Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 121 of 325
Found at i:38825634 original size:27 final size:27
Alignment explanation
Indices: 38825580--38825663 Score: 118
Period size: 27 Copynumber: 3.1 Consensus size: 27
38825570 AGCATTGCTG
* *
38825580 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
38825606 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
38825633 CCAGAACAGAT-ATATGTGGCATAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
38825660 CCAG
1 CCAG
38825664 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 15 0.28
27 38 0.72
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:38827102 original size:24 final size:24
Alignment explanation
Indices: 38827067--38827143 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
38827057 CCGACCTTGT
*
38827067 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
38827091 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
* *
38827115 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
38827139 TCTCC
1 TCTCC
38827144 TGACAGACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.23, C:0.42, G:0.03, T:0.32
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:38837177 original size:40 final size:40
Alignment explanation
Indices: 38837122--38837343 Score: 295
Period size: 40 Copynumber: 5.6 Consensus size: 40
38837112 TATTCGAATG
* * *
38837122 ATATCCGGGTTAAGTCCTGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * *
38837162 ATATCCAGGCTAAGTCCCAAAGGCATTTGTGCTATTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
38837202 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * * *
38837242 ATATCTGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * *
38837282 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATT
*
38837322 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
38837344 TACTTGGGTT
Statistics
Matches: 161, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
39 14 0.09
40 145 0.90
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
Found at i:38845634 original size:40 final size:40
Alignment explanation
Indices: 38845579--38845800 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
38845569 TATTCGAATG
*
38845579 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
*
38845619 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
38845659 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * * *
38845699 ATATCTGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * *
38845739 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATT
*
38845779 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
38845801 TACTTGGGTT
Statistics
Matches: 167, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 14 0.08
40 151 0.90
41 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
Found at i:38854225 original size:48 final size:48
Alignment explanation
Indices: 38854143--38854329 Score: 200
Period size: 48 Copynumber: 3.9 Consensus size: 48
38854133 ATACTAGGGT
* * *
38854143 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTTA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTATA
* * * *
38854191 TATGAGAGCTAGTGTAAGACCATGTCT-GAGACATGGCATTGGCCTCGACA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGA-ACATGGCATCGGCCT--ATA
* * *
38854241 TGTG-GA-CTAGTGTAAGACCATGTTTGGAACATGGCATCGGCCCCGATA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGG--CCTATA
* *
38854289 TATGAAAGCCAGTGTAAGACCATGTTTGGAACATGGAATCG
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCG
38854330 ACATGTAACA
Statistics
Matches: 115, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
47 2 0.02
48 71 0.62
49 5 0.04
50 37 0.32
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (48 bp):
TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTATA
Found at i:38855369 original size:27 final size:27
Alignment explanation
Indices: 38855321--38855738 Score: 336
Period size: 27 Copynumber: 15.4 Consensus size: 27
38855311 ATTATCAAAG
*
38855321 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
*
38855348 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTATTT
38855375 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTATTT
* * *
38855402 TACCCTCGATTTACAGAGTTACTGTTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
38855429 TACCCTTGAATTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTATTT
** *
38855456 TACCCTCGATTTACAAAATTACCGTTC
1 TACCCTCGATTTACAAAATTACTATTT
* ** *
38855483 TACCCTCAATTTGTAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
* * *
38855510 TACCCTCGATTTAGAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
* * ***
38855537 TACCCTCAATTTAGAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTATTT
* ** ***
38855564 TACCC-CTAGTTTGTAAAATTACTAAAA
1 TACCCTCGA-TTTACAAAATTACTATTT
* ** ***
38855591 TACCCCCTGATTTGTAAAATTACTAAAA
1 TACCCTC-GATTTACAAAATTACTATTT
* * ***
38855619 TACCCTCGACTGGTA-AAAATTACCAAAG
1 TACCCTCGA-T-TTACAAAATTACTATTT
* * *
38855647 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTATTT
* * * * *
38855674 TACCCTCAATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAAAATTACTATTT
* **
38855701 TACCCTTGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTATTT
38855728 TACCCTCGATT
1 TACCCTCGATT
38855739 GTGAAATTAC
Statistics
Matches: 329, Mismatches: 56, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
26 4 0.01
27 277 0.84
28 46 0.14
29 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTATTT
Found at i:38855606 original size:28 final size:28
Alignment explanation
Indices: 38855551--38855623 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
38855541 CTCAATTTAG
38855551 AAAATTACTAAAATA-CCCCTAGTTTGT
1 AAAATTACTAAAATACCCCCTAGTTTGT
38855578 AAAATTACTAAAATACCCCCT-GATTTGT
1 AAAATTACTAAAATACCCCCTAG-TTTGT
38855606 AAAATTACTAAAATACCC
1 AAAATTACTAAAATACCC
38855624 TCGACTGGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
27 16 0.36
28 28 0.64
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (28 bp):
AAAATTACTAAAATACCCCCTAGTTTGT
Found at i:38855635 original size:55 final size:55
Alignment explanation
Indices: 38855545--38855669 Score: 137
Period size: 55 Copynumber: 2.3 Consensus size: 55
38855535 TTTACCCTCA
* * * * *
38855545 ATTTAGAAAATTACTAAAATACCCCTAGTTTGT-AAAATTACTAAAATACCCCCTG
1 ATTTATAAAATTACTAAAATACCCCGAGCTGGTAAAAATTACCAAAATACCCCC-G
* * *
38855600 ATTTGTAAAATTACTAAAATACCCTCGA-CTGGTAAAAATTACCAAAGTACCCTCG
1 ATTTATAAAATTACTAAAATACCC-CGAGCTGGTAAAAATTACCAAAATACCCCCG
*
38855655 ATTTATAGAATTACT
1 ATTTATAAAATTACT
38855670 GTTTTACCCT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
55 39 0.67
56 19 0.33
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (55 bp):
ATTTATAAAATTACTAAAATACCCCGAGCTGGTAAAAATTACCAAAATACCCCCG
Found at i:38855637 original size:28 final size:27
Alignment explanation
Indices: 38855196--38855669 Score: 179
Period size: 27 Copynumber: 17.5 Consensus size: 27
38855186 ATATCCTAAG
* *
38855196 TTGTAAAATTACCAAAGTACCCTCGGA-
1 TTGTAAAATTACTAAAATACCCTC-GAT
* ** *
38855223 TTATAAAATTACCCAAATATCCTCGAT
1 TTGTAAAATTACTAAAATACCCTCGAT
*
38855250 TTGTAAAATTA-TCGAAATACCCTC-AGT
1 TTGTAAAATTACT-AAAATACCCTCGA-T
* * * *
38855277 TTGCAAAATTATTGAAATACCCTCGAC
1 TTGTAAAATTACTAAAATACCCTCGAT
* *
38855304 ATGTAAAATTA-TCAAAGTACCCTCGAT
1 TTGTAAAATTACT-AAAATACCCTCGAT
** * ***
38855331 TTACAAAATTACCATTTTACCCTCGAT
1 TTGTAAAATTACTAAAATACCCTCGAT
** ****
38855358 TTACAAAATTACTGTTTTACCCTCGAT
1 TTGTAAAATTACTAAAATACCCTCGAT
** ***
38855385 TTACAAAATTACTATTTTACCCTCGAT
1 TTGTAAAATTACTAAAATACCCTCGAT
** * * **** * *
38855412 TTACAGAGTTACTGTTTTACCCTTGAA
1 TTGTAAAATTACTAAAATACCCTCGAT
** ***
38855439 TTACAAAATTACTATTTTACCCTCGAT
1 TTGTAAAATTACTAAAATACCCTCGAT
** ***** *
38855466 TTACAAAATTACCGTTCTACCCTCAAT
1 TTGTAAAATTACTAAAATACCCTCGAT
* ***
38855493 TTGTAAAATTACCATTTTACCCTCGAT
1 TTGTAAAATTACTAAAATACCCTCGAT
* * *** *
38855520 TTAG-AGAATTACCATTTTACCCTCAAT
1 TT-GTAAAATTACTAAAATACCCTCGAT
*
38855547 TTAG-AAAATTACTAAAATACCC-CTAGT
1 TT-GTAAAATTACTAAAATACCCTCGA-T
*
38855574 TTGTAAAATTACTAAAATACCCCCTGAT
1 TTGTAAAATTACTAAAATACCCTC-GAT
*
38855602 TTGTAAAATTACTAAAATACCCTCGAC
1 TTGTAAAATTACTAAAATACCCTCGAT
* * *
38855629 TGGTAAAAATTACCAAAGTACCCTCGAT
1 TTGT-AAAATTACTAAAATACCCTCGAT
* *
38855657 TTATAGAATTACT
1 TTGTAAAATTACT
38855670 GTTTTACCCT
Statistics
Matches: 371, Mismatches: 63, Indels: 26
0.81 0.14 0.06
Matches are distributed among these distances:
26 7 0.02
27 313 0.84
28 50 0.13
29 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (27 bp):
TTGTAAAATTACTAAAATACCCTCGAT
Found at i:38855723 original size:191 final size:189
Alignment explanation
Indices: 38855456--38855813 Score: 470
Period size: 191 Copynumber: 1.9 Consensus size: 189
38855446 ATTACTATTT
*
38855456 TACCCTCGATTTACAAAATTACCGTTCTACCCTCAATTTGTAAAATTACCATTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTACCGTTCTACCCTCAATTTATAAAATTACCATTTTACCCTCGATT
* * **
38855521 TAGAGAATTACCATTTTACCCTCAATT-TAGAAAATTACTAAAATACCCCTAGT-TTGTAAAATT
66 TACAAAATTACCATTTTACCCTCAATTGT-G-AAATTACTAAAATACCCCTA-TAGGGTAAAATT
* *
38855584 ACTAAAATACCCCCT-GATTTGTAAAATTACTAAAATACCCTCGACTGGTAAAAATTACCAAAG
128 ACCAAAACA-CCCCTAG-TTTGTAAAATTACTAAAATACCCTCGACTGGTAAAAATTACCAAAG
* * * * * *** *
38855647 TACCCTCGATTTATAGAATTACTGTTTTACCCTCAATTTATAGAATTATTGTTTTACCCTTGATT
1 TACCCTCGATTTACAAAATTACCGTTCTACCCTCAATTTATAAAATTACCATTTTACCCTCGATT
* * * *
38855712 TACAAAATTACCGTTTTACCCTCGATTGTGAAATTACTGAAATACCCCTATAGGGTAGAATTACC
66 TACAAAATTACCATTTTACCCTCAATTGTGAAATTACTAAAATACCCCTATAGGGTAAAATTACC
38855777 AAAACACCCCTAGTTTGTAAAATTACTAAAATACCCT
131 AAAACACCCCTAGTTTGTAAAATTACTAAAATACCCT
38855814 TGTAAGGTAG
Statistics
Matches: 144, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
189 30 0.21
190 34 0.24
191 79 0.55
192 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (189 bp):
TACCCTCGATTTACAAAATTACCGTTCTACCCTCAATTTATAAAATTACCATTTTACCCTCGATT
TACAAAATTACCATTTTACCCTCAATTGTGAAATTACTAAAATACCCCTATAGGGTAAAATTACC
AAAACACCCCTAGTTTGTAAAATTACTAAAATACCCTCGACTGGTAAAAATTACCAAAG
Found at i:38855773 original size:27 final size:27
Alignment explanation
Indices: 38855743--38855999 Score: 250
Period size: 27 Copynumber: 9.6 Consensus size: 27
38855733 TCGATTGTGA
*
38855743 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
* * ** *
38855770 AATTACCAAAACACCCCTAGT-TTGTAA
1 AATTACCGAAATACCCCTA-TAGGGTAG
** * * *
38855797 AATTACTAAAATACCCTTGTAAGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
** *
38855824 AATTACTAAAATA-CCCTAGTAAGGTAG
1 AATTACCGAAATACCCCTA-TAGGGTAG
*
38855851 AATTACCG-AATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
*
38855877 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
* *
38855904 AATTATCGCAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
*
38855931 AATTACCGAAATACCCTTATAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
** * * *
38855958 AATTACTAAAATACCCTTGTAGGGTGG
1 AATTACCGAAATACCCCTATAGGGTAG
*
38855985 AATTACCGAGATACC
1 AATTACCGAAATACC
38856000 TTGTGGGGTA
Statistics
Matches: 193, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
26 23 0.12
27 169 0.88
28 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTATAGGGTAG
Found at i:38855855 original size:134 final size:134
Alignment explanation
Indices: 38855743--38856017 Score: 347
Period size: 134 Copynumber: 2.1 Consensus size: 134
38855733 TCGATTGTGA
* ** *
38855743 AATTACTGAAATACCCCTATAGGGTAGAATTACCAAAACACCCCTAGT-TTGTAAAATTACTAAA
1 AATTACCGAAATACCCCTATAGGGTAGAATTACCAAAACACCCCTA-TAGGGTAAAATTACCAAA
*
38855807 ATACCCTTGTAAGGTAGAATTACTAAAATACCCTAGTAAGGTAGAATTACCGAATACCCCTGTAG
65 ATACCCTTATAAGGTAGAATTACTAAAATACCCTAGTAAGGTAGAATTACCGAATACCCCTGTAG
38855872 GGTAG
130 GGTAG
* * ** * * *
38855877 AATTACCGAAATACCCCTGTAGGGTAGAATTATCGCAATACCCCTATAGGGTAGAATTACCGAAA
1 AATTACCGAAATACCCCTATAGGGTAGAATTACCAAAACACCCCTATAGGGTAAAATTACCAAAA
* * * * * *
38855942 TACCCTTATAGGGTAGAATTACTAAAATACCCTTGTAGGGTGGAATTACCGAGATA-CCTTGTGG
66 TACCCTTATAAGGTAGAATTACTAAAATACCCTAGTAAGGTAGAATTACCGA-ATACCCCTGTAG
*
38856006 GGTAA
130 GGTAG
38856011 AATTACC
1 AATTACC
38856018 ATTTTGCCCC
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
133 1 0.01
134 116 0.97
135 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (134 bp):
AATTACCGAAATACCCCTATAGGGTAGAATTACCAAAACACCCCTATAGGGTAAAATTACCAAAA
TACCCTTATAAGGTAGAATTACTAAAATACCCTAGTAAGGTAGAATTACCGAATACCCCTGTAGG
GTAG
Found at i:38856300 original size:27 final size:26
Alignment explanation
Indices: 38856262--38856312 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
38856252 CTCGCTGCAA
*
38856262 TCTGGTGGCTTCGCCACATATATCTGT
1 TCTGGTGACTTCGCCACA-ATATCTGT
*
38856289 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACTTCGCCACAATATCT
38856313 AGCAGCCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (26 bp):
TCTGGTGACTTCGCCACAATATCTGT
Found at i:38856359 original size:67 final size:67
Alignment explanation
Indices: 38856247--38856396 Score: 255
Period size: 67 Copynumber: 2.2 Consensus size: 67
38856237 AATCGTTCTG
* * *
38856247 GCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAATATC
1 GCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTCTTCTGGTGACTTCATCAAAATATC
38856312 TA
66 TA
*
38856314 GCAGCCTCGCTGCAATCTGGTGGCTTCGTCACATATATCTCTTCTGGTGACTTCATCAAAATATC
1 GCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTCTTCTGGTGACTTCATCAAAATATC
*
38856379 TG
66 TA
38856381 GCAGCCTCGCTGCAAT
1 GCAGCCTCGCTGCAAT
38856397 TTCTGTGGTG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 78 1.00
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.31
Consensus pattern (67 bp):
GCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTCTTCTGGTGACTTCATCAAAATATC
TA
Found at i:38856508 original size:6 final size:6
Alignment explanation
Indices: 38856499--38856681 Score: 144
Period size: 6 Copynumber: 29.8 Consensus size: 6
38856489 TTGCATTCAC
* *
38856499 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTA ATTCTG ATTCT- ATTACCT-
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * *
38856548 ATTCTG ATTTTG GTTCTG GTTCTG ATTCTG ATTCTG -TTACCTG ATACTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG
* * *
38856597 ATTCTG ATTCTG -TTACCTA ATTCTG ATTCTG GTTCTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
*
38856646 -TCACCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
38856682 AGTTATGATA
Statistics
Matches: 144, Mismatches: 18, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
5 12 0.08
6 111 0.77
7 16 0.11
8 5 0.03
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:38856533 original size:25 final size:25
Alignment explanation
Indices: 38856502--38856633 Score: 127
Period size: 25 Copynumber: 5.6 Consensus size: 25
38856492 CATTCACATT
38856502 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTGATA
* * *
38856527 CTAATTCTGATTCTATTACCT-ATT
1 CTGATTCTGATTCTGTTACCTGATA
* * *
38856551 CTGA-T-T--TT-GGTT--CTGGTT
1 CTGATTCTGATTCTGTTACCTGATA
38856569 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTGATA
* *
38856594 CTGATTCTGATTCTGTTACCTAATT
1 CTGATTCTGATTCTGTTACCTGATA
*
38856619 CTGATTCTGGTTCTG
1 CTGATTCTGATTCTG
38856634 ATTTTGATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
17 2 0.02
18 6 0.07
19 3 0.03
20 3 0.03
22 3 0.03
23 4 0.05
24 5 0.06
25 60 0.70
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTGATA
Found at i:38856635 original size:37 final size:37
Alignment explanation
Indices: 38856588--38856686 Score: 144
Period size: 37 Copynumber: 2.6 Consensus size: 37
38856578 ATTCTGTTAC
*
38856588 CTGATACTGATTCTGATTCTGTTACCTAATTCTGATT
1 CTGATTCTGATTCTGATTCTGTTACCTAATTCTGATT
* * * *
38856625 CTGGTTCTGATTTTGATTCTGTCACCTGATTCTGATT
1 CTGATTCTGATTCTGATTCTGTTACCTAATTCTGATT
38856662 CTGATTCTGATTCTGATTCTAGTTA
1 CTGATTCTGATTCTGATTCT-GTTA
38856687 TGATAATGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 50 0.94
38 3 0.06
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTTACCTAATTCTGATT
Found at i:38859222 original size:50 final size:51
Alignment explanation
Indices: 38859099--38859239 Score: 202
Period size: 48 Copynumber: 2.8 Consensus size: 51
38859089 ACACGACATT
38859099 TATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-AGCCTCGA
1 TATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAGCCTCGA
* * *
38859149 CATGTG-G-GCTAGTGTAAGACCATGTTTGGGACATGGCATCGA-CAC-CGA
1 TATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAGC-CTCGA
*
38859197 TATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 TATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
38859240 GCATCTTACC
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
48 40 0.50
49 4 0.05
50 36 0.45
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (51 bp):
TATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAGCCTCGA
Found at i:38861064 original size:46 final size:46
Alignment explanation
Indices: 38860997--38861122 Score: 189
Period size: 46 Copynumber: 2.7 Consensus size: 46
38860987 AACCTGCCCC
* * * * * *
38860997 TAAGTGAACTTGAACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
38861043 TAAGTGAACTCGGACTCAACTCAACCAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
38861089 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
38861123 TGCTCAACCA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:38861141 original size:46 final size:45
Alignment explanation
Indices: 38861035--38861133 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 45
38861025 CTCGGGCGTT
* *
38861035 CGCATCCATAAGTGAACTCGGACTCAACTCAACCAGTTCGGACATT
1 CGCAACCATAAGTGAACTCGGACTCAACTCAACCAGTTCGGA-ATG
* *
38861081 CGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATG
1 CGCAACCATAAGTGAACTCGGACTCAACTCAACCAGTTCGGAATG
*
38861125 CTCAACCAT
1 CGCAACCAT
38861134 CCTAGTGACA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 9 0.18
46 40 0.82
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (45 bp):
CGCAACCATAAGTGAACTCGGACTCAACTCAACCAGTTCGGAATG
Found at i:38874493 original size:17 final size:17
Alignment explanation
Indices: 38874458--38874511 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
38874448 CATGTGGCCT
* * *
38874458 GCCCGTGTGGGCCATAC
1 GCCCGTATGGCCCACAC
* * *
38874475 GCTCGTGTGGCCTACAC
1 GCCCGTATGGCCCACAC
38874492 GCCCGTATGGCCCACAC
1 GCCCGTATGGCCCACAC
38874509 GCC
1 GCC
38874512 TATGTTGCCC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.13, C:0.41, G:0.30, T:0.17
Consensus pattern (17 bp):
GCCCGTATGGCCCACAC
Found at i:38880371 original size:25 final size:25
Alignment explanation
Indices: 38880342--38880389 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38880332 TTCAATACAG
* *
38880342 TATACTACCTATAGTAGTTTCAGAA
1 TATACTACCAATAATAGTTTCAGAA
*
38880367 TATACTATCAATAATAGTTTCAG
1 TATACTACCAATAATAGTTTCAG
38880390 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (25 bp):
TATACTACCAATAATAGTTTCAGAA
Found at i:38882633 original size:40 final size:41
Alignment explanation
Indices: 38882573--38882653 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 41
38882563 GTAACAGTTT
*
38882573 GGGCCTTAGCCCATCTCAGTA-CAGTATCGAAT-ATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAGTATC-AATCATGCAGTA
*
38882613 GGGCCTTAGCCCATCACAGTATCAGTGTCAATCATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAGTATCAATCATGCAGTA
38882654 TTTAGTAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 23 0.62
41 14 0.38
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (41 bp):
GGGCCTTAGCCCATCACAGTATCAGTATCAATCATGCAGTA
Found at i:38890385 original size:16 final size:16
Alignment explanation
Indices: 38890364--38890395 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38890354 CCTACCAAAA
38890364 CTTTACGCTTAGTAAG
1 CTTTACGCTTAGTAAG
38890380 CTTTACGCTTAGTAAG
1 CTTTACGCTTAGTAAG
38890396 TCCATGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
CTTTACGCTTAGTAAG
Found at i:38896818 original size:13 final size:13
Alignment explanation
Indices: 38896800--38896824 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38896790 TAATGGTATA
38896800 TTGAATCCATGAT
1 TTGAATCCATGAT
38896813 TTGAATCCATGA
1 TTGAATCCATGA
38896825 AAATTTAGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:38898393 original size:47 final size:47
Alignment explanation
Indices: 38898339--38898884 Score: 907
Period size: 47 Copynumber: 11.6 Consensus size: 47
38898329 TATTTGAATA
38898339 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
38898386 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
38898433 AATGTGAAAGTGTATATATGTGATAAGCCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38898480 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCTGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
38898527 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38898576 AATGTGAAAGTGTATAAATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
38898623 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38898670 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
38898717 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
38898766 AATGTGAAA--GTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
38898811 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38898858 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
38898885 TCCCGAAGGG
Statistics
Matches: 468, Mismatches: 25, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
45 44 0.09
47 337 0.72
49 87 0.19
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:38898660 original size:190 final size:190
Alignment explanation
Indices: 38898339--38898884 Score: 956
Period size: 190 Copynumber: 2.9 Consensus size: 190
38898329 TATTTGAATA
38898339 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
38898402 TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGCCCTAAT
66 TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
*
38898467 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCTGATGTGATG
131 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
38898527 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
38898592 AATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
66 TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
*
38898657 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGTCTAATAGCCGATGTGATG
131 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
38898717 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * * * *
38898780 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGT
66 TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
* * *
38898845 GGCCAATGTGATGGATGTGAAAGTGTATAAATGTGATAAG
131 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
38898885 TCCCGAAGGG
Statistics
Matches: 343, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
188 113 0.33
190 230 0.67
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (190 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
Found at i:38900403 original size:40 final size:40
Alignment explanation
Indices: 38900345--38900449 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 40
38900335 GAGTGAAATG
* *
38900345 TCCGGGCTAAATCTCGAAGAGCATTTGTGCTAGTGATGTA
1 TCCGGACTAAGTCTCGAAGAGCATTTGTGCTAGTGATGTA
*
38900385 TTCGGACTAAGT-TCCGAAGAGCATTTGTGCTAGTGATGTA
1 TCCGGACTAAGTCT-CGAAGAGCATTTGTGCTAGTGATGTA
*
38900425 TCCGGGCTAAGTCTCGAAGAGCATT
1 TCCGGACTAAGTCTCGAAGAGCATT
38900450 CGTGTAACGA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 1 0.02
40 56 0.97
41 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (40 bp):
TCCGGACTAAGTCTCGAAGAGCATTTGTGCTAGTGATGTA
Found at i:38901875 original size:93 final size:93
Alignment explanation
Indices: 38901762--38901933 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
38901752 CGCCCATAAG
* *
38901762 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38901827 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
38901855 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38901920 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
38901934 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:38901930 original size:46 final size:46
Alignment explanation
Indices: 38901755--38901930 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
38901745 TGTAACCCGC
* * *
38901755 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
38901801 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
38901851 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
38901894 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
38901931 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:38909443 original size:93 final size:93
Alignment explanation
Indices: 38909330--38909501 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
38909320 CGCCCATAAG
* *
38909330 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38909395 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
38909423 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38909488 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
38909502 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:38909498 original size:46 final size:46
Alignment explanation
Indices: 38909323--38909498 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
38909313 TGTAACCCGC
* * *
38909323 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
38909369 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
38909419 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
38909462 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
38909499 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:38910841 original size:40 final size:40
Alignment explanation
Indices: 38910786--38910946 Score: 198
Period size: 40 Copynumber: 4.0 Consensus size: 40
38910776 GGATATTACA
*
38910786 ATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCGAAGAGC
1 ATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGC
* * *
38910826 ATTCGTGCTAGTGATGTATCTGGACTAAGTTCCGAAGAGC
1 ATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGC
* * *
38910866 ATTCGTGCTAGTGATATATCCGTGCTAA-ACCCTGAAGAGC
1 ATTCGTGCTAGTGATGTATCCGGGCTAAGTCCC-GAAGAGC
* * * * *
38910906 ATTTGTGCTGGTGTTTTATCCGGGCTAGGTCCCGAAGAGC
1 ATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGC
38910946 A
1 A
38910947 ATCATGCTGG
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 2 0.02
40 97 0.95
41 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
ATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGC
Found at i:38913162 original size:13 final size:13
Alignment explanation
Indices: 38913144--38913168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38913134 TAATGGTATA
38913144 TTGAATCCATGAT
1 TTGAATCCATGAT
38913157 TTGAATCCATGA
1 TTGAATCCATGA
38913169 AAATTTAGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:38914737 original size:47 final size:47
Alignment explanation
Indices: 38914683--38915085 Score: 666
Period size: 47 Copynumber: 8.6 Consensus size: 47
38914673 TATTTGAATA
38914683 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
38914730 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
**
38914777 AATGTGAAAGTGTATATATGTGATAAGGCCTAATCACCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
38914824 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38914871 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
38914918 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
38914967 AATGTGAAA--GTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
38915012 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38915059 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
38915086 TCCCGAAGGG
Statistics
Matches: 334, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
45 44 0.13
47 248 0.74
49 42 0.13
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:38919795 original size:19 final size:19
Alignment explanation
Indices: 38919767--38919835 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
38919757 ACTTATTTGA
38919767 AAAATCATTTTGATGTGTT
1 AAAATCATTTTGATGTGTT
* * * *
38919786 AAAATGATTTTAACTAT-TGA
1 AAAATCATTTTGA-TGTGT-T
38919806 AAAATCATTTTGATGTGTT
1 AAAATCATTTTGATGTGTT
*
38919825 AAAATTATTTT
1 AAAATCATTTT
38919836 AACTTAATTA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 24 0.63
20 14 0.37
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (19 bp):
AAAATCATTTTGATGTGTT
Found at i:38919806 original size:39 final size:39
Alignment explanation
Indices: 38919763--38919839 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
38919753 TCTGACTTAT
38919763 TTGAAAAATCATTTTGATGTGTTAAAATGATTTTAACTA
1 TTGAAAAATCATTTTGATGTGTTAAAATGATTTTAACTA
*
38919802 TTGAAAAATCATTTTGATGTGTTAAAATTATTTTAACT
1 TTGAAAAATCATTTTGATGTGTTAAAATGATTTTAACT
38919840 TAATTAAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (39 bp):
TTGAAAAATCATTTTGATGTGTTAAAATGATTTTAACTA
Found at i:38919828 original size:20 final size:20
Alignment explanation
Indices: 38919766--38919828 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
38919756 GACTTATTTG
38919766 AAAAATCATTTTGATGTGTT
1 AAAAATCATTTTGATGTGTT
* * * *
38919786 -AAAATGATTTTAACTAT-TG
1 AAAAATCATTTTGA-TGTGTT
38919805 AAAAATCATTTTGATGTGTT
1 AAAAATCATTTTGATGTGTT
38919825 AAAA
1 AAAA
38919829 TTATTTTAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (20 bp):
AAAAATCATTTTGATGTGTT
Found at i:38919852 original size:39 final size:38
Alignment explanation
Indices: 38919766--38919857 Score: 132
Period size: 39 Copynumber: 2.4 Consensus size: 38
38919756 GACTTATTTG
38919766 AAAAATCATTTTGATGTGTTAAAATGATTTTAACTATT
1 AAAAATCATTTTGATGTGTTAAAATGATTTTAACTATT
*
38919804 GAAAAATCATTTTGATGTGTTAAAATTATTTTAACTTAATT
1 -AAAAATCATTTTGATGTGTTAAAATGATTTTAAC-T-ATT
*
38919845 -AAGATCATTTTGA
1 AAAAATCATTTTGA
38919858 ATTGGTTAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 45 0.92
40 1 0.02
41 3 0.06
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (38 bp):
AAAAATCATTTTGATGTGTTAAAATGATTTTAACTATT
Found at i:38925103 original size:27 final size:27
Alignment explanation
Indices: 38925052--38925104 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
38925042 CAACTGTTAC
*
38925052 TGATTTTGAGAATGGGCTAGGCCCAAT
1 TGATTTTGAGAATGGGCTAGACCCAAT
38925079 TGATTTTGATG-A-GGGCTGAGACCCAA
1 TGATTTTGA-GAATGGGCT-AGACCCAA
38925105 GTGAAATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 5 0.22
27 17 0.74
28 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (27 bp):
TGATTTTGAGAATGGGCTAGACCCAAT
Found at i:38928180 original size:85 final size:85
Alignment explanation
Indices: 38928037--38928215 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
38928027 GGCCGGCCAT
*
38928037 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGGATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38928102 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
38928122 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38928187 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
38928207 GAGCATGGG
1 GAGCATGGG
38928216 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:38929518 original size:79 final size:82
Alignment explanation
Indices: 38929382--38929564 Score: 234
Period size: 79 Copynumber: 2.3 Consensus size: 82
38929372 TCGAATGATG
* *
38929382 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
38929446 TGTGCGAGTTACTA-AT
66 TGTGCGAGTTACTATAA
* * * **
38929462 TCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
38929524 TTGTGCGAGTTACTATAA
65 TTGTGCGAGTTACTATAA
*
38929542 T-CGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
38929565 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.64
80 31 0.34
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATAA
Found at i:38929573 original size:40 final size:40
Alignment explanation
Indices: 38929382--38929566 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
38929372 TCGAATGATG
* * * *
38929382 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
38929422 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
38929462 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
38929501 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
38929542 T-CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
38929567 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 11 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:38929588 original size:79 final size:79
Alignment explanation
Indices: 38929435--38929589 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
38929425 GGACTAAGAT
* **
38929435 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
38929500 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
38929514 CCGAAGGCATTTGTGCGAGTTACTATAAT-CGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
38929577 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
38929590 ATTCTGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
79 41 0.61
80 26 0.39
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:38936164 original size:85 final size:85
Alignment explanation
Indices: 38936021--38936199 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
38936011 GGCCGGCCAT
38936021 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38936086 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
38936106 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38936171 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
38936191 GAGCATGGG
1 GAGCATGGG
38936200 CAATAAAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:38937500 original size:79 final size:81
Alignment explanation
Indices: 38937364--38937546 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
38937354 TCGAATGATG
* *
38937364 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
38937428 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
38937443 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
38937505 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
38937523 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
38937547 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:38937562 original size:40 final size:40
Alignment explanation
Indices: 38937365--38937548 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
38937355 CGAATGATGT
* * * *
38937365 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
38937405 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
38937445 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
38937483 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
38937524 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
38937549 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:38937570 original size:79 final size:79
Alignment explanation
Indices: 38937417--38937571 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
38937407 GGACTAAGAT
* **
38937417 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
38937482 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
38937496 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
38937559 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
38937572 ATTCTGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 41 0.61
80 24 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:38939383 original size:22 final size:22
Alignment explanation
Indices: 38939330--38939384 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
38939320 TATTGCCTTT
* * *
38939330 AGCCATCCTATTTACGGTGTTG
1 AGCCATCCTGTCTACGGCGTTG
38939352 AGCCATCCTGTCTACGGCGTTG
1 AGCCATCCTGTCTACGGCGTTG
*
38939374 AGCCGTCCTGT
1 AGCCATCCTGT
38939385 TGACTTAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.15, C:0.29, G:0.25, T:0.31
Consensus pattern (22 bp):
AGCCATCCTGTCTACGGCGTTG
Found at i:38940193 original size:19 final size:18
Alignment explanation
Indices: 38940152--38940185 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38940142 TTTTCACAAA
*
38940152 GTTTTAACATGGCAAGAG
1 GTTTTAACATAGCAAGAG
38940170 GTTTTAA-ATAGCAAGA
1 GTTTTAACATAGCAAGA
38940186 AGGGTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (18 bp):
GTTTTAACATAGCAAGAG
Found at i:38952978 original size:40 final size:40
Alignment explanation
Indices: 38952916--38953173 Score: 306
Period size: 40 Copynumber: 6.5 Consensus size: 40
38952906 AATCCAAGTA
* * * *
38952916 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
38952955 CCTTCGGGACATAGCCCGGATATAGTAACTCGTACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
38952995 CCTTCAGGACTTAGCCCAGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
38953035 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
38953075 CCTTTGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
38953115 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
38953155 CCTCCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
38953174 TTATCATCTG
Statistics
Matches: 191, Mismatches: 25, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
39 12 0.06
40 179 0.94
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:38956301 original size:83 final size:83
Alignment explanation
Indices: 38956162--38956328 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
38956152 TAAATGTGAG
*
38956162 GTCCTTAAGATGTAAATGGGCTATTGGAATTATGCATGGACAAAATTGGACATTACTTAGTGGTT
1 GTCCTTAAGATGTAAATGGGCCATTGGAATTATGCATGGACAAAATTGGACATTACTTAGTGGTT
38956227 TTTAAATGAAATGAAAAA
66 TTTAAATGAAATGAAAAA
38956245 GTCCTTAAGATGTAAATGGGCCATTGGAATTATGCATGGACAAAATTGGACATTACTTAGTGGTT
1 GTCCTTAAGATGTAAATGGGCCATTGGAATTATGCATGGACAAAATTGGACATTACTTAGTGGTT
38956310 TTTAAATGAAATGAAAAA
66 TTTAAATGAAATGAAAAA
38956328 G
1 G
38956329 GTTATATTAG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (83 bp):
GTCCTTAAGATGTAAATGGGCCATTGGAATTATGCATGGACAAAATTGGACATTACTTAGTGGTT
TTTAAATGAAATGAAAAA
Found at i:38959773 original size:23 final size:22
Alignment explanation
Indices: 38959722--38959773 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
38959712 CCTCGTCTTT
*
38959722 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
38959744 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
38959767 TTCTTTT
1 TTCTTTT
38959774 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:38972230 original size:85 final size:85
Alignment explanation
Indices: 38972087--38972265 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
38972077 GGCCGGCCGT
38972087 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38972152 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
38972172 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38972237 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
38972257 GAGCATGGG
1 GAGCATGGG
38972266 CAATAAAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:38973586 original size:40 final size:40
Alignment explanation
Indices: 38973435--38973579 Score: 179
Period size: 40 Copynumber: 3.6 Consensus size: 40
38973425 CGAATGATGT
* * * *
38973435 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
*
38973475 CCGGGCTAAGAT-CCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
38973514 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
38973555 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
38973580 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
39 2 0.02
40 80 0.88
41 9 0.10
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:38973586 original size:80 final size:80
Alignment explanation
Indices: 38973434--38973612 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 80
38973424 TCGAATGATG
* *
38973434 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGGCTAAGATCCGAAGGCATTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGGCTAAGATCCGAAGGCATTG
**
38973499 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * *
38973514 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGGCTAAGAT-CCGAAGGCAT
* *
38973577 TTGAACGAGTAGCTATA
64 TGGAACGAGTAGCTAAA
* *
38973594 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
38973613 TACGTGATTC
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
79 17 0.20
80 60 0.71
81 7 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGGCTAAGATCCGAAGGCATTG
GAACGAGTAGCTAAA
Found at i:38985708 original size:60 final size:60
Alignment explanation
Indices: 38985635--38985756 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
38985625 GTATCAAGTT
38985635 GGTAATAAGGTATTCTTGAAAGTATCTCCATGGAAGAAGGTTTTAAGATTCGGTAGAGAA
1 GGTAATAAGGTATTCTTGAAAGTATCTCCATGGAAGAAGGTTTTAAGATTCGGTAGAGAA
* *
38985695 GGTAATAAGGTATTCTTGAAAGTATCTCTATGGAAGAAGGTTTTGAGATTCGGTAGAGAA
1 GGTAATAAGGTATTCTTGAAAGTATCTCCATGGAAGAAGGTTTTAAGATTCGGTAGAGAA
38985755 GG
1 GG
38985757 CAAGTTGAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (60 bp):
GGTAATAAGGTATTCTTGAAAGTATCTCCATGGAAGAAGGTTTTAAGATTCGGTAGAGAA
Found at i:38997836 original size:19 final size:19
Alignment explanation
Indices: 38997814--38997883 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
38997804 TGTTACACAG
38997814 ATGAATTACTGTTATACGA
1 ATGAATTACTGTTATACGA
* * *
38997833 ATGAAGTACTGTTTATAAGG
1 ATGAATTACTG-TTATACGA
* *
38997853 ATGAGTTGCTGTTAT-CGA
1 ATGAATTACTGTTATACGA
*
38997871 ATGAATTATTGTT
1 ATGAATTACTGTT
38997884 TATATGATTG
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
18 11 0.28
19 14 0.36
20 14 0.36
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.40
Consensus pattern (19 bp):
ATGAATTACTGTTATACGA
Found at i:38997884 original size:38 final size:39
Alignment explanation
Indices: 38997813--38997887 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
38997803 GTGTTACACA
38997813 GATGAATTACTGTTATACGAATGAAGTACTGTTTATAAG
1 GATGAATTACTGTTATACGAATGAAGTACTGTTTATAAG
* * * *
38997852 GATGAGTTGCTGTTAT-CGAATGAATTATTGTTTATA
1 GATGAATTACTGTTATACGAATGAAGTACTGTTTATA
38997888 TGATTGAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 18 0.56
39 14 0.44
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (39 bp):
GATGAATTACTGTTATACGAATGAAGTACTGTTTATAAG
Found at i:39005907 original size:19 final size:19
Alignment explanation
Indices: 39005879--39005918 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39005869 TTTCAAGAAT
*
39005879 ACTCTGTCCTCGAAGTGGA
1 ACTCTATCCTCGAAGTGGA
* *
39005898 ACTCTATCCTTGAATTGGA
1 ACTCTATCCTCGAAGTGGA
39005917 AC
1 AC
39005919 AAAATCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (19 bp):
ACTCTATCCTCGAAGTGGA
Found at i:39007966 original size:43 final size:42
Alignment explanation
Indices: 39007854--39008004 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 42
39007844 CAATGCCAAC
* *
39007854 GTCCCAGACGTGGTCTTACATGT-AATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACACGTAAATCAAATAT-GATGCCA-T
* * *
39007897 ATCCCAGACAGGGTCTTGCACG-AAATCAAATATGATGCCGAT
1 GTCCCAGACATGGTCTTACACGTAAATCAAATATGATGCC-AT
* *
39007939 GTCCCAAACATGGTCTTACACGTAAATCATAAGT-TGATGCCAAC
1 GTCCCAGACATGGTCTTACACGTAAATCA-AA-TATGATGCC-AT
* *
39007983 GTCTCAGACGTGGTCTTACACG
1 GTCCCAGACATGGTCTTACACG
39008005 ATAACACATA
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
42 25 0.28
43 34 0.38
44 29 0.33
45 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGTAAATCAAATATGATGCCAT
Found at i:39010121 original size:93 final size:93
Alignment explanation
Indices: 39010009--39010179 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
39009999 GCCCATAAGT
* *
39010009 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
39010074 TGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
39010102 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
39010167 CGAGTTCGGATGC
66 CGAGCTCGGATGC
39010180 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:39010176 original size:46 final size:46
Alignment explanation
Indices: 39010001--39010176 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
39009991 TGTAACCCGC
* *
39010001 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
39010047 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
39010093 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
39010140 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
39010177 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 69 0.63
47 31 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:39012117 original size:29 final size:29
Alignment explanation
Indices: 39012080--39012163 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
39012070 GATAACAAGA
*
39012080 AAACC-GAATAAAGAAATCCAAGATAGAG
1 AAACCAGAATAAAGAAATCCAAGATAAAG
39012108 AAACCAGAATAAAGAAATCC-AGAATAAAG
1 AAACCAGAATAAAGAAATCCAAG-ATAAAG
* * *
39012137 AGATCCAGGATAAAGAAACCCAAGATA
1 A-AACCAGAATAAAGAAATCCAAGATA
39012164 CGATACTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.15
29 20 0.42
30 19 0.40
31 2 0.04
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (29 bp):
AAACCAGAATAAAGAAATCCAAGATAAAG
Found at i:39012129 original size:15 final size:15
Alignment explanation
Indices: 39012076--39012154 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
39012066 CAAAGATAAC
*
39012076 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
39012090 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
39012105 GAGAAA-CCAGAATA
1 AAGAAATCCAGAATA
39012119 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
39012134 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
39012149 AAGAAA
1 AAGAAA
39012155 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
14 20 0.36
15 35 0.64
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:39012163 original size:15 final size:15
Alignment explanation
Indices: 39012087--39012163 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
39012077 AGAAAACCGA
39012087 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
39012102 ATAGAGAAA-CC-AG
1 ATAAAGAAATCCAAG
39012115 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
39012130 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
39012146 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
39012161 ATA
1 ATA
39012164 CGATACTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
13 2 0.04
14 10 0.19
15 39 0.75
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:39013534 original size:13 final size:13
Alignment explanation
Indices: 39013516--39013542 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39013506 AATATTTATC
39013516 ACATATGTATCAT
1 ACATATGTATCAT
39013529 ACATATGTATCAT
1 ACATATGTATCAT
39013542 A
1 A
39013543 AACTTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (13 bp):
ACATATGTATCAT
Found at i:39014756 original size:13 final size:13
Alignment explanation
Indices: 39014738--39014763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39014728 AGGGTTCTTA
39014738 TTCCAGATTTAAT
1 TTCCAGATTTAAT
39014751 TTCCAGATTTAAT
1 TTCCAGATTTAAT
39014764 CTCGTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TTCCAGATTTAAT
Found at i:39016938 original size:11 final size:11
Alignment explanation
Indices: 39016922--39016974 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
39016912 TTGGAGTAAC
39016922 AAAAAAATCAA
1 AAAAAAATCAA
* *
39016933 AAAAAATTGAA
1 AAAAAAATCAA
*
39016944 AAAAAATTCAA
1 AAAAAAATCAA
39016955 AAAAAAAGTCACA
1 AAAAAAA-TCA-A
39016968 AAAAAAA
1 AAAAAAA
39016975 ATCGAAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
11 25 0.69
12 3 0.08
13 8 0.22
ACGTcount: A:0.77, C:0.08, G:0.04, T:0.11
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:39016946 original size:12 final size:11
Alignment explanation
Indices: 39016922--39016960 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
39016912 TTGGAGTAAC
39016922 AAAAAAA-TCA
1 AAAAAAATTCA
*
39016932 AAAAAAATTGA
1 AAAAAAATTCA
39016943 AAAAAAATTCA
1 AAAAAAATTCA
39016954 AAAAAAA
1 AAAAAAA
39016961 AGTCACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:39016975 original size:19 final size:18
Alignment explanation
Indices: 39016953--39017036 Score: 57
Period size: 18 Copynumber: 4.5 Consensus size: 18
39016943 AAAAAAATTC
39016953 AAAAAAAAAGTCACAAAAA
1 AAAAAAAAAGT-ACAAAAA
** *
39016972 AAAATCGAAA-TTC-AAAA
1 AAAA-AAAAAGTACAAAAA
*
39016989 AAAAAAGAAGTGAGCAAAAA
1 AAAAAAAAAGT-A-CAAAAA
39017009 AGAAAAAAAAGTA-AAAAA
1 A-AAAAAAAAGTACAAAAA
39017027 AAGAAAAAAA
1 AA-AAAAAAA
39017037 AAAGTGAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
16 2 0.04
17 10 0.20
18 14 0.28
19 6 0.12
20 9 0.18
21 9 0.18
ACGTcount: A:0.76, C:0.06, G:0.11, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAGTACAAAAA
Found at i:39017009 original size:21 final size:20
Alignment explanation
Indices: 39016985--39017046 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
39016975 ATCGAAATTC
* *
39016985 AAAAAAAAAAGAAGTGAGCAA
1 AAAAAAAAAAAAAGTGA-AAA
* *
39017006 AAAAGAAAAAAAAGTAAAAA
1 AAAAAAAAAAAAAGTGAAAA
39017026 AAAGAAAAAAAAAAGTGAAAA
1 AAA-AAAAAAAAAAGTGAAAA
39017047 GTCTTGCGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 5 0.15
21 29 0.85
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAAAAGTGAAAA
Found at i:39017038 original size:10 final size:9
Alignment explanation
Indices: 39017004--39017037 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
39016994 AGAAGTGAGC
39017004 AAAAAAGAA
1 AAAAAAGAA
39017013 AAAAAAGTAA
1 AAAAAAG-AA
39017023 AAAAAAGAA
1 AAAAAAGAA
39017032 AAAAAA
1 AAAAAA
39017038 AAGTGAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:39017935 original size:18 final size:18
Alignment explanation
Indices: 39017914--39017948 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39017904 AGAAAAGAAA
39017914 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
39017932 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
39017949 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:39020030 original size:10 final size:10
Alignment explanation
Indices: 39020014--39020071 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
39020004 CAACTCCGAC
39020014 CAGCTCAATT
1 CAGCTCAATT
* *
39020024 GAGCTCATTT
1 CAGCTCAATT
39020034 CAGCTCAA-T
1 CAGCTCAATT
39020043 CGAGCTCAATT
1 C-AGCTCAATT
*
39020054 TAGCTACAATT
1 CAGCT-CAATT
39020065 CAGCTCA
1 CAGCTCA
39020072 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:39020037 original size:20 final size:20
Alignment explanation
Indices: 39020014--39020074 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
39020004 CAACTCCGAC
39020014 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
39020034 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
39020055 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
39020075 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:39025071 original size:23 final size:22
Alignment explanation
Indices: 39025019--39025071 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39025009 TCCACGTCTT
*
39025019 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39025041 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39025064 TTTCTTTT
1 TTTCTTTT
39025072 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39029899 original size:18 final size:18
Alignment explanation
Indices: 39029878--39029912 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39029868 TTTTTCTTTT
39029878 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
39029896 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
39029913 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:39030875 original size:21 final size:19
Alignment explanation
Indices: 39030835--39030882 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
39030825 TTTTGTCACT
* *
39030835 TATTTTTTTTCTTTTTTTC
1 TATTTTTTTTCATTTCTTC
39030854 TATTTTTTTTCGAATTTCTTC
1 TATTTTTTTTC--ATTTCTTC
39030875 T-TTTTTTT
1 TATTTTTTT
39030883 AAATCCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 7 0.28
21 7 0.28
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.79
Consensus pattern (19 bp):
TATTTTTTTTCATTTCTTC
Found at i:39035568 original size:30 final size:30
Alignment explanation
Indices: 39035534--39035617 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
39035524 TAAACTAAAA
*
39035534 TGAGCTCAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
39035564 TGAGCTGAGGC-TAAACTCCTAAGCTTAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
39035594 TGAGCTAAGGTTTAGCTCGTGAGC
1 TGAGCTAAGCTTTAGCTCGTGAGC
39035618 AGAATATGAG
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
29 2 0.05
30 35 0.90
31 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:39037909 original size:16 final size:16
Alignment explanation
Indices: 39037885--39037915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39037875 TTGCCTCTCT
*
39037885 TTTCTTTTTCTTTTTA
1 TTTCATTTTCTTTTTA
39037901 TTTCATTTTCTTTTT
1 TTTCATTTTCTTTTT
39037916 CTTCTTTTGC
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:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCATTTTCTTTTTA
Found at i:39037928 original size:15 final size:15
Alignment explanation
Indices: 39037886--39037943 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
39037876 TGCCTCTCTT
*
39037886 TTCTTTTTCTTTTTAT
1 TTCTTTTTCTTTTT-C
*
39037902 TTCATTTTCTTTTTC
1 TTCTTTTTCTTTTTC
*
39037917 TTCTTTTGCTTTTTC
1 TTCTTTTTCTTTTTC
*
39037932 TTTTTTTTCTTT
1 TTCTTTTTCTTT
39037944 GTTTTCTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
15 23 0.64
16 13 0.36
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (15 bp):
TTCTTTTTCTTTTTC
Found at i:39037930 original size:21 final size:21
Alignment explanation
Indices: 39037884--39037943 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
39037874 CTTGCCTCTC
* *
39037884 TTTTCTTTTTCTTTTTATTTCA
1 TTTTCTTTTTCTTCTT-TTGCA
*
39037906 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTCTTCTTTTGCA
*
39037927 TTTTCTTTTTTTTCTTT
1 TTTTCTTTTTCTTCTTT
39037944 GTTTTCTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTTCTTCTTTTGCA
Found at i:39040081 original size:18 final size:20
Alignment explanation
Indices: 39040050--39040091 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
39040040 AAAATCAGTC
*
39040050 AAAAAAGTCAAAA-T-AATA
1 AAAAAAGACAAAATTCAATA
*
39040068 AAAAAAGACGAAATTCAATA
1 AAAAAAGACAAAATTCAATA
39040088 AAAA
1 AAAA
39040092 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAAGACAAAATTCAATA
Found at i:39046523 original size:11 final size:12
Alignment explanation
Indices: 39046481--39046523 Score: 63
Period size: 11 Copynumber: 3.7 Consensus size: 12
39046471 TCAGATTTTT
39046481 TTTTCTTTTCGAA
1 TTTT-TTTTCGAA
39046494 TTTTTTTT-GAA
1 TTTTTTTTCGAA
39046505 TTTTTTTTCG-A
1 TTTTTTTTCGAA
39046516 TTTTTTTT
1 TTTTTTTT
39046524 ACTTGTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 20 0.69
12 5 0.17
13 4 0.14
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:39046539 original size:40 final size:41
Alignment explanation
Indices: 39046465--39046541 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
39046455 CATTAAACAC
* * * *
39046465 TTTTTTTCAGATTTTTTTTTCTTTTCGAATTTTTTTTGAAT
1 TTTTTTTCAGATTTTTTTTACTTGTAGAACTTTTTTTGAAT
*
39046506 TTTTTTTC-GATTTTTTTTACTTGTATAACTTTTTTT
1 TTTTTTTCAGATTTTTTTTACTTGTAGAACTTTTTTT
39046542 TGTACTATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 23 0.74
41 8 0.26
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.71
Consensus pattern (41 bp):
TTTTTTTCAGATTTTTTTTACTTGTAGAACTTTTTTTGAAT
Found at i:39046539 original size:41 final size:41
Alignment explanation
Indices: 39046465--39046543 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
39046455 CATTAAACAC
* * *
39046465 TTTTTTTCAGATTTTTTTTTCTTTTCGAATTTTTTTTGAAT
1 TTTTTTTCAGATTTTTTTTACTTGTAGAATTTTTTTTGAAT
*
39046506 TTTTTTTC-GATTTTTTTTACTTGTATAACTTTTTTTTG
1 TTTTTTTCAGATTTTTTTTACTTGTAGAA-TTTTTTTTG
39046544 TACTATATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 16 0.48
41 17 0.52
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.71
Consensus pattern (41 bp):
TTTTTTTCAGATTTTTTTTACTTGTAGAATTTTTTTTGAAT
Found at i:39049165 original size:30 final size:30
Alignment explanation
Indices: 39049129--39049226 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
39049119 GGCTCACTCC
39049129 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
39049159 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
39049189 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
39049219 TAGCTCAT
1 TAGCTCAT
39049227 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:39051857 original size:5 final size:5
Alignment explanation
Indices: 39051838--39051901 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
39051828 TCTTGTAAAG
* *
39051838 AGAAA ACAAA A-AAA AGAAA AGAAAA AGCAAA AGAAG A-AAA AGAAA ACGAAA
1 AGAAA AGAAA AGAAA AGAAA AG-AAA AG-AAA AGAAA AGAAA AGAAA A-GAAA
39051889 TA-AAA AGAAA AGA
1 -AGAAA AGAAA AGA
39051902 GAGGCAAGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
4 8 0.16
5 26 0.53
6 14 0.29
7 1 0.02
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.02
Consensus pattern (5 bp):
AGAAA
Found at i:39051868 original size:21 final size:21
Alignment explanation
Indices: 39051834--39051901 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
39051824 ACATTCTTGT
39051834 AAAGAGAAAA-CAAAAAAAAGA
1 AAAGA-AAAAGCAAAAAAAAGA
*
39051855 AAAGAAAAAGC-AAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAAG-A
*
39051876 AAAGAAAACG-AAATAAAAAGA
1 AAAGAAAAAGCAAA-AAAAAGA
39051897 AAAGA
1 AAAGA
39051902 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 11 0.28
21 24 0.60
22 5 0.12
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.01
Consensus pattern (21 bp):
AAAGAAAAAGCAAAAAAAAGA
Found at i:39051869 original size:12 final size:11
Alignment explanation
Indices: 39051848--39051901 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
39051838 AGAAAACAAA
39051848 AAAAAGAAAAG
1 AAAAAGAAAAG
39051859 AAAAAGCAAAAG
1 AAAAAG-AAAAG
*
39051871 -AAGA-AAAAG
1 AAAAAGAAAAG
* *
39051880 AAAACG-AAAT
1 AAAAAGAAAAG
39051890 AAAAAGAAAAG
1 AAAAAGAAAAG
39051901 A
1 A
39051902 GAGGCAAGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 5 0.15
10 10 0.30
11 13 0.39
12 5 0.15
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:39051874 original size:15 final size:14
Alignment explanation
Indices: 39051856--39051901 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
39051846 AAAAAAAGAA
39051856 AAGAAAAAGCAAAAG
1 AAGAAAAAG-AAAAG
39051871 AAGAAAAAGAAAACG
1 AAGAAAAAGAAAA-G
*
39051886 AAATAAAAAGAAAAG
1 -AAGAAAAAGAAAAG
39051901 A
1 A
39051902 GAGGCAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 12 0.43
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.02
Consensus pattern (14 bp):
AAGAAAAAGAAAAG
Found at i:39051999 original size:12 final size:12
Alignment explanation
Indices: 39051982--39052006 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39051972 TTTGGAAAGC
39051982 AAAAAGAAAATG
1 AAAAAGAAAATG
39051994 AAAAAGAAAATG
1 AAAAAGAAAATG
39052006 A
1 A
39052007 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:39052016 original size:30 final size:31
Alignment explanation
Indices: 39051982--39052063 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
39051972 TTTGGAAAGC
*
39051982 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
39052012 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
39052042 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
39052064 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:39055615 original size:30 final size:30
Alignment explanation
Indices: 39055581--39055678 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
39055571 AGCTCACTCC
39055581 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
39055611 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
39055641 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
39055671 TAGCTCAT
1 TAGCTCAT
39055679 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:39057585 original size:12 final size:12
Alignment explanation
Indices: 39057568--39057592 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39057558 AATTATAGAT
39057568 TCAAAAAAAAAA
1 TCAAAAAAAAAA
39057580 TCAAAAAAAAAA
1 TCAAAAAAAAAA
39057592 T
1 T
39057593 TGAGAAAAAA
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:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (12 bp):
TCAAAAAAAAAA
Found at i:39059821 original size:12 final size:12
Alignment explanation
Indices: 39059804--39059838 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39059794 AGAGCAAAAA
39059804 AAAGAAAAGAAT
1 AAAGAAAAGAAT
*
39059816 AAAGAAAAGAGT
1 AAAGAAAAGAAT
*
39059828 GAAGAAAAGAA
1 AAAGAAAAGAA
39059839 GAAAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (12 bp):
AAAGAAAAGAAT
Found at i:39067920 original size:6 final size:6
Alignment explanation
Indices: 39067909--39067942 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
39067899 AATTTTTTTC
* *
39067909 TCAATA TCAATA TCAATA TCAATC TCAATC TCAA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAA
39067943 ATTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (6 bp):
TCAATA
Found at i:39067994 original size:21 final size:20
Alignment explanation
Indices: 39067950--39067994 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39067940 CAAATTCTTT
*
39067950 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
39067970 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
39067991 TTTC
1 TTTC
39067995 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:39068938 original size:32 final size:33
Alignment explanation
Indices: 39068880--39068956 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 33
39068870 ATTTCAATCA
**
39068880 CTTTTTTTTTTTCAATTTTG-ATTTTTTTTCTT
1 CTTTTTTTTTTTCAATTCCGAATTTTTTTTCTT
39068912 CTTTTTTTGTTTT-AATTCCGAATTTTTTTTTCTT
1 CTTTTTTT-TTTTCAATTCCGAA-TTTTTTTTCTT
39068946 CTTTTTTTTTT
1 CTTTTTTTTTT
39068957 CTTCAATACT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 13 0.32
33 8 0.20
34 19 0.47
ACGTcount: A:0.09, C:0.10, G:0.04, T:0.77
Consensus pattern (33 bp):
CTTTTTTTTTTTCAATTCCGAATTTTTTTTCTT
Found at i:39068951 original size:14 final size:14
Alignment explanation
Indices: 39068934--39068960 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39068924 TAATTCCGAA
39068934 TTTTTTTTTCTTCT
1 TTTTTTTTTCTTCT
39068948 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
39068961 AATACTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTCTTCT
Found at i:39069020 original size:14 final size:14
Alignment explanation
Indices: 39069001--39069066 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
39068991 GAATACAAAC
39069001 TTTTTTTTTTTGAA
1 TTTTTTTTTTTGAA
**
39069015 TTTTTTTTTTCAAA
1 TTTTTTTTTTTGAA
39069029 TTTTTTTTTTTTCGAA
1 -TTTTTTTTTTT-GAA
*
39069045 TTTTTTTTTAT-ATA
1 TTTTTTTTTTTGA-A
39069059 TTTTTTTT
1 TTTTTTTT
39069067 ACAATACCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.02
14 21 0.48
15 20 0.45
16 2 0.05
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTTGAA
Found at i:39069022 original size:16 final size:16
Alignment explanation
Indices: 39069001--39069053 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
39068991 GAATACAAAC
39069001 TTTTTTTTTTT-GAA-
1 TTTTTTTTTTTCGAAT
*
39069015 -TTTTTTTTTTCAAAT
1 TTTTTTTTTTTCGAAT
39069030 TTTTTTTTTTTCGAAT
1 TTTTTTTTTTTCGAAT
39069046 TTTTTTTT
1 TTTTTTTT
39069054 ATATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 10 0.29
14 2 0.06
16 22 0.65
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTTTCGAAT
Found at i:39069037 original size:30 final size:30
Alignment explanation
Indices: 39069001--39069066 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
39068991 GAATACAAAC
39069001 TTTTTTTTTTT-GAATTTTTTTTT-TCAAAT
1 TTTTTTTTTTTCGAATTTTTTTTTAT-AAAT
*
39069030 TTTTTTTTTTTCGAATTTTTTTTTATATAT
1 TTTTTTTTTTTCGAATTTTTTTTTATAAAT
39069060 TTTTTTT
1 TTTTTTT
39069067 ACAATACCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 11 0.32
30 22 0.65
31 1 0.03
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (30 bp):
TTTTTTTTTTTCGAATTTTTTTTTATAAAT
Found at i:39076576 original size:22 final size:22
Alignment explanation
Indices: 39076548--39076589 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
39076538 TTGAACCATC
39076548 ACCATTTCGTACCAAATCCCTT
1 ACCATTTCGTACCAAATCCCTT
*
39076570 ACCATTTCGTACCAATTCCC
1 ACCATTTCGTACCAAATCCC
39076590 AAATACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.38, G:0.05, T:0.31
Consensus pattern (22 bp):
ACCATTTCGTACCAAATCCCTT
Found at i:39081659 original size:19 final size:19
Alignment explanation
Indices: 39081635--39081674 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39081625 AGCTCCCATG
39081635 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
39081654 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
39081673 TA
1 TA
39081675 TCAGCTCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:39085089 original size:23 final size:22
Alignment explanation
Indices: 39085037--39085089 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39085027 TCCACGTCTT
*
39085037 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39085059 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39085082 TTTCTTTT
1 TTTCTTTT
39085090 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39085134 original size:16 final size:16
Alignment explanation
Indices: 39085113--39085150 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
39085103 CTTTTTGCTC
39085113 TTTTTCATTCTCTTTT
1 TTTTTCATTCTCTTTT
39085129 TTTTTCATTCTCTTTT
1 TTTTTCATTCTCTTTT
39085145 TCTTTT
1 T-TTTT
39085151 TCCTCACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCATTCTCTTTT
Found at i:39087484 original size:13 final size:13
Alignment explanation
Indices: 39087460--39087494 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
39087450 TAAACTAAGT
39087460 AAATAAATAAATAA
1 AAATAAA-AAATAA
39087474 AAATAAAAAATAA
1 AAATAAAAAATAA
39087487 AAATAAAA
1 AAATAAAA
39087495 CTTTACAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:39088111 original size:10 final size:9
Alignment explanation
Indices: 39088095--39088120 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39088085 TTATACAAGT
39088095 TAAAAAAAA
1 TAAAAAAAA
39088104 TAAAAAAAA
1 TAAAAAAAA
39088113 TAAAAAAA
1 TAAAAAAA
39088121 GTGATTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:39090979 original size:40 final size:41
Alignment explanation
Indices: 39090924--39091005 Score: 157
Period size: 40 Copynumber: 2.0 Consensus size: 41
39090914 GGTTTGTACG
39090924 AATGGTTGGTAATGCCATTTGGCCTTACAAATGCT-CCAGC
1 AATGGTTGGTAATGCCATTTGGCCTTACAAATGCTCCCAGC
39090964 AATGGTTGGTAATGCCATTTGGCCTTACAAATGCTCCCAGC
1 AATGGTTGGTAATGCCATTTGGCCTTACAAATGCTCCCAGC
39091005 A
1 A
39091006 CTTTTATGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 35 0.85
41 6 0.15
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (41 bp):
AATGGTTGGTAATGCCATTTGGCCTTACAAATGCTCCCAGC
Found at i:39095070 original size:41 final size:41
Alignment explanation
Indices: 39095013--39095095 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
39095003 GGTTTGTACG
39095013 AATGGTTGGTAATGCCATTTGGCCTTACAAATGCTCCCAGC
1 AATGGTTGGTAATGCCATTTGGCCTTACAAATGCTCCCAGC
39095054 AATGGTTGGTAATGCCATTTGGCCTTACAAATGCTCCCAGC
1 AATGGTTGGTAATGCCATTTGGCCTTACAAATGCTCCCAGC
39095095 A
1 A
39095096 CTTTTATGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
AATGGTTGGTAATGCCATTTGGCCTTACAAATGCTCCCAGC
Found at i:39100320 original size:18 final size:18
Alignment explanation
Indices: 39100299--39100333 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39100289 TTTTTCTTTT
39100299 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
39100317 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
39100334 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:39112483 original size:15 final size:15
Alignment explanation
Indices: 39112463--39112510 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39112453 TCAAAGGTGG
39112463 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
39112478 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
39112493 -TTTATGGATATAAA
1 GTTTATGGATATGAA
39112507 GTTT
1 GTTT
39112511 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:39115994 original size:30 final size:30
Alignment explanation
Indices: 39115906--39116003 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 30
39115896 TTAAACTAAA
* *
39115906 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * * *
39115936 TTGACCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
39115966 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
39115996 ATGAGCTA
1 ATGAGCTA
39116004 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:39120562 original size:13 final size:12
Alignment explanation
Indices: 39120532--39120587 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
39120522 AATGTGAAAC
*
39120532 AAAAAGAAATTG
1 AAAAAGAAGTTG
39120544 AAAAAGAAGTTG
1 AAAAAGAAGTTG
*
39120556 AAGAAAGAAG-AG
1 AA-AAAGAAGTTG
*
39120568 AAAATG-AGTTAG
1 AAAAAGAAGTT-G
39120580 AAAAAGAA
1 AAAAAGAA
39120588 ACAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 22 0.63
13 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:39124400 original size:30 final size:29
Alignment explanation
Indices: 39124301--39124402 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
39124291 CGAGTTTAAA
*
39124301 CTAAAATGAGCTAA-GCTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGCTTAGCTCGTGAG
* * * * *
39124329 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGCTTAGCTCGTGAG
* *
39124359 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGCTTAGCTCGTGAG
39124389 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
39124403 GGAGTGAGCT
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
28 5 0.09
29 10 0.18
30 39 0.70
31 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGCTTAGCTCGTGAG
Found at i:39126542 original size:12 final size:12
Alignment explanation
Indices: 39126527--39126557 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39126517 TTCTTTTTGC
39126527 TTTTCAAAGGCT
1 TTTTCAAAGGCT
39126539 TTTTCAAAGGCT
1 TTTTCAAAGGCT
39126551 TTTTCAA
1 TTTTCAA
39126558 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:39126615 original size:5 final size:5
Alignment explanation
Indices: 39126605--39126666 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
39126595 CTCTTGCCTC
* *
39126605 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTCTT GCTTT TCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCT-TT TCTTT TC-TTT
39126652 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
39126667 GTTTCTCTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 4 0.09
5 30 0.64
6 12 0.26
7 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:39126640 original size:11 final size:11
Alignment explanation
Indices: 39126607--39126666 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
39126597 CTTGCCTCTC
39126607 TTTTCTTTT-T
1 TTTTCTTTTCT
*
39126617 ATTTCATTTTCT
1 TTTTC-TTTTCT
39126629 TTTTC--TTCT
1 TTTTCTTTTCT
* *
39126638 CTTGCTTTTCT
1 TTTTCTTTTCT
39126649 TTTTCTTTTC-
1 TTTTCTTTTCT
39126659 TTTTCTTT
1 TTTTCTTT
39126667 GTTTCTCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 7 0.17
10 12 0.30
11 16 0.40
12 5 0.12
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTCTTTTCT
Done.