Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 137 of 208
Found at i:41833369 original size:25 final size:24
Alignment explanation
Indices: 41833332--41833380 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
41833322 CAATAAACAT
41833332 GTATTCTACAAGTACCTTTTGTGGC
1 GTATTCTACAAGTACC-TTTGTGGC
** *
41833357 GTATTCTGTAAGTGCCTTTGTGGC
1 GTATTCTACAAGTACCTTTGTGGC
41833381 ATTTTTGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.41
Consensus pattern (24 bp):
GTATTCTACAAGTACCTTTGTGGC
Found at i:41834762 original size:24 final size:24
Alignment explanation
Indices: 41834725--41834774 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
41834715 CAAGACTTAC
41834725 TAAGGGGTCACATACTAAATCACA
1 TAAGGGGTCACATACTAAATCACA
* * *
41834749 TAAGGGTTCGCATATTAAATCACA
1 TAAGGGGTCACATACTAAATCACA
41834773 TA
1 TA
41834775 CTCAATTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (24 bp):
TAAGGGGTCACATACTAAATCACA
Found at i:41834793 original size:36 final size:36
Alignment explanation
Indices: 41834732--41835044 Score: 383
Period size: 36 Copynumber: 8.7 Consensus size: 36
41834722 TACTAAGGGG
* * * *
41834732 TCACATACTAAATCACATAAGGGTTCGCATATTAAA
1 TCACATACTAAATTACATGAAGGTTCGCATACTAAA
* * * *
41834768 TCACATACTCAATTACATGATGGTTCACATGCTAAA
1 TCACATACTAAATTACATGAAGGTTCGCATACTAAA
* * * *
41834804 TTATATACTAAATTACATTAAGGTTTGCATACTAAA
1 TCACATACTAAATTACATGAAGGTTCGCATACTAAA
* *
41834840 TCACATACTGAATTACATAAAGGTTCGCATACTAAA
1 TCACATACTAAATTACATGAAGGTTCGCATACTAAA
* * * *
41834876 TCACATATTAAATTACATGAGGGTTGGTATACTAAA
1 TCACATACTAAATTACATGAAGGTTCGCATACTAAA
* * *
41834912 TAATATACTAAATTACATGAAGGTTTGCATACTAAA
1 TCACATACTAAATTACATGAAGGTTCGCATACTAAA
* * *
41834948 TCATATACTAAATTACATGAGGGTTTGCATACTAAA
1 TCACATACTAAATTACATGAAGGTTCGCATACTAAA
41834984 TCACATACTAAATTACATGAAGGTTCGCATACTAAA
1 TCACATACTAAATTACATGAAGGTTCGCATACTAAA
* * *
41835020 TCATATACTAAATTACTTGAGGGTT
1 TCACATACTAAATTACATGAAGGTT
41835045 TAACATAGTG
Statistics
Matches: 237, Mismatches: 40, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 237 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (36 bp):
TCACATACTAAATTACATGAAGGTTCGCATACTAAA
Found at i:41834921 original size:108 final size:108
Alignment explanation
Indices: 41834732--41835045 Score: 448
Period size: 108 Copynumber: 2.9 Consensus size: 108
41834722 TACTAAGGGG
* * * * *
41834732 TCACATACTAAATCACATAAGGGTTCGCATATTAAATCACATACTCAATTACATGATGGTTCACA
1 TCACATACTAAATTACATAAGGGTTCGCATACTAAATCACATACTAAATTACATGAAGGTTCGCA
* * *
41834797 TGCTAAATTATATACTAAATTACATTAAGGTTTGCATACTAAA
66 TACTAAATAATATACTAAATTACATGAAGGTTTGCATACTAAA
* * * * * *
41834840 TCACATACTGAATTACATAAAGGTTCGCATACTAAATCACATATTAAATTACATGAGGGTTGGTA
1 TCACATACTAAATTACATAAGGGTTCGCATACTAAATCACATACTAAATTACATGAAGGTTCGCA
41834905 TACTAAATAATATACTAAATTACATGAAGGTTTGCATACTAAA
66 TACTAAATAATATACTAAATTACATGAAGGTTTGCATACTAAA
* * *
41834948 TCATATACTAAATTACATGAGGGTTTGCATACTAAATCACATACTAAATTACATGAAGGTTCGCA
1 TCACATACTAAATTACATAAGGGTTCGCATACTAAATCACATACTAAATTACATGAAGGTTCGCA
* * *
41835013 TACTAAATCATATACTAAATTACTTGAGGGTTT
66 TACTAAATAATATACTAAATTACATGAAGGTTT
41835046 AACATAGTGG
Statistics
Matches: 181, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 181 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (108 bp):
TCACATACTAAATTACATAAGGGTTCGCATACTAAATCACATACTAAATTACATGAAGGTTCGCA
TACTAAATAATATACTAAATTACATGAAGGTTTGCATACTAAA
Found at i:41835186 original size:24 final size:24
Alignment explanation
Indices: 41835150--41835206 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
41835140 TATCATTTAC
*
41835150 TAAGGGTTTGCAGTACAGTTAGCA
1 TAAGGGTTCGCAGTACAGTTAGCA
41835174 TAAGGGTTCGCAGTACAGTTAGCA
1 TAAGGGTTCGCAGTACAGTTAGCA
41835198 TAAGGGTTC
1 TAAGGGTTC
41835207 ACATAATAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (24 bp):
TAAGGGTTCGCAGTACAGTTAGCA
Found at i:41836489 original size:27 final size:26
Alignment explanation
Indices: 41836459--41836608 Score: 90
Period size: 28 Copynumber: 5.3 Consensus size: 26
41836449 AATAAATCTT
*
41836459 TATA-ATTTTTACATGTTTTTATTTCTA
1 TATATATTTTTA-ATATTTTTATTT-TA
*
41836486 TATATATTTATAATATTTTATATTTTA
1 TATATATTTTTAATATTTT-TATTTTA
41836513 TATAGTATTTTT-ATAATTTTTATTTTA
1 TATA-TATTTTTAAT-ATTTTTATTTTA
* * *
41836540 TGTAATTGATTTTTTTATTTTTTTATTTTAA
1 TAT-A-T-A-TTTTTAATATTTTTATTTT-A
* *
41836571 TTTAATAATTTTACAT-TTTTTATATTTA
1 TAT-ATATTTTTA-ATATTTTTAT-TTTA
41836599 TATAATATTT
1 TAT-ATATTT
41836609 ATATAAGTTT
Statistics
Matches: 101, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
27 27 0.27
28 44 0.44
29 7 0.07
30 16 0.16
31 7 0.07
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (26 bp):
TATATATTTTTAATATTTTTATTTTA
Found at i:41836503 original size:9 final size:10
Alignment explanation
Indices: 41836484--41836531 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
41836474 TTTTTATTTC
41836484 TATATATATT
1 TATATATATT
41836494 TATA-ATATT
1 TATATATATT
41836503 T-TATAT-TT
1 TATATATATT
41836511 TATATAGTATT
1 TATATA-TATT
*
41836522 TTTATA-ATT
1 TATATATATT
41836531 T
1 T
41836532 TTATTTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
8 5 0.15
9 16 0.48
10 5 0.15
11 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TATATATATT
Found at i:41836510 original size:28 final size:28
Alignment explanation
Indices: 41836474--41836646 Score: 87
Period size: 30 Copynumber: 6.2 Consensus size: 28
41836464 TTTTTACATG
*
41836474 TTTTTAT-TTCTATATA-TA-TTTATAA
1 TTTTTATATTTTATATAGTATTTTATAA
41836499 TATTTTATATTTTATATAGTATTTTTATAA
1 T-TTTTATATTTTATATAGTA-TTTTATAA
* * * *
41836529 -TTTT-TATTTTATGTAATTGATTTTTTTA
1 TTTTTATATTTTATAT-AGT-ATTTTATAA
* * * * *
41836557 TTTTTTTATTTTAATTTAATAATTTTACAT
1 TTTTTATATTTT-ATATAGT-ATTTTATAA
*
41836587 TTTTTATA-TTTATATAATATTTATATAA
1 TTTTTATATTTTATATAGTATTT-TATAA
41836615 GTTTTTAATATATTT-TATA-TA--TTATAA
1 -TTTTT-ATAT-TTTATATAGTATTTTATAA
41836642 TTTTT
1 TTTTT
41836647 TTAATATTCT
Statistics
Matches: 117, Mismatches: 16, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
25 1 0.01
26 11 0.09
27 26 0.22
28 24 0.21
29 13 0.11
30 32 0.27
31 7 0.06
32 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTTTATATTTTATATAGTATTTTATAA
Found at i:41837563 original size:2 final size:2
Alignment explanation
Indices: 41837556--41837599 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
41837546 TTTTCTCTTT
41837556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41837597 TA T
1 TA T
41837600 TAAGTGTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41845496 original size:31 final size:31
Alignment explanation
Indices: 41845461--41845544 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
41845451 TTAACAACCG
* *
41845461 AATGAGTTAAATAAAAACTTCTAGA-TAGTTT
1 AATGACTTAAATAAAAACTT-TAGAGTAGTTA
* *
41845492 AATGACTTAATTAAAAACTTTCGAGTAGTTA
1 AATGACTTAAATAAAAACTTTAGAGTAGTTA
* * *
41845523 AATAATTTTAATAAAAACTTTA
1 AATGACTTAAATAAAAACTTTA
41845545 CTGAGCAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
30 3 0.07
31 40 0.93
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTAGAGTAGTTA
Found at i:41861585 original size:14 final size:15
Alignment explanation
Indices: 41861568--41861596 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41861558 GAGTATGGTA
41861568 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
41861582 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
41861597 TACTAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:41868957 original size:30 final size:29
Alignment explanation
Indices: 41868923--41869125 Score: 148
Period size: 29 Copynumber: 6.9 Consensus size: 29
41868913 AACGTCGATC
*
41868923 ATCGACAAATGAAAAGGGATAGCTTCGGCT
1 ATCGA-AAATGAAAAGGGATAGCTTCGACT
* *
41868953 ATCGAATACGAAAAGGGATAGCTTCGACT
1 ATCGAAAATGAAAAGGGATAGCTTCGACT
** * * *
41868982 ATCGATTATGAAAAGGGAT-GGTGACGACC
1 ATCGAAAATGAAAAGGGATAGCT-TCGACT
*
41869011 ATC-AACAATGAAAAGGGATGGCTTCGACT
1 ATCGAA-AATGAAAAGGGATAGCTTCGACT
* *
41869040 ATC-AAACTATGAAAAGGGATAGCTTTGGCT
1 ATCGAAA--ATGAAAAGGGATAGCTTCGACT
* * *
41869070 ATC-AAATTATGAAAAGGGAT-GGTGACGACC
1 ATCGAAA--ATGAAAAGGGATAGCT-TCGACT
41869100 ATC-AAATTATGAAAAGGGATAGCTTC
1 ATCGAAA--ATGAAAAGGGATAGCTTC
41869126 AGTTGTTGCA
Statistics
Matches: 142, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.03
29 68 0.48
30 68 0.48
31 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (29 bp):
ATCGAAAATGAAAAGGGATAGCTTCGACT
Found at i:41868969 original size:29 final size:30
Alignment explanation
Indices: 41868931--41869179 Score: 195
Period size: 30 Copynumber: 8.4 Consensus size: 30
41868921 TCATCGACAA
*
41868931 ATGAAAAGGGATAGCTTCGGCTATCGAA-T
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
*
41868960 ACGAAAAGGGATAGCTTCGACTATCG-ATT
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
* * * **
41868989 ATGAAAAGGGAT-GGTGACGACCATC-AACA
1 ATGAAAAGGGATAGCT-TCGACTATCGAATT
* * *
41869018 ATGAAAAGGGATGGCTTCGACTATCAAACT
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
* * *
41869048 ATGAAAAGGGATAGCTTTGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
* * * *
41869078 ATGAAAAGGGAT-GGTGACGACCATCAAATT
1 ATGAAAAGGGATAGCT-TCGACTATCGAATT
* * * * *
41869108 ATGAAAAGGGATAGCTTC-AGTTGTTGCACT
1 ATGAAAAGGGATAGCTTCGA-CTATCGAATT
* **
41869138 ATGAAAAGGGATAACTTCGGTTATCGAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
*
41869168 ACGAAAAGGGAT
1 ATGAAAAGGGAT
41869180 GGGTCAACCA
Statistics
Matches: 174, Mismatches: 37, Indels: 17
0.76 0.16 0.07
Matches are distributed among these distances:
28 3 0.02
29 66 0.38
30 103 0.59
31 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGACTATCGAATT
Found at i:41879583 original size:25 final size:25
Alignment explanation
Indices: 41879554--41879650 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 25
41879544 CTACAAACTC
41879554 TCTAGATAATATGCCACAAAGGCTT
1 TCTAGATAATATGCCACAAAGGCTT
* * *
41879579 TCTAGGTAAAACGCCACAAAGGCTCT
1 TCTAGATAATATGCCACAAAGGCT-T
* * *
41879605 TC-AAATAATCTGCCACAAAGGCTC
1 TCTAGATAATATGCCACAAAGGCTT
* *
41879629 TCCAGGTAAT-TCGCCACAAAGG
1 TCTAGATAATAT-GCCACAAAGG
41879651 TTTAGTTTGG
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
24 3 0.05
25 52 0.90
26 3 0.05
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (25 bp):
TCTAGATAATATGCCACAAAGGCTT
Found at i:41882367 original size:25 final size:25
Alignment explanation
Indices: 41882227--41882370 Score: 126
Period size: 25 Copynumber: 5.8 Consensus size: 25
41882217 CACACCATAA
* * * *
41882227 CTCTCAGGAGCTTCCTGATATCTAG
1 CTCTCACGAGCTTCCCGATATTTGG
* * * *
41882252 CTCTCACAAGCCTCCCGTTATTTAG
1 CTCTCACGAGCTTCCCGATATTTGG
* * * * *
41882277 CTCTTATGAGCATCTCGATATGTGG
1 CTCTCACGAGCTTCCCGATATTTGG
**
41882302 CTCTCACGAGCTTCCTAATATTTGG
1 CTCTCACGAGCTTCCCGATATTTGG
*
41882327 CTCCCACGAGCTTCCCGATATTTGG
1 CTCTCACGAGCTTCCCGATATTTGG
* *
41882352 CTTTCATGAGCTTCCCGAT
1 CTCTCACGAGCTTCCCGAT
41882371 TAACGGCTCT
Statistics
Matches: 92, Mismatches: 27, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 92 1.00
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (25 bp):
CTCTCACGAGCTTCCCGATATTTGG
Found at i:41882447 original size:25 final size:25
Alignment explanation
Indices: 41882400--41882448 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
41882390 CCTGATAATT
* *
41882400 AGCTCACATGAGCTTTCCGTTATAC
1 AGCTCACATGAGCTTCCCATTATAC
41882425 AGCTCACATGAGCTTCCCATTATA
1 AGCTCACATGAGCTTCCCATTATA
41882449 TGGCTCGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.31
Consensus pattern (25 bp):
AGCTCACATGAGCTTCCCATTATAC
Found at i:41882454 original size:25 final size:25
Alignment explanation
Indices: 41882299--41882467 Score: 76
Period size: 25 Copynumber: 6.8 Consensus size: 25
41882289 TCTCGATATG
* * * * *
41882299 TGGCTCTCACGAGCTTCCTAATATT
1 TGGCTCACATGAGCTTCCCATTATA
* * *
41882324 TGGCTCCCACGAGCTTCCCGA-TATT
1 TGGCTCACATGAGCTTCCC-ATTATA
**
41882349 TGGCTTTCATGAGCTTCCCGATTA-A
1 TGGCTCACATGAGCTTCCC-ATTATA
* *** * *
41882374 CGGCTCTTTTGAGCTTCCTGATAAT-
1 TGGCTCACATGAGCTTCC-CATTATA
* * *
41882399 TAGCTCACATGAGCTTTCCGTTATA
1 TGGCTCACATGAGCTTCCCATTATA
**
41882424 CAGCTCACATGAGCTTCCCATTATA
1 TGGCTCACATGAGCTTCCCATTATA
*
41882449 TGGCTCGA-AAGAGCTTCCC
1 TGGCTC-ACATGAGCTTCCC
41882468 GTTTACATGC
Statistics
Matches: 111, Mismatches: 27, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
24 3 0.03
25 104 0.94
26 4 0.04
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCATTATA
Found at i:41882487 original size:25 final size:25
Alignment explanation
Indices: 41882407--41882487 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
41882397 ATTAGCTCAC
*
41882407 ATGAGCTTTCCGTTATACA-GCTC-A
1 ATGAGCTTCCCGTT-TACATGCTCGA
* *
41882431 CATGAGCTTCCC-ATTATATGGCTCGA
1 -ATGAGCTTCCCGTTTACAT-GCTCGA
* *
41882457 AAGAGCTTCCCGTTTACATGCTCGT
1 ATGAGCTTCCCGTTTACATGCTCGA
41882482 ATGAGC
1 ATGAGC
41882488 ATACATGTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
23 3 0.07
24 1 0.02
25 34 0.77
26 6 0.14
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCGTTTACATGCTCGA
Found at i:41886962 original size:19 final size:20
Alignment explanation
Indices: 41886941--41886978 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
41886931 TTTTTCAATT
41886941 TTTTTA-AAAAAA-TTAAAA
1 TTTTTAGAAAAAATTTAAAA
41886959 TTTTTAGAAAAAATTTAAAA
1 TTTTTAGAAAAAATTTAAAA
41886979 AGTTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
TTTTTAGAAAAAATTTAAAA
Found at i:41887007 original size:22 final size:21
Alignment explanation
Indices: 41886968--41887008 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41886958 ATTTTTAGAA
**
41886968 AAAATTTAAAAAGTTTTATTC
1 AAAATTTAAAAACATTTATTC
41886989 AAAATTTGAAAAACATTTAT
1 AAAATTT-AAAAACATTTAT
41887009 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAATTTAAAAACATTTATTC
Found at i:41887358 original size:33 final size:34
Alignment explanation
Indices: 41887321--41887387 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
41887311 AAATAAATTC
* *
41887321 AATTCTTTTT-ATATCAAGTAAATATAATTATTT
1 AATTCTTTTTCACATCAAATAAATATAATTATTT
*
41887354 AATTCTTTTTCACATTAAATAAATATAATTATTT
1 AATTCTTTTTCACATCAAATAAATATAATTATTT
41887388 TTGTATACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 10 0.33
34 20 0.67
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.51
Consensus pattern (34 bp):
AATTCTTTTTCACATCAAATAAATATAATTATTT
Found at i:41891194 original size:6 final size:6
Alignment explanation
Indices: 41891183--41891215 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
41891173 TCATTCCCAT
41891183 CTGCAG CTGCAG CTGCAG CTGCAG CTGCAG CTG
1 CTGCAG CTGCAG CTGCAG CTGCAG CTGCAG CTG
41891216 TAGCAGTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.18
Consensus pattern (6 bp):
CTGCAG
Found at i:41892348 original size:47 final size:47
Alignment explanation
Indices: 41892296--41892392 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
41892286 GTACAAATTT
41892296 TATGAGTGCAGAATTTACATCATAAAATCATGTTAATAAAATTTAAG
1 TATGAGTGCAGAATTTACATCATAAAATCATGTTAATAAAATTTAAG
*
41892343 TATGAGTGCAGAATTTACATTATAAAATCATGTTAATAAAATTTAAG
1 TATGAGTGCAGAATTTACATCATAAAATCATGTTAATAAAATTTAAG
41892390 TAT
1 TAT
41892393 CGAATATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (47 bp):
TATGAGTGCAGAATTTACATCATAAAATCATGTTAATAAAATTTAAG
Found at i:41893314 original size:29 final size:28
Alignment explanation
Indices: 41893259--41893331 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
41893249 ATGCATTATA
41893259 AAAGAAGAAAAGAAAAATAAAGGAAAAT
1 AAAGAAGAAAAGAAAAATAAAGGAAAAT
* * *
41893287 AAAGAA-AAAAGAGAGAAATAATGTAAAAG
1 AAAGAAGAAAAGA-A-AAATAAAGGAAAAT
* *
41893316 AAAAAAGAAAATAAAA
1 AAAGAAGAAAAGAAAA
41893332 GAATTAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
27 6 0.16
28 9 0.24
29 17 0.46
30 5 0.14
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.08
Consensus pattern (28 bp):
AAAGAAGAAAAGAAAAATAAAGGAAAAT
Found at i:41894217 original size:26 final size:26
Alignment explanation
Indices: 41894181--41894234 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
41894171 AGTTATGTGA
41894181 TAATCAAGTTTTGGGAAAGCCTACCT
1 TAATCAAGTTTTGGGAAAGCCTACCT
41894207 TAATCAAGTTTTGGGAAAGCCTACCT
1 TAATCAAGTTTTGGGAAAGCCTACCT
41894233 TA
1 TA
41894235 CTCCAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (26 bp):
TAATCAAGTTTTGGGAAAGCCTACCT
Found at i:41901121 original size:34 final size:34
Alignment explanation
Indices: 41901071--41901187 Score: 144
Period size: 34 Copynumber: 3.4 Consensus size: 34
41901061 ATGGTATGGC
*
41901071 ATTCTAATATGATATATGTTTTTGAAAATATGAT
1 ATTCTAATATGATATATGTTTTTGGAAATATGAT
* * * *
41901105 ATTCTAATCTGGTATATGTTTCTGGAAATATGAC
1 ATTCTAATATGATATATGTTTTTGGAAATATGAT
* * * *
41901139 ATTCTGATTTGATATATGTTTTTGGTAATGTGAT
1 ATTCTAATATGATATATGTTTTTGGAAATATGAT
*
41901173 ATTCTGATATGATAT
1 ATTCTAATATGATAT
41901188 TTGTATATGT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 70 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (34 bp):
ATTCTAATATGATATATGTTTTTGGAAATATGAT
Found at i:41903052 original size:17 final size:19
Alignment explanation
Indices: 41903025--41903064 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
41903015 ATTTCATGTA
41903025 TTTTATAATATTTTA-AAT
1 TTTTATAATATTTTAGAAT
41903043 TTTTAT-ATATTTTAGAAT
1 TTTTATAATATTTTAGAAT
41903061 TTTT
1 TTTT
41903065 CGTGAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTATAATATTTTAGAAT
Found at i:41906175 original size:17 final size:17
Alignment explanation
Indices: 41906153--41906203 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
41906143 ATGTAGTCAT
*
41906153 TTGAAAAACTTTCAAAA
1 TTGAAAAACTTTAAAAA
* *
41906170 TTGAAATATTTTAAAAA
1 TTGAAAAACTTTAAAAA
*
41906187 TT-AAAAATGTTTAAAAA
1 TTGAAAAA-CTTTAAAAA
41906204 CTATTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (17 bp):
TTGAAAAACTTTAAAAA
Found at i:41911407 original size:14 final size:13
Alignment explanation
Indices: 41911384--41911425 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
41911374 CTGTCCCCTA
41911384 ATTTTTTATTTTT
1 ATTTTTTATTTTT
41911397 ATTTATTTATTTTT
1 ATTT-TTTATTTTT
* *
41911411 -TCTTTTATTATT
1 ATTTTTTATTTTT
41911423 ATT
1 ATT
41911426 ATTATTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 8 0.33
13 7 0.29
14 9 0.38
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:41911504 original size:31 final size:30
Alignment explanation
Indices: 41911466--41911534 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
41911456 CAAATTTTGT
* *
41911466 TATATATATATACATTCATACATTTTTATAA
1 TATATATATACACATACATA-ATTTTTATAA
*
41911497 TATATATATACACATACATATTTTTTATAA
1 TATATATATACACATACATAATTTTTATAA
*
41911527 TTTATATA
1 TATATATA
41911535 CATATGCCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (30 bp):
TATATATATACACATACATAATTTTTATAA
Found at i:41911512 original size:27 final size:30
Alignment explanation
Indices: 41911467--41911537 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
41911457 AAATTTTGTT
41911467 ATATATATATACATTCATAC-A-TTTTTATA
1 ATATATATATACA-TCATACAATTTTTTATA
41911496 ATATATATATACA-CATACATATTTTTTATA
1 ATATATATATACATCATACA-ATTTTTTATA
41911526 AT-T-TATATACAT
1 ATATATATATACAT
41911538 ATGCCTACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
27 5 0.13
28 8 0.21
29 15 0.39
30 10 0.26
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (30 bp):
ATATATATATACATCATACAATTTTTTATA
Found at i:41913888 original size:24 final size:25
Alignment explanation
Indices: 41913843--41913895 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
41913833 TCTTTTTGCA
* *
41913843 TTCATTCCATGCATCTGTATTACAT
1 TTCATTCCATGCATCTGCATTAAAT
* *
41913868 TTCATTGCAT-CATTTGCATTAAAT
1 TTCATTCCATGCATCTGCATTAAAT
41913892 TTCA
1 TTCA
41913896 CGAAAGAGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (25 bp):
TTCATTCCATGCATCTGCATTAAAT
Found at i:41916657 original size:32 final size:30
Alignment explanation
Indices: 41916620--41916686 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
41916610 AAAAAAGGAG
*
41916620 AAAAAAGAAGAGAAAAAAACAAAAAATAAAA
1 AAAAAAGAA-AGAAAAAAACAAAAAACAAAA
* * *
41916651 ATAAAAAGAAATAAGAAAATAAAAAACAAAA
1 A-AAAAAGAAAGAAAAAAACAAAAAACAAAA
41916682 AAAAA
1 AAAAA
41916687 CCTCTACTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 4 0.13
31 19 0.61
32 8 0.26
ACGTcount: A:0.84, C:0.03, G:0.07, T:0.06
Consensus pattern (30 bp):
AAAAAAGAAAGAAAAAAACAAAAAACAAAA
Found at i:41917154 original size:19 final size:18
Alignment explanation
Indices: 41917120--41917172 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
41917110 ACTTAACTTG
41917120 AAAAAAAAGAACAAAAAGA
1 AAAAAAAAGAA-AAAAAGA
41917139 AAAAGAAAAGAAAAAAAGA
1 AAAA-AAAAGAAAAAAAGA
*
41917158 ACGAAAAAAGAAAAA
1 A-AAAAAAAGAAAAA
41917173 GGAGAGGCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAGA
Found at i:41918259 original size:44 final size:44
Alignment explanation
Indices: 41918183--41918269 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
41918173 ACCAGCCTTA
** * * ** * *
41918183 TCTCCCTGGGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTG
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTG
41918227 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTT
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTT
41918270 ATCTTCTCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTG
Found at i:41918390 original size:45 final size:45
Alignment explanation
Indices: 41918340--41918659 Score: 439
Period size: 45 Copynumber: 7.1 Consensus size: 45
41918330 GTGGAGTAAG
* *
41918340 TCGAAGATTGCAGGTCTTATCTTCCTGTATTGGCAGCAAAGTAGA
1 TCGAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA
*
41918385 TCGAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGA
1 TCGAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA
*
41918430 -CTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGA
1 TC-GAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA
*
41918475 TCGAAGATAGCAGGTCTTGTCTTCCTGTATTGGTAGCAAAGTAGA
1 TCGAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA
* * * *
41918520 -CTGAAGATAGCAGATCTTGTCTTCCAGTATTGGCAACGAAGTAGA
1 TC-GAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA
** * * *
41918565 TTAAAGATAGTAGGTCTTGTCTTCCTGTATTGGCAACGAAGTAGA
1 TCGAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA
* * *
41918610 TCGAAGATAGCAGATCTTTTCTTCCTGTATTGGCAGCGAAA-CAGA
1 TCGAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGC-AAAGTAGA
41918655 TCGAA
1 TCGAA
41918660 AACACCAGCC
Statistics
Matches: 245, Mismatches: 25, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
44 2 0.01
45 240 0.98
46 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (45 bp):
TCGAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA
Found at i:41918831 original size:50 final size:49
Alignment explanation
Indices: 41918777--41919116 Score: 164
Period size: 50 Copynumber: 6.8 Consensus size: 49
41918767 TTGTCATTAC
* *
41918777 AGTGGAATAGATTGAAGCTACAATGGCGAATCTTACTTCTCTGGCAATGT
1 AGTGGAATAGATTGAAGCTACAACGGCGAATCTTACTTC-CTAGCAATGT
* * * * ** *
41918827 AGTGGAACAGGTTGAAGCTACAACAGCAAATCTTGTTTCCTCG-ATATTGT
1 AGTGGAATAGATTGAAGCTACAACGGCGAATCTTACTTCCTAGCA-A-TGT
* ** * * * * * *
41918877 AATTAAAAAGATTGAAGCCATAACGACGAATCTTACTTCCCTAGCAGTGC
1 AGTGGAATAGATTGAAGCTACAACGGCGAATCTTACTT-CCTAGCAATGT
** ** *
41918927 AGCAGAATAGATTGAAGCTACAACGGCGAATCTTACTTCCCCG-ATATTGC
1 AGTGGAATAGATTGAAGCTACAACGGCGAATCTTACTTCCTAGCA-A-TGT
* ** * * * * * * *
41918977 AATTAAAAAAATTGAAGCCACAACGGCGAATCTTACTTCCTTGGTAGTGC
1 AGTGGAATAGATTGAAGCTACAACGGCGAATCTTACTTCC-TAGCAATGT
** * * * ** * *
41919027 AGCAGAACAGATTGAAGCTACAACGACGAATCTTGCTTCCCCGACATTGC
1 AGTGGAATAGATTGAAGCTACAACGGCGAATCTTACTTCCTAG-CAATGT
* ** * *
41919077 AATTAAAAAGATTGAAGC-ACAACGGCGGATCTTACTTCCT
1 AGTGGAATAGATTGAAGCTACAACGGCGAATCTTACTTCCT
41919117 CGACATTGTA
Statistics
Matches: 215, Mismatches: 66, Indels: 19
0.72 0.22 0.06
Matches are distributed among these distances:
48 2 0.01
49 26 0.12
50 180 0.84
51 5 0.02
52 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (49 bp):
AGTGGAATAGATTGAAGCTACAACGGCGAATCTTACTTCCTAGCAATGT
Found at i:41918959 original size:100 final size:100
Alignment explanation
Indices: 41918785--41919115 Score: 430
Period size: 100 Copynumber: 3.3 Consensus size: 100
41918775 ACAGTGGAAT
* * * * * * ** *
41918785 AGATTGAAGCTACAATGGCGAATCTTACTTCTCTGGCAATGTAGTGGAACAGGTTGAAGCTACAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCAGTGCAGCAGAACAGATTGAAGCTACAA
* * * * *
41918850 CAGCAAATCTTGTTTCCTCGATATTGTAATTAAAA
66 CGGCGAATCTTGCTTCCCCGATATTGCAATTAAAA
* * *
41918885 AGATTGAAGCCATAACGACGAATCTTACTTCCCTAGCAGTGCAGCAGAATAGATTGAAGCTACAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCAGTGCAGCAGAACAGATTGAAGCTACAA
*
41918950 CGGCGAATCTTACTTCCCCGATATTGCAATTAAAA
66 CGGCGAATCTTGCTTCCCCGATATTGCAATTAAAA
* * * *
41918985 AAATTGAAGCCACAACGGCGAATCTTACTTCCTTGGTAGTGCAGCAGAACAGATTGAAGCTACAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCAGTGCAGCAGAACAGATTGAAGCTACAA
* *
41919050 CGACGAATCTTGCTTCCCCGACATTGCAATTAAAA
66 CGGCGAATCTTGCTTCCCCGATATTGCAATTAAAA
*
41919085 AGATTGAAG-CACAACGGCGGATCTTACTTCC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCC
41919116 TCGACATTGT
Statistics
Matches: 201, Mismatches: 30, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
99 21 0.10
100 180 0.90
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (100 bp):
AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCAGTGCAGCAGAACAGATTGAAGCTACAA
CGGCGAATCTTGCTTCCCCGATATTGCAATTAAAA
Found at i:41919352 original size:44 final size:45
Alignment explanation
Indices: 41919250--41919357 Score: 164
Period size: 44 Copynumber: 2.4 Consensus size: 45
41919240 GTCTTAGCCT
* * *
41919250 CCTGAAGTTGCAGTGGGGCAGACTGAAGATAACGAGTCTTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTGAAGATAACGAATCCTATCTC
* *
41919295 CCTGAAGTTGCAGTGGAGCAGACTGAAGCT-ACTAATCCTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTGAAGATAACGAATCCTATCTC
41919339 CCTGAAGTTGCAGTGGAGC
1 CCTGAAGTTGCAGTGGAGC
41919358 GAATTAAACC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
44 30 0.52
45 28 0.48
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (45 bp):
CCTGAAGTTGCAGTGGAGCAGACTGAAGATAACGAATCCTATCTC
Found at i:41921186 original size:27 final size:29
Alignment explanation
Indices: 41921155--41921224 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
41921145 AAATTTTGTT
*
41921155 ATATATATACATTCATAC-A-TTTTTATA
1 ATATATATACATACATACAATTTTTTATA
* *
41921182 ATATATATATAAACATACATATTTTTTATA
1 ATATATATACATACATACA-ATTTTTTATA
*
41921212 ATTTATATACATA
1 ATATATATACATA
41921225 TACCTACTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 15 0.44
29 1 0.03
30 18 0.53
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATATATACATACATACAATTTTTTATA
Found at i:41926545 original size:21 final size:21
Alignment explanation
Indices: 41926524--41926814 Score: 153
Period size: 21 Copynumber: 14.0 Consensus size: 21
41926514 CTTTCCGTTT
* *
41926524 AACTCTTACGAGCTTCTGTTT
1 AACTCTTATGAGCTTCTGTTC
* *
41926545 AACTCATATGAG-TTTTCGTTC
1 AACTCTTATGAGCTTCT-GTTC
* * *
41926566 AACTCTTTTCAGCTTCTATTC
1 AACTCTTATGAGCTTCTGTTC
*
41926587 AACTCTTATGAGTTTCTGTTC
1 AACTCTTATGAGCTTCTGTTC
* *
41926608 AGCTCTTATGAGCTTCTGTTT
1 AACTCTTATGAGCTTCTGTTC
* * *
41926629 ATCT-TATATGAGTTTCCGTTC
1 AACTCT-TATGAGCTTCTGTTC
* * * *
41926650 AGCTCTTTTAAGCTTCTGTTT
1 AACTCTTATGAGCTTCTGTTC
* * * *
41926671 AACCCTAATG-GGTTTTCGTTC
1 AACTCTTATGAGCTTCT-GTTC
* * * *
41926692 AATTCTTTTAAGCTTCTGTTT
1 AACTCTTATGAGCTTCTGTTC
* *
41926713 AACCCTTATGAG-TTTTCGTTC
1 AACTCTTATGAGCTTCT-GTTC
* * *
41926734 AGCTCTTTTGAGCTTCTGTTT
1 AACTCTTATGAGCTTCTGTTC
* * * * *
41926755 TACCCTTATGGGTTTCTGTTT
1 AACTCTTATGAGCTTCTGTTC
* *
41926776 AGCTCTTATGAGCTTTTGTTC
1 AACTCTTATGAGCTTCTGTTC
* *
41926797 AGCT-TT-CGAGCTTCTGTT
1 AACTCTTATGAGCTTCTGTT
41926815 AATGATATAC
Statistics
Matches: 194, Mismatches: 68, Indels: 18
0.69 0.24 0.06
Matches are distributed among these distances:
19 10 0.05
20 13 0.07
21 160 0.82
22 11 0.06
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.47
Consensus pattern (21 bp):
AACTCTTATGAGCTTCTGTTC
Found at i:41926629 original size:84 final size:84
Alignment explanation
Indices: 41926526--41926795 Score: 335
Period size: 84 Copynumber: 3.2 Consensus size: 84
41926516 TTCCGTTTAA
* * * * * *
41926526 CTCTTACGAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAACTCTTTTCAGCTTCTATTCAACT
1 CTCTTATGAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAGCTCTTTTAAGCTTCTGTTTAACC
*
41926591 CTTATGAGTTTCTGTTCAG
66 CTTATGGGTTTCTGTTCAG
* * *
41926610 CTCTTATGAGCTTCTGTTTATCTTATATGAGTTTCCGTTCAGCTCTTTTAAGCTTCTGTTTAACC
1 CTCTTATGAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAGCTCTTTTAAGCTTCTGTTTAACC
* *
41926675 CTAATGGGTTT-TCGTTCAA
66 CTTATGGGTTTCT-GTTCAG
* * * * * * *
41926694 TTCTTTTAAGCTTCTGTTTAACCCTTATGAGTTTTCGTTCAGCTCTTTTGAGCTTCTGTTTTACC
1 CTCTTATGAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAGCTCTTTTAAGCTTCTGTTTAACC
*
41926759 CTTATGGGTTTCTGTTTAG
66 CTTATGGGTTTCTGTTCAG
*
41926778 CTCTTATGAGCTTTTGTT
1 CTCTTATGAGCTTCTGTT
41926796 CAGCTTTCGA
Statistics
Matches: 155, Mismatches: 29, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
83 1 0.01
84 153 0.99
85 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.48
Consensus pattern (84 bp):
CTCTTATGAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAGCTCTTTTAAGCTTCTGTTTAACC
CTTATGGGTTTCTGTTCAG
Found at i:41926760 original size:42 final size:42
Alignment explanation
Indices: 41926533--41926795 Score: 280
Period size: 42 Copynumber: 6.3 Consensus size: 42
41926523 TAACTCTTAC
* * *
41926533 GAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAACTCTTTT
1 GAGCTTCTGTTTAACCCTTATGAGTTTTCGTTCAGCTCTTTT
* * * * *
41926575 CAGCTTCTATTCAACTCTTATGAG-TTTCTGTTCAGCTCTTAT
1 GAGCTTCTGTTTAACCCTTATGAGTTTTC-GTTCAGCTCTTTT
* * *
41926617 GAGCTTCTGTTT-ATCTTATATGAGTTTCCGTTCAGCTCTTTT
1 GAGCTTCTGTTTAACCCT-TATGAGTTTTCGTTCAGCTCTTTT
* * * **
41926659 AAGCTTCTGTTTAACCCTAATGGGTTTTCGTTCAATTCTTTT
1 GAGCTTCTGTTTAACCCTTATGAGTTTTCGTTCAGCTCTTTT
*
41926701 AAGCTTCTGTTTAACCCTTATGAGTTTTCGTTCAGCTCTTTT
1 GAGCTTCTGTTTAACCCTTATGAGTTTTCGTTCAGCTCTTTT
* * * *
41926743 GAGCTTCTGTTTTACCCTTATG-GGTTTCTGTTTAGCTCTTAT
1 GAGCTTCTGTTTAACCCTTATGAGTTTTC-GTTCAGCTCTTTT
*
41926785 GAGCTTTTGTT
1 GAGCTTCTGTT
41926796 CAGCTTTCGA
Statistics
Matches: 184, Mismatches: 32, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
41 11 0.06
42 167 0.91
43 6 0.03
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (42 bp):
GAGCTTCTGTTTAACCCTTATGAGTTTTCGTTCAGCTCTTTT
Found at i:41926790 original size:126 final size:126
Alignment explanation
Indices: 41926515--41926795 Score: 352
Period size: 126 Copynumber: 2.2 Consensus size: 126
41926505 CTTGTTTTAC
* * * *
41926515 TTTCCGTTTAACTCTTACGAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAACTCTTTTCAGCT
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTTAACCCATATGAGTTTTCGTTCAACTCTTTTAAGCT
* * *
41926580 TCTATTCAACTCTTATGAGTTTCTGTTCAGCTCTTATGAGCTTCTGTTTATCTTATATGAG
66 TCTATTCAACCCTTATGAGTTTCTGTTCAGCTCTTATGAGCTTCTGTTTACCCTATATGAG
* * * * *
41926641 TTTCCGTTCAGCTCTTTTAAGCTTCTGTTTAACCC-TAATGGGTTTTCGTTCAATTCTTTTAAGC
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTTAACCCAT-ATGAGTTTTCGTTCAACTCTTTTAAGC
* * * *
41926705 TTCTGTTTAACCCTTATGAGTTT-TCGTTCAGCTCTTTTGAGCTTCTGTTTTACCCT-TATGGG
65 TTCTATTCAACCCTTATGAGTTTCT-GTTCAGCTCTTATGAGCTTCTG-TTTACCCTATATGAG
* *
41926767 TTTCTGTTTAGCTCTTATGAGCTTTTGTT
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTT
41926796 CAGCTTTCGA
Statistics
Matches: 131, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
125 2 0.02
126 123 0.94
127 6 0.05
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.48
Consensus pattern (126 bp):
TTTCCGTTTAGCTCTTATGAGCTTCTGTTTAACCCATATGAGTTTTCGTTCAACTCTTTTAAGCT
TCTATTCAACCCTTATGAGTTTCTGTTCAGCTCTTATGAGCTTCTGTTTACCCTATATGAG
Found at i:41927885 original size:22 final size:22
Alignment explanation
Indices: 41927861--41927939 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
41927851 ATGGCTTGTT
**
41927861 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGGC
* * *
41927883 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
41927905 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
41927927 TAACGTACTAAGC
1 TAACGTACTAAGC
41927940 ACTGTGTGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:41929090 original size:35 final size:35
Alignment explanation
Indices: 41929051--41929120 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
41929041 GTCTAGGATC
*
41929051 ACATATCTCTGAAGATCACCTTCCATATTTGCCAA
1 ACATATCTCTGAAGATCACCTTCCATATTTACCAA
* *
41929086 ACATATCTTTGAAGATCACTTTCCATATTTACCAA
1 ACATATCTCTGAAGATCACCTTCCATATTTACCAA
41929121 GCTCCGGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (35 bp):
ACATATCTCTGAAGATCACCTTCCATATTTACCAA
Found at i:41933662 original size:35 final size:35
Alignment explanation
Indices: 41933615--41933685 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
41933605 TCTAGGATCA
*
41933615 CATATCTCTGAAGATCACATTCCATATTTGCCAAG
1 CATATCTCTGAAGATCACATTCCATATTTACCAAG
* ** *
41933650 CATATCTTTGAAGATCATTTTCTATATTTACCAAG
1 CATATCTCTGAAGATCACATTCCATATTTACCAAG
41933685 C
1 C
41933686 TCCGAATATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.37
Consensus pattern (35 bp):
CATATCTCTGAAGATCACATTCCATATTTACCAAG
Found at i:41942858 original size:16 final size:17
Alignment explanation
Indices: 41942837--41942873 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
41942827 AAATAAAATG
41942837 CAAAAA-AACACAA-AAA
1 CAAAAATAA-ACAACAAA
41942853 CAAAAATAAACAACAAA
1 CAAAAATAAACAACAAA
41942870 CAAA
1 CAAA
41942874 CGCCATCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.78, C:0.19, G:0.00, T:0.03
Consensus pattern (17 bp):
CAAAAATAAACAACAAA
Found at i:41946633 original size:38 final size:38
Alignment explanation
Indices: 41946589--41946712 Score: 176
Period size: 38 Copynumber: 3.3 Consensus size: 38
41946579 AATTACACCA
*
41946589 GCACAAAGCCTGAATATCACTGGTACAAAGCCTGCTAG
1 GCACAAAGCCTGAATATCACTGGCACAAAGCCTGCTAG
* *
41946627 CCACAAAGCCTGAATATCACTAGCACAAAGCCTGCTAG
1 GCACAAAGCCTGAATATCACTGGCACAAAGCCTGCTAG
* * * *
41946665 GCACAAAGCCCGAATATCACCGGCACGAAGCCTACTAG
1 GCACAAAGCCTGAATATCACTGGCACAAAGCCTGCTAG
*
41946703 GCACAGAGCC
1 GCACAAAGCC
41946713 CGAACTAATG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.35, C:0.31, G:0.20, T:0.14
Consensus pattern (38 bp):
GCACAAAGCCTGAATATCACTGGCACAAAGCCTGCTAG
Found at i:41948473 original size:18 final size:18
Alignment explanation
Indices: 41948450--41948484 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41948440 CTAATTAACA
41948450 TAGAGGTAGACGTAGCAG
1 TAGAGGTAGACGTAGCAG
*
41948468 TAGAGGTAGAGGTAGCA
1 TAGAGGTAGACGTAGCA
41948485 TTGACTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.40, T:0.17
Consensus pattern (18 bp):
TAGAGGTAGACGTAGCAG
Found at i:41954312 original size:24 final size:23
Alignment explanation
Indices: 41954272--41954321 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
41954262 AATATATTTT
*
41954272 TTAAATAATTAACATAA-TAGATA
1 TTAAAAAATTAACATAATTA-ATA
*
41954295 TTAAAAAATTTAATATAATTAATA
1 TTAAAAAA-TTAACATAATTAATA
41954319 TTA
1 TTA
41954322 GTAATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 14 0.61
25 2 0.09
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAAAAATTAACATAATTAATA
Found at i:41955211 original size:18 final size:17
Alignment explanation
Indices: 41955188--41955235 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
41955178 TATAAATCAT
41955188 AAAAATAATAAATTTTA
1 AAAAATAATAAATTTTA
*
41955205 GAAAAATTATTAAATTTTA
1 -AAAAA-TAATAAATTTTA
41955224 ATAAAAT-ATAAA
1 A-AAAATAATAAA
41955236 AAGTTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 4 0.15
18 7 0.27
19 15 0.58
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAAATAATAAATTTTA
Found at i:41955229 original size:19 final size:20
Alignment explanation
Indices: 41955186--41955230 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
41955176 ATTATAAATC
*
41955186 ATAAAAATAATAAATTTTAG
1 ATAAAATTAATAAATTTTAG
*
41955206 A-AAAATTATTAAATTTTA-
1 ATAAAATTAATAAATTTTAG
41955224 ATAAAAT
1 ATAAAAT
41955231 ATAAAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 20 0.91
20 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAAAATTAATAAATTTTAG
Found at i:41955287 original size:37 final size:38
Alignment explanation
Indices: 41955216--41955305 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 38
41955206 AAAAATTATT
* * *
41955216 AAATTTTAATAAAATATAAAAAGTTATAATTTTTTATAA
1 AAATTATAA-AAAATATAAAAAATTATAAATTTTTATAA
* *
41955255 AAATTGTAAAAAATA-AAAAAATTGTAAATTTTTATAA
1 AAATTATAAAAAATATAAAAAATTATAAATTTTTATAA
*
41955292 AAATCATAAAAAAT
1 AAATTATAAAAAAT
41955306 TAACAACTCG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 31 0.69
38 6 0.13
39 8 0.18
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (38 bp):
AAATTATAAAAAATATAAAAAATTATAAATTTTTATAA
Found at i:41955324 original size:37 final size:37
Alignment explanation
Indices: 41955242--41955324 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
41955232 TAAAAAGTTA
** *
41955242 TAATTTTTTATAAAAATTGTAAAAAATAAAAAAATTG
1 TAATTTTTTATAAAAATCATAAAAAATAAAAAAATCG
* * * *
41955279 TAAATTTTTATAAAAATCATAAAAAATTAACAACTCG
1 TAATTTTTTATAAAAATCATAAAAAATAAAAAAATCG
*
41955316 TAGTTTTTT
1 TAATTTTTT
41955325 TCAATTAAAG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (37 bp):
TAATTTTTTATAAAAATCATAAAAAATAAAAAAATCG
Found at i:41955518 original size:8 final size:8
Alignment explanation
Indices: 41955507--41955559 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
41955497 GACTTTATAA
41955507 AATTTTAT
1 AATTTTAT
*
41955515 AATTTTTT
1 AATTTTAT
41955523 ATATTTCTAT
1 A-ATTT-TAT
41955533 ATATTTTAT
1 A-ATTTTAT
*
41955542 AACTTTTAC
1 AA-TTTTAT
41955551 AATTTTAT
1 AATTTTAT
41955559 A
1 A
41955560 TATATATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
8 15 0.39
9 15 0.39
10 8 0.21
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (8 bp):
AATTTTAT
Found at i:41955522 original size:10 final size:10
Alignment explanation
Indices: 41955441--41955612 Score: 60
Period size: 10 Copynumber: 17.5 Consensus size: 10
41955431 GTACGATAAC
41955441 TTTTATAATTT
1 TTTTATAA-TT
41955452 TTTTATGAA--
1 TTTTAT-AATT
*
41955461 ATTTAT-ATT
1 TTTTATAATT
41955470 TTTT-TACATT
1 TTTTATA-ATT
*
41955480 TTGTATAATT
1 TTTTATAATT
*
41955490 TTCTTATGA--
1 TT-TTATAATT
* **
41955499 CTTTATAAAA
1 TTTTATAATT
41955509 TTTTATAATT
1 TTTTATAATT
41955519 TTTTAT-A-T
1 TTTTATAATT
* *
41955527 TTCTAT-ATA
1 TTTTATAATT
*
41955536 TTTTATAA-C
1 TTTTATAATT
*
41955545 TTTTACAATT
1 TTTTATAATT
41955555 TTATATATATATT
1 TT-T-TATA-ATT
*
41955568 TTTTATGA-T
1 TTTTATAATT
*
41955577 TTTTATATTT
1 TTTTATAATT
*
41955587 TTCTTCTAATT
1 TT-TTATAATT
* *
41955598 TTTAATAAAT
1 TTTTATAATT
41955608 TTTTA
1 TTTTA
41955613 ATATTTAAAT
Statistics
Matches: 118, Mismatches: 26, Indels: 35
0.66 0.15 0.20
Matches are distributed among these distances:
7 1 0.01
8 13 0.11
9 29 0.25
10 40 0.34
11 24 0.20
12 6 0.05
13 5 0.04
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:41955619 original size:18 final size:18
Alignment explanation
Indices: 41955593--41955649 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
41955583 ATTTTTCTTC
*
41955593 TAATTTTTAATAAATTTT
1 TAATATTTAATAAATTTT
**
41955611 TAATATTTAA-ATTTTTAT
1 TAATATTTAATAAATTT-T
*
41955629 TAAAATTTAATAATATTTT
1 TAATATTTAATAA-ATTTT
41955648 TA
1 TA
41955650 GCTTTTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.13
18 19 0.63
19 4 0.13
20 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATATTTAATAAATTTT
Found at i:41955625 original size:26 final size:28
Alignment explanation
Indices: 41955594--41955646 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
41955584 TTTTTCTTCT
*
41955594 AATTTTTAAT-AAATTT-TTAATATTTA
1 AATTTTTAATAAAATTTAATAATATTTA
*
41955620 AATTTTTATTAAAATTTAATAATATTT
1 AATTTTTAATAAAATTTAATAATATTT
41955647 TTAGCTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 6 0.26
28 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
AATTTTTAATAAAATTTAATAATATTTA
Found at i:41965645 original size:28 final size:29
Alignment explanation
Indices: 41965610--41965669 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
41965600 TTAAAACTTT
*
41965610 AAAAATT-AAAAATA-TATAAATTATTTAA
1 AAAAATTAAAAAACATTA-AAATTATTTAA
41965638 AAAAATTAAAAAACATTAAAATTATTTAA
1 AAAAATTAAAAAACATTAAAATTATTTAA
41965667 AAA
1 AAA
41965670 GTATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.24
29 20 0.69
30 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAAATTAAAAAACATTAAAATTATTTAA
Found at i:41965677 original size:28 final size:27
Alignment explanation
Indices: 41965607--41965677 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 27
41965597 CTTTTAAAAC
*
41965607 TTTAAAAAT-TAAAAATATATAAATTA
1 TTTAAAAATATAAAAACATATAAATTA
*
41965633 TTTAAAAAAATTAAAAAACAT-TAAAATTA
1 TTTAAAAATA-T-AAAAACATAT-AAATTA
41965662 TTTAAAAAGTATAAAA
1 TTTAAAAA-TATAAAA
41965678 TATATTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 8 0.22
28 6 0.16
29 22 0.59
30 1 0.03
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (27 bp):
TTTAAAAATATAAAAACATATAAATTA
Found at i:41972089 original size:31 final size:31
Alignment explanation
Indices: 41972035--41972115 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
41972025 TTAATTAAAA
* * * * *
41972035 AAAAG-TTACATTTTAGTCTTTAAATTATTT
1 AAAAGTTTTCATTTAAGTCATTAAACTATTC
41972065 AAAAGTTTTCATTTAAGTCATTAAACTATTC
1 AAAAGTTTTCATTTAAGTCATTAAACTATTC
*
41972096 AAAAGTTTTTATTTAAGTCA
1 AAAAGTTTTCATTTAAGTCA
41972116 CTGAACTGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 5 0.11
31 39 0.89
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (31 bp):
AAAAGTTTTCATTTAAGTCATTAAACTATTC
Found at i:41974741 original size:3 final size:3
Alignment explanation
Indices: 41974735--41974804 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
41974725 ATCATTACAT
* * * *
41974735 TTA TTA TTA TTA TTA TTA TTG TTA TTG TTA TTA TTA CTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41974783 TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA
41974805 GTTTTATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41976634 original size:23 final size:24
Alignment explanation
Indices: 41976608--41976658 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
41976598 GTTCAATTCG
*
41976608 GTACCCACTTTTTT-CTTAATTTA
1 GTACCCAATTTTTTACTTAATTTA
** *
41976631 GTACTTAATTTTTTATTTAATTTA
1 GTACCCAATTTTTTACTTAATTTA
41976655 GTAC
1 GTAC
41976659 TTAAACTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.55
Consensus pattern (24 bp):
GTACCCAATTTTTTACTTAATTTA
Found at i:41976639 original size:12 final size:12
Alignment explanation
Indices: 41976622--41976662 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
41976612 CCACTTTTTT
41976622 CTTAATTTAGTA
1 CTTAATTTAGTA
**
41976634 CTTAATTTTTTA
1 CTTAATTTAGTA
*
41976646 TTTAATTTAGTA
1 CTTAATTTAGTA
41976658 CTTAA
1 CTTAA
41976663 ACTTGTCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (12 bp):
CTTAATTTAGTA
Found at i:41981686 original size:31 final size:31
Alignment explanation
Indices: 41981648--41981710 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
41981638 TATATAACAA
41981648 TACGTTAGCATCCAATAAACTTGAGAAGTTT
1 TACGTTAGCATCCAATAAACTTGAGAAGTTT
41981679 TACGTTAGCATCCAATAAACTTGAGAAGTTT
1 TACGTTAGCATCCAATAAACTTGAGAAGTTT
41981710 T
1 T
41981711 CTTTTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (31 bp):
TACGTTAGCATCCAATAAACTTGAGAAGTTT
Found at i:41989422 original size:11 final size:11
Alignment explanation
Indices: 41989406--41989440 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
41989396 AATAAAACGA
41989406 TTAAAGAAACT
1 TTAAAGAAACT
41989417 TTAAAGAAACT
1 TTAAAGAAACT
41989428 TTAAAGAAACT
1 TTAAAGAAACT
41989439 TT
1 TT
41989441 TAAAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (11 bp):
TTAAAGAAACT
Found at i:41989431 original size:22 final size:24
Alignment explanation
Indices: 41989406--41989449 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
41989396 AATAAAACGA
41989406 TTAAAGAAAC-TTT-AAAGAAACT
1 TTAAAGAAACTTTTAAAAGAAACT
41989428 TTAAAGAAACTTTTAAAAGAAA
1 TTAAAGAAACTTTTAAAAGAAA
41989450 AAATAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 3 0.15
24 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.27
Consensus pattern (24 bp):
TTAAAGAAACTTTTAAAAGAAACT
Found at i:41995981 original size:17 final size:17
Alignment explanation
Indices: 41995959--41995992 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41995949 TATGCAAAAC
*
41995959 AATTTAAAGTAAATAAT
1 AATTTAAAATAAATAAT
41995976 AATTTAAAATAAATAAT
1 AATTTAAAATAAATAAT
41995993 TTACAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATAAT
Found at i:41996277 original size:6 final size:6
Alignment explanation
Indices: 41996266--41996290 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41996256 AAGAGTTTTT
41996266 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
41996291 CAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:41996701 original size:41 final size:41
Alignment explanation
Indices: 41996644--41996726 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
41996634 GGCCAAAACG
41996644 ACGTCGTTTTGGCACCTGACCTGCAGTTGCAAAACGGCGCC
1 ACGTCGTTTTGGCACCTGACCTGCAGTTGCAAAACGGCGCC
41996685 ACGTCGTTTTGGCACCTGACCTGCAGTTGCAAAACGGCGCC
1 ACGTCGTTTTGGCACCTGACCTGCAGTTGCAAAACGGCGCC
41996726 A
1 A
41996727 TTTTGTAGTA
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:0.20, C:0.31, G:0.27, T:0.22
Consensus pattern (41 bp):
ACGTCGTTTTGGCACCTGACCTGCAGTTGCAAAACGGCGCC
Found at i:42009073 original size:27 final size:27
Alignment explanation
Indices: 42009043--42009202 Score: 171
Period size: 27 Copynumber: 6.0 Consensus size: 27
42009033 TATCTGCAGG
42009043 GAAATACCCCCATAAGATAAAATGACC
1 GAAATACCCCCATAAGATAAAATGACC
* *
42009070 GAAATACCCCCATAGGGTAAAATGACC
1 GAAATACCCCCATAAGATAAAATGACC
* *
42009097 GAAATA-CCCCATAGGGTAAAATGACC
1 GAAATACCCCCATAAGATAAAATGACC
* *
42009123 AAAATACCCCTAT-AGAGTAAAATGACC
1 GAAATACCCCCATAAGA-TAAAATGACC
* * * *
42009150 GAAATACCTCCATAGGGTAAAATGACT
1 GAAATACCCCCATAAGATAAAATGACC
** * *
42009177 GTTATACCCCTAAAAGATAAAATGAC
1 GAAATACCCCCATAAGATAAAATGAC
42009203 TGTTATGACC
Statistics
Matches: 111, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
26 26 0.23
27 84 0.76
28 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (27 bp):
GAAATACCCCCATAAGATAAAATGACC
Found at i:42009128 original size:53 final size:53
Alignment explanation
Indices: 42009043--42009175 Score: 203
Period size: 53 Copynumber: 2.5 Consensus size: 53
42009033 TATCTGCAGG
* * * *
42009043 GAAATACCCCCATAAGATAAAATGACCGAAATACCCCCATAGGGTAAAATGACC
1 GAAATA-CCCCATAGGGTAAAATGACCAAAATACCCCCATAGAGTAAAATGACC
*
42009097 GAAATACCCCATAGGGTAAAATGACCAAAATACCCCTATAGAGTAAAATGACC
1 GAAATACCCCATAGGGTAAAATGACCAAAATACCCCCATAGAGTAAAATGACC
42009150 GAAATACCTCCATAGGGTAAAATGAC
1 GAAATACC-CCATAGGGTAAAATGAC
42009176 TGTTATACCC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
53 50 0.68
54 23 0.32
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (53 bp):
GAAATACCCCATAGGGTAAAATGACCAAAATACCCCCATAGAGTAAAATGACC
Found at i:42009636 original size:28 final size:27
Alignment explanation
Indices: 42009589--42009713 Score: 151
Period size: 28 Copynumber: 4.5 Consensus size: 27
42009579 ATTATTGCAT
42009589 TACACTGTTACTGTATTGGGCTAAGGCC
1 TACACTGTT-CTGTATTGGGCTAAGGCC
* * * *
42009617 TATACTGATTCTGTAATGGGCTAACGAC
1 TACACTG-TTCTGTATTGGGCTAAGGCC
42009645 TACACTGGTTCTGTATTGGGCTAAGGCC
1 TACACT-GTTCTGTATTGGGCTAAGGCC
*
42009673 CACACTGTTACTGTATTGGGCTAAGGCC
1 TACACTGTT-CTGTATTGGGCTAAGGCC
* *
42009701 CACACTGTACTGT
1 TACACTGTTCTGT
42009714 CACTGAGTAG
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.08
28 74 0.88
29 3 0.04
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (27 bp):
TACACTGTTCTGTATTGGGCTAAGGCC
Found at i:42011390 original size:20 final size:21
Alignment explanation
Indices: 42011360--42011399 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
42011350 GCTAGGTTGG
42011360 GTAGTAAAAGAAAAAGAAAAC
1 GTAGTAAAAGAAAAAGAAAAC
*
42011381 GTAG-AAAAGAAGAAGAAAA
1 GTAGTAAAAGAAAAAGAAAA
42011400 GAAGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.68, C:0.03, G:0.23, T:0.07
Consensus pattern (21 bp):
GTAGTAAAAGAAAAAGAAAAC
Found at i:42011397 original size:11 final size:10
Alignment explanation
Indices: 42011385--42011418 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
42011375 GAAAACGTAG
42011385 AAAAGAAGAA
1 AAAAGAAGAA
42011395 GAAAAGAAG-A
1 -AAAAGAAGAA
42011405 AAAAGAAGAA
1 AAAAGAAGAA
42011415 AAAA
1 AAAA
42011419 TTTCCAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.36
10 6 0.27
11 8 0.36
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAGAAGAA
Found at i:42011408 original size:20 final size:20
Alignment explanation
Indices: 42011365--42011418 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
42011355 GTTGGGTAGT
* *
42011365 AAAAGAAAAAGAAAACGTAG
1 AAAAGAAGAAGAAAACGAAG
42011385 AAAAGAAGAAGAAAA-GAAG
1 AAAAGAAGAAGAAAACGAAG
42011404 AAAAAGAAGAA-AAAA
1 -AAAAGAAGAAGAAAA
42011419 TTTCCAAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAGAAGAAGAAAACGAAG
Found at i:42012437 original size:13 final size:13
Alignment explanation
Indices: 42012419--42012447 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42012409 TGCCTCGTCC
42012419 AACGTGGCAAGTT
1 AACGTGGCAAGTT
42012432 AACGTGGCAAGTT
1 AACGTGGCAAGTT
42012445 AAC
1 AAC
42012448 TTTGCCTCGT
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:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (13 bp):
AACGTGGCAAGTT
Found at i:42014596 original size:21 final size:20
Alignment explanation
Indices: 42014572--42014610 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42014562 GGACTAATTT
*
42014572 AAAACAATTAGAAATTTTGGG
1 AAAA-AATTAAAAATTTTGGG
*
42014593 AAAAAGTTAAAAATTTTG
1 AAAAAATTAAAAATTTTG
42014611 AAAATAGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAAAATTAAAAATTTTGGG
Found at i:42015206 original size:86 final size:86
Alignment explanation
Indices: 42015107--42015275 Score: 329
Period size: 86 Copynumber: 2.0 Consensus size: 86
42015097 AATAAATCCA
42015107 ACATATCAATTTCAACATAATAAATCCATGACCACAACATACATCACACACACATCATATAATCA
1 ACATATCAATTTCAACATAATAAATCCATGACCACAACATACATCACACACACATCATATAATCA
42015172 CTTCATTCTCAATTTATAGCT
66 CTTCATTCTCAATTTATAGCT
*
42015193 ACATATCAATTTCAACATAATAAATCCATGGCCACAACATACATCACACACACATCATATAATCA
1 ACATATCAATTTCAACATAATAAATCCATGACCACAACATACATCACACACACATCATATAATCA
42015258 CTTCATTCTCAATTTATA
66 CTTCATTCTCAATTTATA
42015276 CCTAGCCTAT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (86 bp):
ACATATCAATTTCAACATAATAAATCCATGACCACAACATACATCACACACACATCATATAATCA
CTTCATTCTCAATTTATAGCT
Found at i:42018368 original size:30 final size:29
Alignment explanation
Indices: 42018334--42018422 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 29
42018324 GGTAGCATTG
42018334 ATATAATGTCAACTTGTGTGAGCAATCTTA
1 ATATAATGTCAACTTGTGTGAGCAA-CTTA
* * * *
42018364 ATATAATGTCAACTTGTATGAGCAGCCCTG
1 ATATAATGTCAACTTGTGTGAGCA-ACTTA
* *
42018394 ATATAATGTCAGCTTGTGTAAGCAACTTA
1 ATATAATGTCAACTTGTGTGAGCAACTTA
42018423 TTCTCGTGTA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 2 0.04
30 46 0.96
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (29 bp):
ATATAATGTCAACTTGTGTGAGCAACTTA
Found at i:42020638 original size:256 final size:256
Alignment explanation
Indices: 42020183--42020696 Score: 929
Period size: 256 Copynumber: 2.0 Consensus size: 256
42020173 ACGCTCGTGG
* *
42020183 TGGCCTCTACAGTCTAACACTATGTTTCGTGGGCTCGGTTCACCACACGAGTGTTCGCAGGCCCA
1 TGGCCTCTACAGTCTAACACCATGTTTCGTGGGCTCGGTTCACCACACGAGTGTTCGCAAGCCCA
42020248 CGTGGCCTCAATCGTCACATTTTTAGCTTTTCGACTTTTTGACTTTTGCCAATTCACAGAAGAGA
66 CGTGGCCTCAATCGTCACATTTTTAGCTTTTCGACTTTTTGACTTTTGCCAATTCACAGAAGAGA
42020313 CAGAGTGATTACACACACTCTTTCAGCTTTACGAAAGTCATGATTTACGGTGTACAGATACACAC
131 CAGAGTGATTACACACACTCTTTCAGCTTTACGAAAGTCATGATTTACGGTGTACAGATACACAC
*
42020378 TTGATTGCGAAACGTACGAATCGTCCACGTGCTCCAAAGCCTATTTTCCATCAAATCATAT
196 TTGATTGCAAAACGTACGAATCGTCCACGTGCTCCAAAGCCTATTTTCCATCAAATCATAT
42020439 TGGCCTCTACAGTCTAACACCATGTTTCGTGGGCTCGGTTCACCACACGAGTGTTCGCAAGCCCA
1 TGGCCTCTACAGTCTAACACCATGTTTCGTGGGCTCGGTTCACCACACGAGTGTTCGCAAGCCCA
* ** *
42020504 TGTGGCCTCAATCGTCGTATTTTTGGCTTTTCGACTTTTTGACTTTTGCCAATTCACAGAAGAGA
66 CGTGGCCTCAATCGTCACATTTTTAGCTTTTCGACTTTTTGACTTTTGCCAATTCACAGAAGAGA
* * *
42020569 CAGTGTGATTACACACACTCTTTCAGCTTTACGAAAGTCATGATTTATGGTGTATAGATACACAC
131 CAGAGTGATTACACACACTCTTTCAGCTTTACGAAAGTCATGATTTACGGTGTACAGATACACAC
*
42020634 TTGATTGCAAAACGTACGAATCGTCCACGTGCTCCAAAGCCTATTTTTCATCAAATCATAT
196 TTGATTGCAAAACGTACGAATCGTCCACGTGCTCCAAAGCCTATTTTCCATCAAATCATAT
42020695 TG
1 TG
42020697 TTAGTCTTCC
Statistics
Matches: 247, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
256 247 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (256 bp):
TGGCCTCTACAGTCTAACACCATGTTTCGTGGGCTCGGTTCACCACACGAGTGTTCGCAAGCCCA
CGTGGCCTCAATCGTCACATTTTTAGCTTTTCGACTTTTTGACTTTTGCCAATTCACAGAAGAGA
CAGAGTGATTACACACACTCTTTCAGCTTTACGAAAGTCATGATTTACGGTGTACAGATACACAC
TTGATTGCAAAACGTACGAATCGTCCACGTGCTCCAAAGCCTATTTTCCATCAAATCATAT
Found at i:42023499 original size:14 final size:14
Alignment explanation
Indices: 42023480--42023508 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42023470 GGACTTAATT
42023480 AATAATAAACTTAA
1 AATAATAAACTTAA
42023494 AATAATAAACTTAA
1 AATAATAAACTTAA
42023508 A
1 A
42023509 GACCTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATAAACTTAA
Found at i:42023573 original size:22 final size:22
Alignment explanation
Indices: 42023542--42023590 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
42023532 ATTAAAATAT
*
42023542 TGTGTGTGCGTGTGCGCGTGCG
1 TGTGTATGCGTGTGCGCGTGCG
*
42023564 TGTGTATGCGTGTGTGCGTGCG
1 TGTGTATGCGTGTGCGCGTGCG
42023586 TGTGT
1 TGTGT
42023591 GTGGTATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.02, C:0.14, G:0.47, T:0.37
Consensus pattern (22 bp):
TGTGTATGCGTGTGCGCGTGCG
Found at i:42023590 original size:12 final size:12
Alignment explanation
Indices: 42023542--42023591 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
42023532 ATTAAAATAT
*
42023542 TGTGTGTGCGTG
1 TGTGCGTGCGTG
*
42023554 TGCGCGTGCGTG
1 TGTGCGTGCGTG
*
42023566 TGT--ATGCGTG
1 TGTGCGTGCGTG
42023576 TGTGCGTGCGTG
1 TGTGCGTGCGTG
42023588 TGTG
1 TGTG
42023592 TGGTATAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 9 0.29
12 22 0.71
ACGTcount: A:0.02, C:0.14, G:0.48, T:0.36
Consensus pattern (12 bp):
TGTGCGTGCGTG
Found at i:42028354 original size:27 final size:26
Alignment explanation
Indices: 42028319--42028759 Score: 452
Period size: 27 Copynumber: 16.4 Consensus size: 26
42028309 CCCTAAAATA
*
42028319 GGTAAAATGACCGAAATACCATCATAG
1 GGTAAAATGACCGAAATACC-CCATAG
* * * *
42028346 GGTAGAATGATCGAAATATTCCCATAA
1 GGTAAAATGACCGAAATA-CCCCATAG
*
42028373 GGTAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* *
42028400 GGTAGAATGATCGAAATACCTCCATAG
1 GGTAAAATGACCGAAATACC-CCATAG
*
42028427 GGTAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* * *
42028454 GATAAAATGACCAAAATACCCCCACAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* *
42028481 GGTAAAATGACCAAAATACCCCAAAG
1 GGTAAAATGACCGAAATACCCCATAG
* *
42028507 GATAAAATAACCGAAATACCCCTATATG
1 GGTAAAATGACCGAAATACCCC-ATA-G
* *
42028535 GGTAAAATGAACAAAATACCCCATAG
1 GGTAAAATGACCGAAATACCCCATAG
* *
42028561 GGTAAAATGATCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
*
42028588 GGTAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* *
42028615 GGTAGAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
* *
42028642 GGTAAAATAACTGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
* *
42028669 GTTAAAATGACTGAAATACCTCCATAG
1 GGTAAAATGACCGAAATACC-CCATAG
* * **
42028696 GGTAGAATAACC-AAATACCATTATAG
1 GGTAAAATGACCGAAATACC-CCATAG
42028722 GGTAAAATGACCGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
*
42028749 GTTAAAATGAC
1 GGTAAAATGAC
42028760 TGTTATACCC
Statistics
Matches: 352, Mismatches: 52, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
26 71 0.20
27 257 0.73
28 24 0.07
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (26 bp):
GGTAAAATGACCGAAATACCCCATAG
Found at i:42028460 original size:81 final size:80
Alignment explanation
Indices: 42028319--42028759 Score: 517
Period size: 81 Copynumber: 5.5 Consensus size: 80
42028309 CCCTAAAATA
* * * ** *
42028319 GGTAAAATGACCGAAATACCATCATAGGGTAGAATGATCGAAATATTCCCATAAGGTAAAATGAC
1 GGTAAAATGACCGAAATACC-CCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAC
42028384 CAAAATACCCCCATAG
65 CAAAATACCCCCATAG
* * * *
42028400 GGTAGAATGATCGAAATACCTCCATAGGGTAAAATGACCAAAATACCCCCATAGGATAAAATGAC
1 GGTAAAATGACCGAAATACC-CCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAC
*
42028465 CAAAATACCCCCACAG
65 CAAAATACCCCCATAG
* * * * * *
42028481 GGTAAAATGACCAAAATACCCCAAAGGATAAAATAACCGAAATACCCCTATATGGGTAAAATGAA
1 GGTAAAATGACCGAAATACCCCATAGGGTAAAATGACCGAAATACCCCCATA-GGGTAAAATGAC
42028546 CAAAATA-CCCCATAG
65 CAAAATACCCCCATAG
* * * *
42028561 GGTAAAATGATCAAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAGAATGAC
1 GGTAAAATGACCGAAATA-CCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAC
*
42028626 CAAAATACCCCTATAG
65 CAAAATACCCCCATAG
* * * * * * *
42028642 GGTAAAATAACTGAAATACCCCTATAGGTTAAAATGACTGAAATACCTCCATAGGGTAGAATAAC
1 GGTAAAATGACCGAAATACCCC-ATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAC
***
42028707 C-AAATACCATTATAG
65 CAAAATACCCCCATAG
*
42028722 GGTAAAATGACCGAAATACCCCTATAGGTTAAAATGAC
1 GGTAAAATGACCGAAATACCCC-ATAGGGTAAAATGAC
42028760 TGTTATACCC
Statistics
Matches: 311, Mismatches: 45, Indels: 9
0.85 0.12 0.02
Matches are distributed among these distances:
80 120 0.39
81 191 0.61
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (80 bp):
GGTAAAATGACCGAAATACCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACC
AAAATACCCCCATAG
Found at i:42028772 original size:134 final size:134
Alignment explanation
Indices: 42028319--42028759 Score: 516
Period size: 134 Copynumber: 3.3 Consensus size: 134
42028309 CCCTAAAATA
** * * * * *
42028319 GGTAAAATGACCGAAATACCATCATAGGGTAGAATGATCGAAATATTCCC-ATAAGG-TAAAATG
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATA-CCCCTA-AAGGATAAAATA
* * * *
42028382 ACCAAAATACCCCCATAGGGTAGAATGA-TCGAAATACCTCCATAGGGTAAAATGACCAAAATAC
64 ACCGAAATACCCCTATAGGGTAAAATGACT-GAAATACCTCCATAGGGTAAAATAACC-AAATAC
42028446 CCCCATAG
127 CCCCATAG
* * *
42028454 GATAAAATGACCAAAATACCCCCACAGGGTAAAATGACCAAAATACCCC-AAAGGATAAAATAAC
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTAAAGGATAAAATAAC
* * *
42028518 CGAAATACCCCTATATGGGTAAAATGAAC-AAAATACC-CCATAGGGTAAAATGATCAAAATACC
66 CGAAATACCCCTATA-GGGTAAAATG-ACTGAAATACCTCCATAGGGTAAAAT-AACCAAATACC
42028581 CCCATAG
128 CCCATAG
* * * *
42028588 GGTAGAATGACCGAAATACCCCCATAGGGTAGAATGACCAAAATACCCCTATAGGGTAAAATAAC
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTAAAGGATAAAATAAC
* * * ***
42028653 TGAAATACCCCTATAGGTTAAAATGACTGAAATACCTCCATAGGGTAGAATAACCAAATACCATT
66 CGAAATACCCCTATAGGGTAAAATGACTGAAATACCTCCATAGGGTAAAATAACCAAATACCCCC
42028718 ATAG
131 ATAG
* *
42028722 GGTAAAATGACCGAAATACCCCTATAGGTTAAAATGAC
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAC
42028760 TGTTATACCC
Statistics
Matches: 261, Mismatches: 37, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
133 6 0.02
134 160 0.61
135 94 0.36
136 1 0.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (134 bp):
GGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTAAAGGATAAAATAAC
CGAAATACCCCTATAGGGTAAAATGACTGAAATACCTCCATAGGGTAAAATAACCAAATACCCCC
ATAG
Found at i:42030893 original size:3 final size:3
Alignment explanation
Indices: 42030885--42030921 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
42030875 AAAGAAACGG
* *
42030885 TGA TGA TGA CGA TGA TGA TCA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
42030922 TTTTTAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:42034197 original size:26 final size:28
Alignment explanation
Indices: 42034149--42034220 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 28
42034139 CTTAATATTT
* *
42034149 AAGTAAATATATATAATA-TAAT-AAT-A
1 AAGTAAATATA-ATAAAAGAAATAAATAA
42034175 AAGTAAATATAATAAAAGAAATAAATAA
1 AAGTAAATATAATAAAAGAAATAAATAA
42034203 AAG-AAATA-AAT-AAAGAAA
1 AAGTAAATATAATAAAAGAAA
42034221 AGAAAAAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 12 0.29
26 17 0.41
27 8 0.20
28 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (28 bp):
AAGTAAATATAATAAAAGAAATAAATAA
Found at i:42034203 original size:13 final size:13
Alignment explanation
Indices: 42034174--42034220 Score: 69
Period size: 13 Copynumber: 3.5 Consensus size: 13
42034164 ATATAATAAT
42034174 AAAGTAAATATAATA
1 AAAG-AAATA-AATA
42034189 AAAGAAATAAATA
1 AAAGAAATAAATA
42034202 AAAGAAATAAAT-
1 AAAGAAATAAATA
42034214 AAAGAAA
1 AAAGAAA
42034221 AGAAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.22
13 16 0.50
14 5 0.16
15 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (13 bp):
AAAGAAATAAATA
Found at i:42034203 original size:22 final size:21
Alignment explanation
Indices: 42034152--42034203 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
42034142 AATATTTAAG
* * *
42034152 TAAATATATATAATATAATAA
1 TAAATAAATATAATAAAAAAA
42034173 TAAAGTAAATATAATAAAAGAAA
1 TAAA-TAAATATAATAAAA-AAA
42034196 TAAATAAA
1 TAAATAAA
42034204 AGAAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 16 0.62
23 6 0.23
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAATAAATATAATAAAAAAA
Found at i:42038250 original size:20 final size:20
Alignment explanation
Indices: 42038225--42038277 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
42038215 CACGGCCTGC
42038225 CCACACGGGCGTGTCCCAAG
1 CCACACGGGCGTGTCCCAAG
* * *
42038245 CCACACAGCCATGTCCCAAG
1 CCACACGGGCGTGTCCCAAG
*
42038265 CCACAGGGGCGTG
1 CCACACGGGCGTG
42038278 CGACCCCTGC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.09
Consensus pattern (20 bp):
CCACACGGGCGTGTCCCAAG
Found at i:42039088 original size:29 final size:29
Alignment explanation
Indices: 42039034--42039090 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
42039024 CCACTAATTG
42039034 ATTATTAAACATATATTATATTATATTAT
1 ATTATTAAACATATATTATATTATATTAT
* *
42039063 ATTATTCAATATA-ATTATATTAATATTA
1 ATTATTAAACATATATTATATT-ATATTA
42039091 ATTGTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTATTAAACATATATTATATTATATTAT
Found at i:42039092 original size:15 final size:15
Alignment explanation
Indices: 42039048--42039093 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
42039038 TTAAACATAT
42039048 ATTATATT-ATATTA
1 ATTATATTAATATTA
*
42039062 TATTAT-TCAATA-TA
1 -ATTATATTAATATTA
42039076 ATTATATTAATATTA
1 ATTATATTAATATTA
42039091 ATT
1 ATT
42039094 GTAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
15 13 0.50
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATATTAATATTA
Found at i:42042795 original size:12 final size:13
Alignment explanation
Indices: 42042762--42042798 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
42042752 ACTTTTCAAA
42042762 AGCACTTTTTCAC
1 AGCACTTTTTCAC
*
42042775 ATCACTTTTTCAC
1 AGCACTTTTTCAC
42042788 AGCA-TTTTTCA
1 AGCACTTTTTCA
42042799 AAAGCTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.43
Consensus pattern (13 bp):
AGCACTTTTTCAC
Found at i:42043305 original size:39 final size:39
Alignment explanation
Indices: 42043243--42043320 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
42043233 AAATTCATAA
*
42043243 ATTAGAATATCTAAATTCATATAATACATGGACAAAAAT
1 ATTAAAATATCTAAATTCATATAATACATGGACAAAAAT
**
42043282 ATTAAAATATCTAAATTTGTATAATACATGGACAAAAAT
1 ATTAAAATATCTAAATTCATATAATACATGGACAAAAAT
42043321 TATAATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (39 bp):
ATTAAAATATCTAAATTCATATAATACATGGACAAAAAT
Found at i:42051590 original size:20 final size:18
Alignment explanation
Indices: 42051548--42051590 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
42051538 TTGAAAATAA
*
42051548 ACATTATTATTAGGTTTT
1 ACATTATTATTAGGCTTT
42051566 A-ATTATTATTAGGACTTT
1 ACATTATTATTAGG-CTTT
42051584 ACCATTA
1 A-CATTA
42051591 ACCAGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 12 0.57
18 5 0.24
20 4 0.19
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (18 bp):
ACATTATTATTAGGCTTT
Found at i:42062675 original size:18 final size:18
Alignment explanation
Indices: 42062648--42062683 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42062638 ATCGATACTT
* *
42062648 TTATGGTAGGTATCGATA
1 TTATGATAGGTACCGATA
42062666 TTATGATAGGTACCGATA
1 TTATGATAGGTACCGATA
42062684 AGGTTTTGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (18 bp):
TTATGATAGGTACCGATA
Found at i:42071063 original size:9 final size:9
Alignment explanation
Indices: 42071049--42071075 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
42071039 AATTCGGTTT
42071049 ATTTCTAAC
1 ATTTCTAAC
42071058 ATTTCTAAC
1 ATTTCTAAC
42071067 ATTTCTAAC
1 ATTTCTAAC
42071076 TTATTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTTCTAAC
Found at i:42075563 original size:11 final size:11
Alignment explanation
Indices: 42075547--42075571 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42075537 ATTGAGGTTC
42075547 TTATATGGTAA
1 TTATATGGTAA
42075558 TTATATGGTAA
1 TTATATGGTAA
42075569 TTA
1 TTA
42075572 GACCATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (11 bp):
TTATATGGTAA
Found at i:42087684 original size:43 final size:42
Alignment explanation
Indices: 42087579--42087735 Score: 152
Period size: 43 Copynumber: 3.6 Consensus size: 42
42087569 ACATTGGGTT
* * * *
42087579 ATCGATATGTGATTACATGTAAGACCATGTATGGGACATCGGC
1 ATCG-TATATGATTACGTGTAAGACCATGTCTGGGACATTGGC
* * *
42087622 ATTGTATTATAATTACGTGTAAGACCATGTCTGGGACATTGTC
1 ATCGTA-TATGATTACGTGTAAGACCATGTCTGGGACATTGGC
* * * *
42087665 ATCGTTATATGATTTCGTGTAAGACCCTATCTGGGACAGTGGC
1 ATCG-TATATGATTACGTGTAAGACCATGTCTGGGACATTGGC
* * *
42087708 ATCGATATGTGATAACATGTAAGACCAT
1 ATCG-TATATGATTACGTGTAAGACCAT
42087736 ATTCGAGATA
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
42 2 0.02
43 88 0.96
44 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (42 bp):
ATCGTATATGATTACGTGTAAGACCATGTCTGGGACATTGGC
Found at i:42100767 original size:22 final size:22
Alignment explanation
Indices: 42100740--42100790 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
42100730 ATTGATACCA
42100740 AGTACGTGAAACATGAGAGCTT
1 AGTACGTGAAACATGAGAGCTT
* **
42100762 AGTACGTTAGCCATGAGAGCTT
1 AGTACGTGAAACATGAGAGCTT
42100784 AGTACGT
1 AGTACGT
42100791 TAGCCATGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (22 bp):
AGTACGTGAAACATGAGAGCTT
Found at i:42100791 original size:22 final size:22
Alignment explanation
Indices: 42100751--42100814 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
42100741 GTACGTGAAA
42100751 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
42100773 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
42100795 CATGAGGGTTTAGTTCGTTA
1 CATGAGAGCTTAGTACGTTA
42100815 AACAATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:42101840 original size:82 final size:82
Alignment explanation
Indices: 42101703--42101866 Score: 283
Period size: 82 Copynumber: 2.0 Consensus size: 82
42101693 ATCATAACAG
*
42101703 TTCCTCACCACATATTATAGTTGATCAAGATTTGGCATATTAGTACATTTATGAAGAACCATACC
1 TTCCTCACCACATATTATAGTAGATCAAGATTTGGCATATTAGTACATTTATGAAGAACCATACC
*
42101768 ATCAAGACATTTTCCAA
66 ATCAAGACAATTTCCAA
* * *
42101785 TTCCTCACCACATATTATAGTAGATTAAGATTTGGCATATTAGTACATTTATGAAGAACTATACT
1 TTCCTCACCACATATTATAGTAGATCAAGATTTGGCATATTAGTACATTTATGAAGAACCATACC
42101850 ATCAAGACAATTTCCAA
66 ATCAAGACAATTTCCAA
42101867 ACCAAAGTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (82 bp):
TTCCTCACCACATATTATAGTAGATCAAGATTTGGCATATTAGTACATTTATGAAGAACCATACC
ATCAAGACAATTTCCAA
Found at i:42102142 original size:16 final size:16
Alignment explanation
Indices: 42102121--42102175 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
42102111 GTTTGGTTCA
*
42102121 CTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
*
42102137 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
42102153 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
42102169 CTGTAAT
1 CTGTAAT
42102176 AGTAATTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:42102432 original size:58 final size:59
Alignment explanation
Indices: 42102353--42102508 Score: 167
Period size: 58 Copynumber: 2.7 Consensus size: 59
42102343 TTTTAATAAG
* * * * *
42102353 ATTATTATTAAAAATGATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAACAAAATTCTTAACATA
** * *
42102411 ATTATTATTAAATATAATTTAAT-AAAATTTTATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAACAAAATTCTTAACATA
*
42102469 ATTATTATT--ATATGAATTTACTAAAATCATAATATATAAT
1 ATTATTATTAAATAT-AATTTAATAAAA--ATAATATATAAT
42102509 ACTATAAAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
56 4 0.05
57 27 0.33
58 40 0.49
60 10 0.12
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAACAAAATTCTTAACATA
Found at i:42102439 original size:10 final size:10
Alignment explanation
Indices: 42102421--42102459 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
42102411 ATTATTATTA
*
42102421 AATATAATTT
1 AATAAAATTT
42102431 AATAAAATTT
1 AATAAAATTT
* *
42102441 TATATAATTT
1 AATAAAATTT
42102451 AATAAAATT
1 AATAAAATT
42102460 CTTAATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AATAAAATTT
Found at i:42102447 original size:20 final size:22
Alignment explanation
Indices: 42102421--42102471 Score: 88
Period size: 20 Copynumber: 2.4 Consensus size: 22
42102411 ATTATTATTA
42102421 AATATAATTTAATAAAATT-TT
1 AATATAATTTAATAAAATTCTT
42102442 -ATATAATTTAATAAAATTCTT
1 AATATAATTTAATAAAATTCTT
42102463 AATATAATT
1 AATATAATT
42102472 ATTATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.64
21 2 0.07
22 8 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATAATTTAATAAAATTCTT
Found at i:42102738 original size:14 final size:14
Alignment explanation
Indices: 42102719--42102757 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
42102709 TCATTAGTTT
42102719 ATATGTCATAAACC
1 ATATGTCATAAACC
* * *
42102733 ATATGTTATTAAGC
1 ATATGTCATAAACC
42102747 ATATGTCATAA
1 ATATGTCATAA
42102758 TTTATTAAGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (14 bp):
ATATGTCATAAACC
Found at i:42105579 original size:12 final size:12
Alignment explanation
Indices: 42105562--42105586 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42105552 GGTGTTCATT
42105562 CGGTTAACCGAC
1 CGGTTAACCGAC
42105574 CGGTTAACCGAC
1 CGGTTAACCGAC
42105586 C
1 C
42105587 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:42105761 original size:9 final size:9
Alignment explanation
Indices: 42105747--42105850 Score: 147
Period size: 9 Copynumber: 11.4 Consensus size: 9
42105737 TTTGGTTAAA
42105747 AATTACCCG
1 AATTACCCG
42105756 AATTACCCG
1 AATTACCCG
42105765 AATTACCCG
1 AATTACCCG
42105774 AATTACCCG
1 AATTACCCG
*
42105783 AATTAACCG
1 AATTACCCG
42105792 AATTACCCG
1 AATTACCCG
*
42105801 AATTAACCG
1 AATTACCCG
*
42105810 AATTAACCG
1 AATTACCCG
42105819 AATTA-CCG
1 AATTACCCG
*
42105827 AAAAATACCCG
1 --AATTACCCG
42105838 AATTACCCG
1 AATTACCCG
42105847 AATT
1 AATT
42105851 TTTTTATTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
8 3 0.03
9 77 0.89
10 4 0.05
11 3 0.03
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:42107179 original size:103 final size:99
Alignment explanation
Indices: 42107102--42107548 Score: 283
Period size: 110 Copynumber: 4.2 Consensus size: 99
42107092 TAAAATTATA
*
42107102 AAAATATAAAAAAGTTCCAAAAATTCAAAAAAAAAGTGTGTTATTTACTTT-TTCAATGGTAAAA
1 AAAAT-TAAAAAA-CTCCAAAAATT-AAAAAAAAA-T-TGTTATTT--TTTCTTCAATGGTAAAA
* *
42107166 TGTCTATCTAAAATTTTAAAAATTTCATTTAAAAATTCAAT
59 TATCTATCTAAAATTTTAAAAATTTCATATAAAAATTCAAT
* * *
42107207 AAAATTATAAAACTCCAAAAATTTAAAAAAAATTGTTATTTTTTCTTGAATGGTAAAATATCTAT
1 AAAATTAAAAAACTCCAAAAATTAAAAAAAAATTGTTATTTTTTCTTCAATGGTAAAATATCTAT
* *
42107272 CTAAATTTTTAAGAAA-TTCATTTAAAAATTCAAT
66 CTAAAATTTTAA-AAATTTCATATAAAAATTCAAT
* * * *
42107306 AAAGTCATAAAAATATAAAAACTCCAAAAGTTTTAAAAAAAAACGTGTTATTTGTTTCTTGAATA
1 AAA---AT-----TA-AAAAACTCCAAAA--ATTAAAAAAAAA-TTGTTATTT-TTTCTTCAATG
* * *
42107371 GTAAAATGTCTATCTAAAATTTTAAGAAACTT-AT-TTAAAATTCAATAAAACT
53 GTAAAATATCTATCTAAAATTTTAA-AAATTTCATATAAAAATTC-----AA-T
* * * * * * * * *
42107423 ATAAATATATAAAAAGTTTCAAAAACTCAATAAAAATGTGTTATTTGCTTCTTGAAGGGTAAATT
1 A-AAAT-TA-AAAAA-CTCCAAAAATTAAAAAAAAAT-TGTTATTT-TTTCTTCAATGGTAAAAT
* * *
42107488 GTCTATCTAAAATTTTAAGAAA-TTCATTTAAAAGTTCAAT
60 ATCTATCTAAAATTTTAA-AAATTTCATATAAAAATTCAAT
42107528 AAAATTATAAAAAGCTCCAAA
1 AAAATTA-AAAAA-CTCCAAA
42107549 TGTTCAAAAA
Statistics
Matches: 286, Mismatches: 29, Indels: 56
0.77 0.08 0.15
Matches are distributed among these distances:
98 3 0.01
99 50 0.17
100 11 0.04
101 1 0.00
102 10 0.03
103 24 0.08
104 10 0.03
105 7 0.02
106 2 0.01
107 2 0.01
108 12 0.04
109 2 0.01
110 65 0.23
111 32 0.11
112 45 0.16
113 2 0.01
115 2 0.01
116 2 0.01
117 2 0.01
118 2 0.01
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (99 bp):
AAAATTAAAAAACTCCAAAAATTAAAAAAAAATTGTTATTTTTTCTTCAATGGTAAAATATCTAT
CTAAAATTTTAAAAATTTCATATAAAAATTCAAT
Found at i:42107389 original size:211 final size:218
Alignment explanation
Indices: 42107061--42107540 Score: 579
Period size: 222 Copynumber: 2.2 Consensus size: 218
42107051 AGTACAAATA
* * * *
42107061 AAAATTTTAAGAAAATCATTTAAAATTTTAATAAAATTATAAAAATATAAAAAAGTTCCAAAAAT
1 AAAATTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAATATAAAAAAGCTCCAAAAAT
* * *
42107126 TCAAAAAAAAAGTGTGTTATTTACTTTTTCAATGGTAAAATGTCTATCTAAAATTTTAA-AAATT
66 TCAAAAAAAAAGCGTGTTATTTACTTTTTCAATAGTAAAATGTCTATCTAAAATTTTAAGAAACT
* *
42107190 TCATTTAAAAATTCAATAAAATTATAAA-ACTCCAAAAA-TTT-A-AA-AAAAAT-TGTTATTT-
131 T-ATTT-AAAATTCAATAAAACTATAAATA-TACAAAAAGTTTAACAATAAAAATGTGTTATTTG
* *
42107248 TTTCTTGAATGGTAAAATATCTATCT
193 CTTCTTGAAGGGTAAAATATCTATCT
* * * *
42107274 AAATTTTTAAGAAATTCATTTAAAAATTCAATAAAGTCATAAAAATAT-AAAAA-CTCCAAAAGT
1 AAAATTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAATATAAAAAAGCTCCAAAA-A
* * *
42107337 TTTAAAAAAAAA-CGTGTTATTT-GTTTCTTGAATAGTAAAATGTCTATCTAAAATTTTAAGAAA
65 TTCAAAAAAAAAGCGTGTTATTTACTTT-TTCAATAGTAAAATGTCTATCTAAAATTTTAAGAAA
*
42107400 CTTATTTAAAATTCAATAAAACTATAAATATATAAAAAGTTTCAAAAACTCAATAAAAATGTGTT
129 CTTATTTAAAATTCAATAAAACTATAAATATACAAAAAGTTT----AA--CAATAAAAATGTGTT
* *
42107465 ATTTGCTTCTTGAAGGGTAAATTGTCTATCT
188 ATTTGCTTCTTGAAGGGTAAAATATCTATCT
*
42107496 AAAATTTTAAGAAATTCATTTAAAAGTTCAATAAAATTATAAAAA
1 AAAATTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAA
42107541 GCTCCAAATG
Statistics
Matches: 226, Mismatches: 25, Indels: 23
0.82 0.09 0.08
Matches are distributed among these distances:
210 29 0.13
211 54 0.24
212 21 0.09
213 42 0.19
216 1 0.00
219 2 0.01
220 6 0.03
221 8 0.04
222 63 0.28
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (218 bp):
AAAATTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAATATAAAAAAGCTCCAAAAAT
TCAAAAAAAAAGCGTGTTATTTACTTTTTCAATAGTAAAATGTCTATCTAAAATTTTAAGAAACT
TATTTAAAATTCAATAAAACTATAAATATACAAAAAGTTTAACAATAAAAATGTGTTATTTGCTT
CTTGAAGGGTAAAATATCTATCT
Found at i:42107496 original size:110 final size:110
Alignment explanation
Indices: 42107205--42107540 Score: 398
Period size: 110 Copynumber: 3.1 Consensus size: 110
42107195 TAAAAATTCA
* * *
42107205 ATAAAATTAT-AAAACTCCAAAA-ATTTAAAAAAAAT-TGTTATTT-TTTCTTGAATGGTAAAAT
1 ATAAAAATATAAAAACTCCAAAAGACTAAAAAAAAATGTGTTATTTGTTTCTTGAATGGTAAAAT
* * *
42107266 ATCTATCTAAATTTTTAAGAAATTCATTTAAAAATTCAAT-AAAGT
66 GTCTATCTAAAATTTTAAGAAATTCATTT-AAAATTCAATAAAACT
** * *
42107311 CATAAAAATATAAAAACTCCAAAAGTTTTAAAAAAAAACGTGTTATTTGTTTCTTGAATAGTAAA
1 -ATAAAAATATAAAAACTCCAAAAG-ACTAAAAAAAAATGTGTTATTTGTTTCTTGAATGGTAAA
42107376 ATGTCTATCTAAAATTTTAAGAAACTT-ATTTAAAATTCAATAAAACT
64 ATGTCTATCTAAAATTTTAAGAAA-TTCATTTAAAATTCAATAAAACT
* * * * * * * *
42107423 ATAAATATATAAAAAGTTTCAAAA-ACTCAATAAAAATGTGTTATTTGCTTCTTGAAGGGTAAAT
1 ATAAAAATATAAAAA-CTCCAAAAGACTAAAAAAAAATGTGTTATTTGTTTCTTGAATGGTAAAA
*
42107487 TGTCTATCTAAAATTTTAAGAAATTCATTTAAAAGTTCAATAAAATT
65 TGTCTATCTAAAATTTTAAGAAATTCATTTAAAA-TTCAATAAAACT
42107534 ATAAAAA
1 ATAAAAA
42107541 GCTCCAAATG
Statistics
Matches: 197, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
107 9 0.05
108 12 0.06
109 2 0.01
110 72 0.37
111 49 0.25
112 51 0.26
113 2 0.01
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.36
Consensus pattern (110 bp):
ATAAAAATATAAAAACTCCAAAAGACTAAAAAAAAATGTGTTATTTGTTTCTTGAATGGTAAAAT
GTCTATCTAAAATTTTAAGAAATTCATTTAAAATTCAATAAAACT
Found at i:42112459 original size:20 final size:22
Alignment explanation
Indices: 42112419--42112460 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
42112409 GTCCCTCGTC
*
42112419 CGTTATGGAGTCGAAGTCAACT
1 CGTTATGGAGTCGAAGGCAACT
42112441 CGTT-TGGAG-CGAAGGCAACT
1 CGTTATGGAGTCGAAGGCAACT
42112461 TGGTCATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 5 0.26
22 4 0.21
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (22 bp):
CGTTATGGAGTCGAAGGCAACT
Found at i:42113191 original size:21 final size:19
Alignment explanation
Indices: 42113165--42113204 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
42113155 TTATTTTTTT
42113165 CAATTAAATTATATATTATAA
1 CAATT-AATT-TATATTATAA
*
42113186 CAATTAATTTTTATTATAA
1 CAATTAATTTATATTATAA
42113205 TTATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
CAATTAATTTATATTATAA
Found at i:42113836 original size:16 final size:16
Alignment explanation
Indices: 42113817--42113851 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42113807 ATATTTTACG
42113817 TTAAAAATTAATTAAT
1 TTAAAAATTAATTAAT
* *
42113833 TTAAAATTTAATTTAT
1 TTAAAAATTAATTAAT
42113849 TTA
1 TTA
42113852 TCATTGATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAAAATTAATTAAT
Found at i:42113992 original size:27 final size:24
Alignment explanation
Indices: 42113962--42114012 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
42113952 AAAATAAAGA
42113962 AAGATAAAAAGATAATAATAAATATTT
1 AAGA-AAAAA-AT-ATAATAAATATTT
* *
42113989 AAGAAAAGAATATATTAAATATTT
1 AAGAAAAAAATATAATAAATATTT
42114013 TCCAATCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 12 0.55
25 2 0.09
26 4 0.18
27 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (24 bp):
AAGAAAAAAATATAATAAATATTT
Found at i:42114841 original size:15 final size:15
Alignment explanation
Indices: 42114821--42114854 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42114811 TTTGGTAAGT
42114821 AATATTCATCAATCA
1 AATATTCATCAATCA
* *
42114836 AATATTTATGAATCA
1 AATATTCATCAATCA
42114851 AATA
1 AATA
42114855 AAAAAGGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (15 bp):
AATATTCATCAATCA
Done.