645555 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
25645466 TGTGTTAACC
*
25645476 CACTGGACGAGGCAGTCGTATGTTAACCCATGTTGCCTTAA
1 CACTGGACGAGGCAGTCGTATGTTAACCAATGTTGCCTTAA
25645517 CACTGGACGAGGCAGTCGTATGTTAACCAATGTTGCCTT
1 CACTGGACGAGGCAGTCGTATGTTAACCAATGTTGCCTT
25645556 CGTAATCTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (41 bp):
CACTGGACGAGGCAGTCGTATGTTAACCAATGTTGCCTTAA
Found at i:25648834 original size:18 final size:17
Alignment explanation
Indices: 25648794--25648834 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
25648784 AAATGTCTTC
25648794 CCAACACGGTTCATTCT
1 CCAACACGGTTCATTCT
**
25648811 TAAACACGGTTCCATTCT
1 CCAACACGGTT-CATTCT
25648829 CCAACA
1 CCAACA
25648835 TAATTGGTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.29, C:0.34, G:0.10, T:0.27
Consensus pattern (17 bp):
CCAACACGGTTCATTCT
Found at i:25657241 original size:2 final size:2
Alignment explanation
Indices: 25657230--25657259 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25657220 ATCTATTTGG
25657230 TA TA -A 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
25657260 TATTCTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25658762 original size:25 final size:25
Alignment explanation
Indices: 25658734--25658786 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
25658724 CCTTAACATA
25658734 ATTTAAGTTT-ATATAAGTTTATATG
1 ATTT-AGTTTGATATAAGTTTATATG
* * *
25658759 ATTTATTTTGTTATAAGTTTTTATG
1 ATTTAGTTTGATATAAGTTTATATG
25658784 ATT
1 ATT
25658787 AAAACTACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.58
Consensus pattern (25 bp):
ATTTAGTTTGATATAAGTTTATATG
Found at i:25663066 original size:2 final size:2
Alignment explanation
Indices: 25663005--25663047 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
25662995 CTAAACTTAA
* *
25663005 CT CT CT CT CT CT CT CT CA CT CT CT CT CT CA CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
25663047 C
1 C
25663048 ATGGATTCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.05, C:0.51, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:25669462 original size:38 final size:38
Alignment explanation
Indices: 25669411--25669488 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
25669401 GAACTAATAG
25669411 TAGAATTGAACATATTCTTTTCAAATAAAATTAGTGGA
1 TAGAATTGAACATATTCTTTTCAAATAAAATTAGTGGA
*
25669449 TAGAATTTAACATATTCTTTTCAAATAAAATTAGTGGA
1 TAGAATTGAACATATTCTTTTCAAATAAAATTAGTGGA
25669487 TA
1 TA
25669489 TTTTCTAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (38 bp):
TAGAATTGAACATATTCTTTTCAAATAAAATTAGTGGA
Found at i:25670729 original size:22 final size:22
Alignment explanation
Indices: 25670704--25670746 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
25670694 GGTTAGTTCG
*
25670704 TATGAGAT-TTATTTTGTTAATA
1 TATG-GATGTTATTGTGTTAATA
*
25670726 TATGGTTGTTATTGTGTTAAT
1 TATGGATGTTATTGTGTTAAT
25670747 TTTTTACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (22 bp):
TATGGATGTTATTGTGTTAATA
Found at i:25671264 original size:17 final size:17
Alignment explanation
Indices: 25671238--25671381 Score: 137
Period size: 17 Copynumber: 8.4 Consensus size: 17
25671228 GAGCTTTTTT
25671238 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* *
25671256 TTTTCAAAACACCGAAAT
1 TTTTTAAAACA-CGAAAA
* **
25671274 TTTTTAAAACAAGAGGA
1 TTTTTAAAACACGAAAA
* *
25671291 TTTTTGAAATACGAAAAA
1 TTTTTAAAACACG-AAAA
*
25671309 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
25671326 TTTTTGAAACACGGAAA
1 TTTTTAAAACACGAAAA
*
25671343 TTTTTGAAA-ACGAAAA
1 TTTTTAAAACACGAAAA
* *
25671359 TTTTTGAAACACAAAAA
1 TTTTTAAAACACGAAAA
25671376 TTTTTA
1 TTTTTA
25671382 GAAGACACTA
Statistics
Matches: 102, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
16 15 0.15
17 56 0.55
18 31 0.30
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.31
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:25671284 original size:35 final size:35
Alignment explanation
Indices: 25671237--25671380 Score: 141
Period size: 35 Copynumber: 4.1 Consensus size: 35
25671227 CGAGCTTTTT
**
25671237 TTTTTTGAAAACACGAAAATTTTCAAAACACCGAAA
1 TTTTTT-AAAACACGAAAATTTTTGAAACACCGAAA
* ** *
25671273 TTTTTTAAAACAAGAGGATTTTTGAAATA-CGAAAA
1 TTTTTTAAAACACGAAAATTTTTGAAACACCG-AAA
* * *
25671308 ATTTTGAAAACACGAAAATTTTTGAAACACGGAAA
1 TTTTTTAAAACACGAAAATTTTTGAAACACCGAAA
* **
25671343 -TTTTTGAAA-ACGAAAATTTTTGAAACACAAAAA
1 TTTTTTAAAACACGAAAATTTTTGAAACACCGAAA
25671376 TTTTT
1 TTTTT
25671381 AGAAGACACT
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
33 22 0.25
34 13 0.15
35 46 0.52
36 7 0.08
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (35 bp):
TTTTTTAAAACACGAAAATTTTTGAAACACCGAAA
Found at i:25671616 original size:20 final size:19
Alignment explanation
Indices: 25671578--25671624 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
25671568 AATATATTTT
25671578 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
25671598 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
25671617 -TTTTGAAA
1 TTTTTGAAA
25671625 AATAGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:25671998 original size:7 final size:7
Alignment explanation
Indices: 25671981--25672077 Score: 81
Period size: 7 Copynumber: 13.1 Consensus size: 7
25671971 GAATTGAAAC
25671981 TCTTTTT
1 TCTTTTT
25671988 T-TTTCTT
1 TCTTT-TT
25671995 T-TTTTCT
1 TCTTTT-T
25672002 TCTTTTT
1 TCTTTTT
25672009 TCCTTTTT
1 T-CTTTTT
25672017 TCCTTTTTT
1 T-C-TTTTT
*
25672026 TCTCTTT
1 TCTTTTT
25672033 TCTTTTT
1 TCTTTTT
*
25672040 TCTTCTT
1 TCTTTTT
25672047 TCTTTTTT
1 TC-TTTTT
*
25672055 TCTTTCT
1 TCTTTTT
*
25672062 TCTTTCTC
1 TCTTT-TT
25672070 TCTTTTT
1 TCTTTTT
25672077 T
1 T
25672078 TCCTGGCCTG
Statistics
Matches: 75, Mismatches: 8, Indels: 14
0.77 0.08 0.14
Matches are distributed among these distances:
6 4 0.05
7 40 0.53
8 25 0.33
9 6 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TCTTTTT
Found at i:25671998 original size:8 final size:8
Alignment explanation
Indices: 25671985--25672079 Score: 81
Period size: 8 Copynumber: 12.0 Consensus size: 8
25671975 TGAAACTCTT
25671985 TTTTTTTC
1 TTTTTTTC
25671993 TTTTTTTC
1 TTTTTTTC
25672001 TTCTTTTTTCC
1 -T-TTTTTT-C
*
25672012 TTTTTTCC
1 TTTTTTTC
25672020 TTTTTTTC
1 TTTTTTTC
*
25672028 -TCTTTTC
1 TTTTTTTC
25672035 -TTTTTTC
1 TTTTTTTC
*
25672042 -TTCTTTC
1 TTTTTTTC
25672049 TTTTTTTC
1 TTTTTTTC
*
25672057 -TTTCTTC
1 TTTTTTTC
* *
25672064 TTTCTCTC
1 TTTTTTTC
25672072 TTTTTTTC
1 TTTTTTTC
25672080 CTGGCCTGCT
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
7 24 0.34
8 32 0.46
9 6 0.09
10 7 0.10
11 1 0.01
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTTC
Found at i:25672009 original size:19 final size:19
Alignment explanation
Indices: 25671981--25672079 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
25671971 GAATTGAAAC
25671981 TCTT-TTTTTTTCTTTTTT
1 TCTTCTTTTTTTCTTTTTT
*
25671999 TCTTCTTTTTTCCTTTTTT
1 TCTTCTTTTTTTCTTTTTT
* *
25672018 CCTT-TTTTTCTCTTTTCTT
1 TCTTCTTTTTTTCTTTT-TT
* *
25672037 TTTTC-TTCTTTCTTTTTT
1 TCTTCTTTTTTTCTTTTTT
25672055 TCTTTCTTCTTTCTCTCTTTTTT
1 TC-TTCTT-TTT-T-TCTTTTTT
25672078 TC
1 TC
25672080 CTGGCCTGCT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
18 17 0.27
19 32 0.51
20 1 0.02
21 2 0.03
22 1 0.02
23 10 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TCTTCTTTTTTTCTTTTTT
Found at i:25672037 original size:15 final size:14
Alignment explanation
Indices: 25671983--25672076 Score: 81
Period size: 15 Copynumber: 6.7 Consensus size: 14
25671973 ATTGAAACTC
25671983 TTTT-TTTTTCTTT
1 TTTTCTTTTTCTTT
25671996 TTTTC---TTCTTT
1 TTTTCTTTTTCTTT
*
25672007 TTTCCTTTTTTCCTTT
1 TTTTC-TTTTT-CTTT
25672023 TTTTCTCTTTTC-TT
1 TTTTCT-TTTTCTTT
25672037 TTTTCTTCTTTCTTT
1 TTTTCTT-TTTCTTT
25672052 TTTTCTTTCTTCTTT
1 TTTTCTTT-TTCTTT
* *
25672067 CTCTCTTTTT
1 TTTTCTTTTT
25672077 TTCCTGGCCT
Statistics
Matches: 67, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
11 10 0.15
13 5 0.07
14 15 0.22
15 25 0.37
16 12 0.18
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:25672209 original size:14 final size:15
Alignment explanation
Indices: 25672192--25672231 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
25672182 GCTGTTTTTT
25672192 CTTTTTTTTTGGGC-
1 CTTTTTTTTTGGGCG
25672206 CTTTTCTTTTTGGGCTG
1 CTTTT-TTTTTGGGC-G
25672223 CTTTTTTTT
1 CTTTTTTTT
25672232 GCTTTGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 4 0.17
17 5 0.22
ACGTcount: A:0.00, C:0.15, G:0.17, T:0.68
Consensus pattern (15 bp):
CTTTTTTTTTGGGCG
Found at i:25672247 original size:31 final size:31
Alignment explanation
Indices: 25672207--25672279 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 31
25672197 TTTTTGGGCC
*
25672207 TTTTCTTTTTGGGCTGCTTT-TTTTTGCTTTG-G
1 TTTT-TTTTTGGGCTGATTTGTTTTT--TTTGTG
25672239 TTTTTTTTTGGGCTGATTTGTTTTTTTTGTG
1 TTTTTTTTTGGGCTGATTTGTTTTTTTTGTG
25672270 TTGTTTTTTT
1 TT-TTTTTTT
25672280 TAATTAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 4 0.11
31 17 0.46
32 16 0.43
ACGTcount: A:0.01, C:0.07, G:0.21, T:0.71
Consensus pattern (31 bp):
TTTTTTTTTGGGCTGATTTGTTTTTTTTGTG
Found at i:25672392 original size:10 final size:10
Alignment explanation
Indices: 25672377--25672407 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
25672367 GATTGTTAAA
25672377 TTTTTTTCTT
1 TTTTTTTCTT
25672387 TTTTTTTCTT
1 TTTTTTTCTT
*
25672397 TTTTCTTCTT
1 TTTTTTTCTT
25672407 T
1 T
25672408 CTTCTTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:25672400 original size:17 final size:17
Alignment explanation
Indices: 25672378--25672424 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
25672368 ATTGTTAAAT
* *
25672378 TTTTTTCTTTTTTTTTC
1 TTTTTTCTTCTTTCTTC
25672395 TTTTTTCTTCTTTCTTC
1 TTTTTTCTTCTTTCTTC
25672412 TTCTTCTTCTTCT
1 TT-TT-TTCTTCT
25672425 CCTCCTACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 17 0.65
18 2 0.08
19 7 0.27
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTCTTTCTTC
Done.