Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 106 of 310
Found at i:33835574 original size:31 final size:31
Alignment explanation
Indices: 33835548--33835649 Score: 168
Period size: 31 Copynumber: 3.3 Consensus size: 31
33835538 TCAGAACTAG
* * * *
33835548 AATCAGAATCAGAATTAGGTGACAGAATCAG
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
33835579 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
33835610 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
33835641 AATCAGAAT
1 AATCAGAAT
33835650 GTGAGTGCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.20
Consensus pattern (31 bp):
AATCAGAATCAGTATCAGGTAACAGAATCAA
Found at i:33835606 original size:19 final size:19
Alignment explanation
Indices: 33835582--33835639 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
33835572 GAATCAGAAT
33835582 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
*
33835601 CAGAATCA--A--A---AT
1 CAGAATCAGTATCAGGTAA
33835613 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
33835632 CAGAATCA
1 CAGAATCA
33835640 AAATCAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 9 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
19 17 0.57
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (19 bp):
CAGAATCAGTATCAGGTAA
Found at i:33836088 original size:27 final size:27
Alignment explanation
Indices: 33836058--33836299 Score: 290
Period size: 27 Copynumber: 9.0 Consensus size: 27
33836048 ATTACCATTT
* *
33836058 TACCCCACAAGGGTATCTCGGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* *
33836085 TACCTTAC-AGGAGTATTTCAGTAATTC
1 TACCCTACAAGG-GTATTTCGGTAATTC
* *
33836112 TACCCTACAGGGGTATTTCGGTATTTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* *
33836139 TACCCTACAAGGGTATTTCAGAAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* **
33836166 TACCCTACAGGGGTATTTTAGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* *
33836193 TACCCTACAGGGGTATTTCAG-AATTTC
1 TACCCTACAAGGGTATTTCGGTAA-TTC
* *
33836220 TACCCTACGAGGGTATTTCGGTATTTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* *
33836247 TACTCTACAAGGGTATTTCGGTATTTC
1 TACCCTACAAGGGTATTTCGGTAATTC
*
33836274 TACCCTACAAGGGTATTTCGATAATT
1 TACCCTACAAGGGTATTTCGGTAATT
33836300 TTATAAATCG
Statistics
Matches: 186, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.03
27 178 0.96
28 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
TACCCTACAAGGGTATTTCGGTAATTC
Found at i:33836175 original size:81 final size:80
Alignment explanation
Indices: 33836054--33836293 Score: 320
Period size: 81 Copynumber: 3.0 Consensus size: 80
33836044 TAAAATTACC
* * *
33836054 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCTTACAGGAGTATTTCAGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGG-GTATTTCAGTAATTCTACCCT
*
33836118 ACAGGGGTATTTCGGT
65 ACAGGGGTATTTCGGA
* * *
33836134 ATTTCTACCCTACAAGGGTATTTCAGAAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACA-GGGTATTTCAGTAATTCTACCCT
*
33836199 ACAGGGGTATTTCAGA
65 ACAGGGGTATTTCGGA
* * * * *
33836215 ATTTCTACCCTACGAGGGTATTTCGGTATTTCTACTCTACAAGGGTATTTCGGTATTTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTAC-AGGGTATTTCAGTAATTCTACCCT
*
33836280 ACAAGGGTATTTCG
65 ACAGGGGTATTTCG
33836294 ATAATTTTAT
Statistics
Matches: 139, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
80 4 0.03
81 132 0.95
82 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (80 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGTATTTCAGTAATTCTACCCTA
CAGGGGTATTTCGGA
Found at i:33836313 original size:27 final size:27
Alignment explanation
Indices: 33836281--33836651 Score: 336
Period size: 27 Copynumber: 13.7 Consensus size: 27
33836271 TTCTACCCTA
* * *
33836281 CAAGGGTATTTCGATAATTTTATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *** * *
33836308 CGAGGGTAAAATGGTAATTCTATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
33836335 CAAGCGTACTTTGGTAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *** **
33836362 CGAGGGTATTTCAATAATTTTACAGGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** *
33836389 CAAGGGTATTTCAGTAATTTCACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
33836416 TAGGGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
33836442 CTAGGGGTATTTTGATAATTTTACAAAC
1 C-AAGGGTATTTTGGTAATTTTACAAAT
*
33836470 CAAGGTTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
33836496 CTAGGGGTATTTTGGTAATTTTATAAAC
1 C-AAGGGTATTTTGGTAATTTTACAAAT
** *
33836524 CAAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
33836551 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
33836578 CAAGGGTATTTTGGTGATTTTATAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
33836604 CTAAGGGTATTTTAGTAATTTTACAAA-
1 C-AAGGGTATTTTGGTAATTTTACAAAT
*
33836631 CTAGGGGTATTTTGGTAATTT
1 C-AAGGGTATTTTGGTAATTT
33836652 GGTAAACTAA
Statistics
Matches: 288, Mismatches: 51, Indels: 10
0.83 0.15 0.03
Matches are distributed among these distances:
26 2 0.01
27 284 0.99
28 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:33836329 original size:81 final size:81
Alignment explanation
Indices: 33836075--33836329 Score: 221
Period size: 81 Copynumber: 3.1 Consensus size: 81
33836065 CAAGGGTATC
* * * *
33836075 TCGGTAATTCTACCTTAC-AGGAGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTATTTC
1 TCGGTAATTCTACCCTACAAGG-GTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGAATTTC
*** * **
33836139 TACCCTACAAGGGTATT
65 TAAAATACGAGGGTAAA
* * * * *
33836156 TCAGAAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGAATTTCT
1 TCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGAATTTCT
*** **
33836221 ACCCTACGAGGGTATT
66 AAAATACGAGGGTAAA
* * * * *
33836237 TCGGTATTTCTACTCTACAAGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGATAATTT-
1 TCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTC-AGAATTTC
33836301 TATAAAT-CGAGGGTAAAA
65 TA-AAATACGAGGGT-AAA
33836319 T-GGTAATTCTA
1 TCGGTAATTCTA
33836330 TAAATCAAGC
Statistics
Matches: 146, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
81 135 0.92
82 11 0.08
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (81 bp):
TCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGAATTTCT
AAAATACGAGGGTAAA
Found at i:33836660 original size:27 final size:27
Alignment explanation
Indices: 33836390--33836651 Score: 344
Period size: 27 Copynumber: 9.7 Consensus size: 27
33836380 TTTACAGGTC
** * *
33836390 AAGGGTATTTCAGTAATTTCACAAATT
1 AAGGGTATTTTGGTAATTTTACAAACT
*
33836417 AGGGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
* * *
33836444 AGGGGTATTTTGATAATTTTACAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
*
33836471 AAGGTTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
* * *
33836498 AGGGGTATTTTGGTAATTTTATAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
** *
33836525 AAGGGTATTTTGGTAATTTTGTAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
*
33836552 AAGGGTATTTTGGTAATTTTACAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
* *
33836579 AAGGGTATTTTGGTGATTTTATAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
*
33836606 AAGGGTATTTTAGTAATTTTACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
*
33836633 AGGGGTATTTTGGTAATTT
1 AAGGGTATTTTGGTAATTT
33836652 GGTAAACTAA
Statistics
Matches: 208, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 208 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAACT
Found at i:33838610 original size:6 final size:6
Alignment explanation
Indices: 33838592--33838704 Score: 72
Period size: 6 Copynumber: 18.3 Consensus size: 6
33838582 AAGAAACATT
* *
33838592 ATCAGA A-CTAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA
* * *
33838641 ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA AT-AGA
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
* *
33838691 AACAAA ATCAGA AT
1 ATCAGA ATCAGA AT
33838705 GTGAATGCAA
Statistics
Matches: 82, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
5 6 0.07
6 64 0.78
7 8 0.10
8 4 0.05
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:33838636 original size:31 final size:31
Alignment explanation
Indices: 33838603--33838704 Score: 150
Period size: 31 Copynumber: 3.3 Consensus size: 31
33838593 TCAGAACTAG
* * * *
33838603 AATCAGAATCAGAATTAGGTGACAGAATCAG
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
33838634 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
* *
33838665 AATCAGAATCAGTATCAGGTAATAGAAACAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
33838696 AATCAGAAT
1 AATCAGAAT
33838705 GTGAATGCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.20
Consensus pattern (31 bp):
AATCAGAATCAGTATCAGGTAACAGAATCAA
Found at i:33838700 original size:37 final size:37
Alignment explanation
Indices: 33838628--33838700 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
33838618 TAGGTGACAG
* *
33838628 AATCAGAATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGAATCAGTATCAGGAAACAAAATCAA
*
33838665 AATCAGAATCAGTATCAGGTAAT-A-GAAACAAAATCA
1 AATCAGAATCAGAATCA-GT-ATCAGGAAACAAAATCA
33838701 GAATGTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 26 0.84
38 3 0.10
39 2 0.06
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (37 bp):
AATCAGAATCAGAATCAGTATCAGGAAACAAAATCAA
Found at i:33839138 original size:27 final size:27
Alignment explanation
Indices: 33839108--33839382 Score: 241
Period size: 27 Copynumber: 10.2 Consensus size: 27
33839098 GGTAAAATGG
* * *
33839108 TAATTTTACCCCATAAGGGTATCTCGA
1 TAATTCTACCCTATAAGGGTATTTCGA
* * *
33839135 TAATTCTACCTTACAAGAGTATTTC-A
1 TAATTCTACCCTATAAGGGTATTTCGA
* *
33839161 GTAATTCTACCCTATAGGGGTATTTCGG
1 -TAATTCTACCCTATAAGGGTATTTCGA
* * *
33839189 TATTTCTACCCTACAAGGGTATTTCGG
1 TAATTCTACCCTATAAGGGTATTTCGA
* *
33839216 TAATTCTACCCTATAGGGGTATTT-TA
1 TAATTCTACCCTATAAGGGTATTTCGA
* * *
33839242 GTAATTCTACCTTATAGGGGTATTTCGG
1 -TAATTCTACCCTATAAGGGTATTTCGA
* * *
33839270 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTATAAGGGTATTTCGA
* * *
33839297 TATTTCTACCCTACAAAGGTATTTC-A
1 TAATTCTACCCTATAAGGGTATTTCGA
* * *
33839323 GTACTTCTACCCTACAAGGGTATTTCGG
1 -TAATTCTACCCTATAAGGGTATTTCGA
* * * *
33839351 CATTTCTACCCTACAAGGGTATTTCGG
1 TAATTCTACCCTATAAGGGTATTTCGA
33839378 TAATT
1 TAATT
33839383 TTGTAAATCG
Statistics
Matches: 207, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
26 1 0.00
27 206 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (27 bp):
TAATTCTACCCTATAAGGGTATTTCGA
Found at i:33839166 original size:54 final size:54
Alignment explanation
Indices: 33839106--33839382 Score: 356
Period size: 54 Copynumber: 5.1 Consensus size: 54
33839096 GGGGTAAAAT
* * * * * * * *
33839106 GGTAATTTTACCCCATAAGGGTATCTCGATAATTCTACCTTACAAGAGTATTTC
1 GGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
*
33839160 AGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
** * * * *
33839214 GGTAATTCTACCCTATAGGGGTATTTTAGTAATTCTACCTTATAGGGGTATTTC
1 GGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
* *
33839268 GGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAAGGTATTTC
1 GGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
* * * * *
33839322 AGTACTTCTACCCTACAAGGGTATTTCGGCATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
33839376 GGTAATT
1 GGTAATT
33839383 TTGTAAATCG
Statistics
Matches: 192, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 192 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
Found at i:33839199 original size:81 final size:81
Alignment explanation
Indices: 33839122--33839382 Score: 371
Period size: 81 Copynumber: 3.2 Consensus size: 81
33839112 TTTACCCCAT
* * *
33839122 AAGGGTATCTCGATAATTCTACCTTACAAGAGTATTTCAGTAATTCTACCCTATAGGGGTATTTC
1 AAGGGTATTTCGGTAATTCTACCCTACAAGAGTATTTCAGTAATTCTACCCTATAGGGGTATTTC
33839187 GGTATTTCTACCCTAC
66 GGTATTTCTACCCTAC
* * * * *
33839203 AAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTAGTAATTCTACCTTATAGGGGTATTTC
1 AAGGGTATTTCGGTAATTCTACCCTACAAGAGTATTTCAGTAATTCTACCCTATAGGGGTATTTC
*
33839268 GGTAATTCTACCCTAC
66 GGTATTTCTACCCTAC
* * * * *
33839284 AGGGGTATTTCGGTATTTCTACCCTACAA-AGGTATTTCAGTACTTCTACCCTACAAGGGTATTT
1 AAGGGTATTTCGGTAATTCTACCCTACAAGA-GTATTTCAGTAATTCTACCCTATAGGGGTATTT
*
33839348 CGGCATTTCTACCCTAC
65 CGGTATTTCTACCCTAC
33839365 AAGGGTATTTCGGTAATT
1 AAGGGTATTTCGGTAATT
33839383 TTGTAAATCG
Statistics
Matches: 156, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
81 156 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (81 bp):
AAGGGTATTTCGGTAATTCTACCCTACAAGAGTATTTCAGTAATTCTACCCTATAGGGGTATTTC
GGTATTTCTACCCTAC
Found at i:33839396 original size:27 final size:27
Alignment explanation
Indices: 33839366--33839761 Score: 284
Period size: 27 Copynumber: 14.7 Consensus size: 27
33839356 CTACCCTACA
* * *
33839366 AGGGTATTTCGGTAATTTTGTAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCT
*** * *
33839393 AGGGTAAAATGGTAATTTTGTAAATCA
1 AGGGTATTTTGGTAATTTTATAAATCT
* * * *
33839420 AGCGTACTTTGGTAATTTTACAAGTCT
1 AGGGTATTTTGGTAATTTTATAAATCT
*** * ** *
33839447 AGGGTATTTCAATAATTTTACAGGTCG
1 AGGGTATTTTGGTAATTTTATAAATCT
* * *
33839474 AGGGTATTTTAGTAATTTCACAAAT-T
1 AGGGTATTTTGGTAATTTTATAAATCT
*
33839500 AGGGGTATTTTGGTAATTTTACAAA-CT
1 A-GGGTATTTTGGTAATTTTATAAATCT
* * *
33839527 AGGGGTATTTTGATAATTTTACAAA-CC
1 A-GGGTATTTTGGTAATTTTATAAATCT
33839554 AGGGGTATTTTGGTAATTTTATAAA-CT
1 A-GGGTATTTTGGTAATTTTATAAATCT
* *
33839581 AGGGGTATTTTGGTAATTTTATAAACCA
1 A-GGGTATTTTGGTAATTTTATAAATCT
* * *
33839609 AAGGTATTTTAGTAATTTTATAAA-CC
1 AGGGTATTTTGGTAATTTTATAAATCT
* * *
33839635 AGGGGTATTTTGGTAATTTTGTAAACCA
1 A-GGGTATTTTGGTAATTTTATAAATCT
* * *
33839663 ATGGTATTTTGGTAATTTTACAAA-CC
1 AGGGTATTTTGGTAATTTTATAAATCT
* * *
33839689 AGAGGTATTTTGGTGATTTTATAAACCA
1 AG-GGTATTTTGGTAATTTTATAAATCT
* * * *
33839717 AGGGTACTTTAGTAATTTTACAAA-CC
1 AGGGTATTTTGGTAATTTTATAAATCT
33839743 AGGGGTATTTTGGTAATTT
1 A-GGGTATTTTGGTAATTT
33839762 GGTAAACTAA
Statistics
Matches: 305, Mismatches: 56, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
26 7 0.02
27 291 0.95
28 7 0.02
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTATAAATCT
Found at i:33839512 original size:81 final size:81
Alignment explanation
Indices: 33839427--33839761 Score: 323
Period size: 81 Copynumber: 4.1 Consensus size: 81
33839417 TCAAGCGTAC
* ***
33839427 TTTGGTAATTTTACAAGTCTA-GGGTATTTCAATAATTTTACAGGTC-GAGGGTATTTTAGTAAT
1 TTTGGTAATTTTACAA-ACTAGGGGTATTTCAATAATTTTACAAACCAG-GGGTATTTTAGTAAT
*
33839490 TTCACAAATTAGGGGTAT
64 TTCACAAACTAGGGGTAT
** *
33839508 TTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACCAGGGGTATTTTGGTAATTT
1 TTTGGTAATTTTACAAACTAGGGGTATTTCAATAATTTTACAAACCAGGGGTATTTTAGTAATTT
* *
33839573 TATAAACTAGGGGTAT
66 CACAAACTAGGGGTAT
* * ** * * * *
33839589 TTTGGTAATTTTATAAACCAAAGGTATTTTAGTAATTTTATAAACCAGGGGTATTTTGGTAATTT
1 TTTGGTAATTTTACAAACTAGGGGTATTTCAATAATTTTACAAACCAGGGGTATTTTAGTAATTT
*** * **
33839654 TGTAAACCAATGGTAT
66 CACAAACTAGGGGTAT
* * *** * * * *
33839670 TTTGGTAATTTTACAAACCAGAGGTATTTTGGTGATTTTATAAACCAAGGGTACTTTAGTAATTT
1 TTTGGTAATTTTACAAACTAGGGGTATTTCAATAATTTTACAAACCAGGGGTATTTTAGTAATTT
* *
33839735 TACAAACCAGGGGTAT
66 CACAAACTAGGGGTAT
33839751 TTTGGTAATTT
1 TTTGGTAATTT
33839762 GGTAAACTAA
Statistics
Matches: 220, Mismatches: 32, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
80 3 0.01
81 216 0.98
82 1 0.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (81 bp):
TTTGGTAATTTTACAAACTAGGGGTATTTCAATAATTTTACAAACCAGGGGTATTTTAGTAATTT
CACAAACTAGGGGTAT
Found at i:33839768 original size:27 final size:27
Alignment explanation
Indices: 33839475--33839761 Score: 367
Period size: 27 Copynumber: 10.6 Consensus size: 27
33839465 TACAGGTCGA
* * * **
33839475 GGGTATTTTAGTAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTATAAACCAG
* *
33839502 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAG
* *
33839529 GGGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAG
*
33839556 GGGTATTTTGGTAATTTTATAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAG
*
33839583 GGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAG
* *
33839610 AGGTATTTTAGTAATTTTATAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAG
* *
33839637 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAG
* *
33839664 TGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAG
* * *
33839691 AGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAG
* * *
33839718 GGGTACTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAG
33839745 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
33839762 GGTAAACTAA
Statistics
Matches: 227, Mismatches: 33, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 227 1.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAG
Found at i:33841189 original size:23 final size:23
Alignment explanation
Indices: 33841163--33841207 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
33841153 TGGCACTCTT
33841163 ATGCAAGTAACAATGGCACTTCG
1 ATGCAAGTAACAATGGCACTTCG
* * * *
33841186 ATGCTAGTGATAGTGGCACTTC
1 ATGCAAGTAACAATGGCACTTC
33841208 AGTGCAAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (23 bp):
ATGCAAGTAACAATGGCACTTCG
Found at i:33848595 original size:42 final size:46
Alignment explanation
Indices: 33848547--33848668 Score: 128
Period size: 48 Copynumber: 2.7 Consensus size: 46
33848537 GTGTTATCAT
*
33848547 GTAAGACCATTTCTGGGATATGGCATT-G-AT-A-TGAGATCCCATA
1 GTAAGACCATATCTGGGATATGGCATTGGCATAAGTGAGATCCCA-A
* * * *
33848590 -TAAGACCATGTCTGGAACATGGCATTGGCATCAAGTTGTGATCCCAA
1 GTAAGACCATATCTGGGATATGGCATTGGCAT-AAG-TGAGATCCCAA
*
33848637 GTAAGACCATATCTGGGATATGGCGTTGGCAT
1 GTAAGACCATATCTGGGATATGGCATTGGCAT
33848669 CTTACTATGT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
42 23 0.36
43 1 0.02
44 2 0.03
46 1 0.02
47 1 0.02
48 36 0.56
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (46 bp):
GTAAGACCATATCTGGGATATGGCATTGGCATAAGTGAGATCCCAA
Found at i:33858585 original size:13 final size:13
Alignment explanation
Indices: 33858567--33858591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33858557 TAAAATTGGT
33858567 TTCAAATTTGGAG
1 TTCAAATTTGGAG
33858580 TTCAAATTTGGA
1 TTCAAATTTGGA
33858592 AGATATGATA
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:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TTCAAATTTGGAG
Found at i:33862206 original size:20 final size:18
Alignment explanation
Indices: 33862181--33862217 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
33862171 TGGAGGACAC
33862181 GGGCGTGTCCTGAGCCACAT
1 GGGCGTGT-CTGA-CCACAT
33862201 GGGCGTGTCTGACCACA
1 GGGCGTGTCTGACCACA
33862218 CGGCCTGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.16, C:0.30, G:0.35, T:0.19
Consensus pattern (18 bp):
GGGCGTGTCTGACCACAT
Found at i:33862664 original size:23 final size:23
Alignment explanation
Indices: 33862634--33862689 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
33862624 GATGAAGTGC
33862634 TGATTTGATTAAATCAGTTGATT
1 TGATTTGATTAAATCAGTTGATT
*
33862657 TGATTTGATTAAGTCAGTTGATT
1 TGATTTGATTAAATCAGTTGATT
33862680 TGATTTGATT
1 TGATTTGATT
33862690 TAGACCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.50
Consensus pattern (23 bp):
TGATTTGATTAAATCAGTTGATT
Found at i:33863579 original size:65 final size:65
Alignment explanation
Indices: 33863475--33863604 Score: 172
Period size: 65 Copynumber: 2.0 Consensus size: 65
33863465 TGCAAGGACA
**
33863475 AAATTGGAAAGTGAATAAATTAATATATGATAAAAGATTAAATAGAATAAAACTTATTTTATATC
1 AAATTGGAAAGTGAATAAATTAATATATGATAAAAGATTAAATAGAATAAAACCCATTTTATATC
* * * * * *
33863540 AAATTGGGAATTGAATTAAA-TAGTATGTGATAAATGATTAAATAGAATTAAACCCATTTTATAT
1 AAATTGGAAAGTGAA-TAAATTAATATATGATAAAAGATTAAATAGAATAAAACCCATTTTATAT
33863604 C
65 C
33863605 TTCTTCTTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 52 0.93
66 4 0.07
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (65 bp):
AAATTGGAAAGTGAATAAATTAATATATGATAAAAGATTAAATAGAATAAAACCCATTTTATATC
Found at i:33863975 original size:51 final size:51
Alignment explanation
Indices: 33863910--33864011 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
33863900 GATTAAATTG
* *
33863910 CAAAGTAGTGAAATTCTTAAAAAAAATTTGAAATTTATGAAATACAGGTGC
1 CAAAGTAGTAAAATTCTTAAAAAAAATTTAAAATTTATGAAATACAGGTGC
** * *
33863961 CAAAGTAGTAAAATTCTTGGAAAAATTTTAAAATTTATGAAATACATGTGC
1 CAAAGTAGTAAAATTCTTAAAAAAAATTTAAAATTTATGAAATACAGGTGC
33864012 TGTAAAAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (51 bp):
CAAAGTAGTAAAATTCTTAAAAAAAATTTAAAATTTATGAAATACAGGTGC
Found at i:33864670 original size:65 final size:65
Alignment explanation
Indices: 33864601--33864771 Score: 243
Period size: 65 Copynumber: 2.6 Consensus size: 65
33864591 TGGTACAACT
* * * *
33864601 TGAAAAGGTTATATACACTTTGTGTGTACACTTGGAAAGGTTAGGTATACTTTGTGTGTACCATA
1 TGAAAAGGATAGATATACTTTGTGTGTACACTTGGAAAGGTTAAGTATACTTTGTGTGTACCATA
* * *
33864666 TGAAAAGGAAAGATATACTTTGTGTGTACACTTGAAAAGTTTAAGTATACTTTGTGTGTACCATA
1 TGAAAAGGATAGATATACTTTGTGTGTACACTTGGAAAGGTTAAGTATACTTTGTGTGTACCATA
* * *
33864731 TGAAAAGGATAGGTATACTCTGTGTCTACCACTTGGAAAGG
1 TGAAAAGGATAGATATACTTTGTGTGTA-CACTTGGAAAGG
33864772 AATGTACACC
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
65 82 0.89
66 10 0.11
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (65 bp):
TGAAAAGGATAGATATACTTTGTGTGTACACTTGGAAAGGTTAAGTATACTTTGTGTGTACCATA
Found at i:33864772 original size:33 final size:33
Alignment explanation
Indices: 33864593--33864772 Score: 179
Period size: 33 Copynumber: 5.5 Consensus size: 33
33864583 TATCCAAATG
* * ** *
33864593 GTACAACTTGAAAAGGTTATATACACTTTGTGT
1 GTACCACTTGAAAAGGATAGGTATACTTTGTGT
* *
33864626 GTA-CACTTGGAAAGGTTAGGTATACTTTGTGT
1 GTACCACTTGAAAAGGATAGGTATACTTTGTGT
* *
33864658 GTACCA-TATGAAAAGGAAAGATATACTTTGTGT
1 GTACCACT-TGAAAAGGATAGGTATACTTTGTGT
** *
33864691 GTA-CACTTGAAAAGTTTAAGTATACTTTGTGT
1 GTACCACTTGAAAAGGATAGGTATACTTTGTGT
*
33864723 GTACCA-TATGAAAAGGATAGGTATACTCTGTGT
1 GTACCACT-TGAAAAGGATAGGTATACTTTGTGT
* *
33864756 CTACCACTTGGAAAGGA
1 GTACCACTTGAAAAGGA
33864773 ATGTACACCT
Statistics
Matches: 121, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
32 54 0.45
33 66 0.55
34 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (33 bp):
GTACCACTTGAAAAGGATAGGTATACTTTGTGT
Found at i:33869073 original size:13 final size:13
Alignment explanation
Indices: 33869057--33869096 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
33869047 TTTAAACCAA
33869057 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
33869070 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
33869083 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
33869096 A
1 A
33869097 ATGAAGAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:33872040 original size:16 final size:16
Alignment explanation
Indices: 33872019--33872049 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
33872009 ATGTAGCAAT
33872019 TTTTTATTTTTTTTTA
1 TTTTTATTTTTTTTTA
33872035 TTTTTATTTTTTTTT
1 TTTTTATTTTTTTTT
33872050 CAGACTATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTATTTTTTTTTA
Found at i:33874201 original size:25 final size:25
Alignment explanation
Indices: 33874168--33874300 Score: 150
Period size: 25 Copynumber: 5.4 Consensus size: 25
33874158 AAATGTGCAA
33874168 ATCAGAGAGCACTGACGTGCTAAAT
1 ATCAGAGAGCACTGACGTGCTAAAT
* * *
33874193 ATCATAGAGCACTGGCGTGCT-AGT
1 ATCAGAGAGCACTGACGTGCTAAAT
33874217 AATCAGAGAGCACT-AGCGTGCTAAAT
1 -ATCAGAGAGCACTGA-CGTGCTAAAT
** *
33874243 ATCAGAGAGCACAAATGTGCT--A-
1 ATCAGAGAGCACTGACGTGCTAAAT
*
33874265 ATCAGAGAGCACTGGCGTGCTAAAT
1 ATCAGAGAGCACTGACGTGCTAAAT
33874290 ATCAGAGAGCA
1 ATCAGAGAGCA
33874301 TGCTGAAGTC
Statistics
Matches: 89, Mismatches: 12, Indels: 14
0.77 0.10 0.12
Matches are distributed among these distances:
22 17 0.19
23 1 0.01
24 3 0.03
25 65 0.73
26 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (25 bp):
ATCAGAGAGCACTGACGTGCTAAAT
Found at i:33874224 original size:50 final size:47
Alignment explanation
Indices: 33874126--33874300 Score: 196
Period size: 47 Copynumber: 3.7 Consensus size: 47
33874116 CACTAATGAA
* * * *
33874126 CAGAGAGCACTGAAGTGCT--TTA-CAGAGAGCACAAATGTGCAAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAACGTGCTAAT
* ***
33874170 CAGAGAGCACTGACGTGCTAAATATCATAGAGCACTGGCGTGCTAGTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAACGTGC---TAAT
*
33874220 CAGAGAGCACT-AGCGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGA-CGTGCTAAATATCAGAGAGCACAAACGTGCTAAT
*
33874267 CAGAGAGCACTGGCGTGCTAAATATCAGAGAGCA
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCA
33874301 TGCTGAAGTC
Statistics
Matches: 109, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
44 18 0.17
46 2 0.02
47 49 0.45
49 1 0.01
50 39 0.36
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (47 bp):
CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAACGTGCTAAT
Found at i:33874285 original size:47 final size:47
Alignment explanation
Indices: 33874148--33874300 Score: 207
Period size: 47 Copynumber: 3.2 Consensus size: 47
33874138 AAGTGCTTTA
* *
33874148 CAGAGAGCACAAATGTGCAAATCAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGGCGTGCTAAATAT
* **** *
33874195 CATAGAGCACTGGCGTGCTAGTAATCAGAGAGCACTAGCGTGCTAAATAT
1 CAGAGAGCACAAATGTGC---TAATCAGAGAGCACTGGCGTGCTAAATAT
33874245 CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGGCGTGCTAAATAT
1 CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGGCGTGCTAAATAT
33874292 CAGAGAGCA
1 CAGAGAGCA
33874301 TGCTGAAGTC
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
47 50 0.56
50 39 0.44
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (47 bp):
CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGGCGTGCTAAATAT
Found at i:33876713 original size:135 final size:135
Alignment explanation
Indices: 33876471--33876746 Score: 543
Period size: 135 Copynumber: 2.0 Consensus size: 135
33876461 CTCCTCCATG
33876471 GCTATTTTTCAGCTGATGAATATGAAGAGAAATGAAGAGAATTCTAGATATTCCAATTTAGTCCC
1 GCTATTTTTCAGCTGATGAATATGAAGAGAAATGAAGAGAATTCTAGATATTCCAATTTAGTCCC
33876536 ATTTTTATTTAGCCAATTTTGGCAATTTTCCAATTTTACCCTTATTTCATCCATTTCCTGATTTT
66 ATTTTTATTTAGCCAATTTTGGCAATTTTCCAATTTTACCCTTATTTCATCCATTTCCTGATTTT
33876601 TCTCA
131 TCTCA
33876606 GCTATTTTTCAGCTGATGAATATGAAGAGAAATGAAGAGAATTCTAGATATTCCAATTTAGTCCC
1 GCTATTTTTCAGCTGATGAATATGAAGAGAAATGAAGAGAATTCTAGATATTCCAATTTAGTCCC
*
33876671 ATTTTTATTTAGCCAATTTTGGCAATTTTCCAATTTTGCCCTTATTTCATCCATTTCCTGATTTT
66 ATTTTTATTTAGCCAATTTTGGCAATTTTCCAATTTTACCCTTATTTCATCCATTTCCTGATTTT
33876736 TCTCA
131 TCTCA
33876741 GCTATT
1 GCTATT
33876747 GCAGCCAAAA
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 140 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (135 bp):
GCTATTTTTCAGCTGATGAATATGAAGAGAAATGAAGAGAATTCTAGATATTCCAATTTAGTCCC
ATTTTTATTTAGCCAATTTTGGCAATTTTCCAATTTTACCCTTATTTCATCCATTTCCTGATTTT
TCTCA
Found at i:33877171 original size:20 final size:21
Alignment explanation
Indices: 33877135--33877182 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
33877125 TCTTACGAGC
*
33877135 TTTC-GTTAACTCATTT-GAG
1 TTTCAGTTAACCCATTTGGAG
* *
33877154 TTTCAGTTAACCCTTTTGGGG
1 TTTCAGTTAACCCATTTGGAG
33877175 TTTCAGTT
1 TTTCAGTT
33877183 CAGCTCTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.17
20 10 0.42
21 10 0.42
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.48
Consensus pattern (21 bp):
TTTCAGTTAACCCATTTGGAG
Found at i:33877237 original size:21 final size:21
Alignment explanation
Indices: 33877213--33877287 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 21
33877203 TAGCCTTCGG
33877213 GCTTCCGTCTAGCACTTGTGT
1 GCTTCCGTCTAGCACTTGTGT
*
33877234 GCTTCAGT-TAGC-CTTCG-G-
1 GCTTCCGTCTAGCACTT-GTGT
* *
33877252 GCTTCTGTCTAGCACTTATGT
1 GCTTCCGTCTAGCACTTGTGT
33877273 GCTTCCG-CTAG-ACTT
1 GCTTCCGTCTAGCACTT
33877288 CTGGCTTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
18 7 0.16
19 12 0.27
20 13 0.29
21 13 0.29
ACGTcount: A:0.12, C:0.28, G:0.23, T:0.37
Consensus pattern (21 bp):
GCTTCCGTCTAGCACTTGTGT
Found at i:33877243 original size:39 final size:39
Alignment explanation
Indices: 33877195--33877277 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
33877185 GCTCTGATGA
* *
33877195 GCTTTAGTTAGCCTTCGGGCTTCCGTCTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
*
33877234 GCTTCAGTTAGCCTTCGGGCTTCTGTCTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
33877273 GCTTC
1 GCTTC
33877278 CGCTAGACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.11, C:0.27, G:0.24, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
Found at i:33877294 original size:39 final size:39
Alignment explanation
Indices: 33877207--33877294 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 39
33877197 TTTAGTTAGC
* * *
33877207 CTTCGGGCTTCCGTCTAGCACTTGTGTGCTTCAGTTAGC
1 CTTCGGGCTTCCGTCTAGCACTTATGTGCTTCAGCTAGA
* *
33877246 CTTCGGGCTTCTGTCTAGCACTTATGTGCTTCCGCTAGA
1 CTTCGGGCTTCCGTCTAGCACTTATGTGCTTCAGCTAGA
*
33877285 CTTCTGGCTT
1 CTTCGGGCTT
33877295 TAGATCACGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.10, C:0.28, G:0.24, T:0.38
Consensus pattern (39 bp):
CTTCGGGCTTCCGTCTAGCACTTATGTGCTTCAGCTAGA
Found at i:33883464 original size:149 final size:149
Alignment explanation
Indices: 33883282--33883795 Score: 1028
Period size: 149 Copynumber: 3.4 Consensus size: 149
33883272 TGTAACTTTA
33883282 TTTGTTAACCCAATGATCTACTGATAAGAACGCTGTCTGTAAAAGACACTTTCATCCAATGAAGA
1 TTTGTTAACCCAATGATCTACTGATAAGAACGCTGTCTGTAAAAGACACTTTCATCCAATGAAGA
33883347 GCTTTACTTCCACTCGCAACAATATTTATGTTGGGTCTACTTCATATTAAAATTTTTTCTAGGTT
66 GCTTTACTTCCACTCGCAACAATATTTATGTTGGGTCTACTTCATATTAAAATTTTTTCTAGGTT
33883412 GCTTAGTAAAATTGATAAT
131 GCTTAGTAAAATTGATAAT
33883431 TTTGTTAACCCAATGATCTACTGATAAGAACGCTGTCTGTAAAAGACACTTTCATCCAATGAAGA
1 TTTGTTAACCCAATGATCTACTGATAAGAACGCTGTCTGTAAAAGACACTTTCATCCAATGAAGA
33883496 GCTTTACTTCCACTCGCAACAATATTTATGTTGGGTCTACTTCATATTAAAATTTTTTCTAGGTT
66 GCTTTACTTCCACTCGCAACAATATTTATGTTGGGTCTACTTCATATTAAAATTTTTTCTAGGTT
33883561 GCTTAGTAAAATTGATAAT
131 GCTTAGTAAAATTGATAAT
33883580 TTTGTTAACCCAATGATCTACTGATAAGAACGCTGTCTGTAAAAGACACTTTCATCCAATGAAGA
1 TTTGTTAACCCAATGATCTACTGATAAGAACGCTGTCTGTAAAAGACACTTTCATCCAATGAAGA
33883645 GCTTTACTTCCACTCGCAACAATATTTATGTTGGGTCTACTTCATATTAAAATTTTTTCTAGGTT
66 GCTTTACTTCCACTCGCAACAATATTTATGTTGGGTCTACTTCATATTAAAATTTTTTCTAGGTT
33883710 GCTTAGTAAAATTGATAAT
131 GCTTAGTAAAATTGATAAT
33883729 TTTGTTAACCCAATGATCTACTGATAAGAACGCTGTCTGTAAAAGACACTTTCATCCAATGAAGA
1 TTTGTTAACCCAATGATCTACTGATAAGAACGCTGTCTGTAAAAGACACTTTCATCCAATGAAGA
33883794 GC
66 GC
33883796 CATGACCTTT
Statistics
Matches: 365, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 365 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (149 bp):
TTTGTTAACCCAATGATCTACTGATAAGAACGCTGTCTGTAAAAGACACTTTCATCCAATGAAGA
GCTTTACTTCCACTCGCAACAATATTTATGTTGGGTCTACTTCATATTAAAATTTTTTCTAGGTT
GCTTAGTAAAATTGATAAT
Found at i:33886450 original size:69 final size:69
Alignment explanation
Indices: 33886339--33886546 Score: 407
Period size: 69 Copynumber: 3.0 Consensus size: 69
33886329 GATAGGAAAA
33886339 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
33886404 GCTG
66 GCTG
33886408 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
33886473 GCTG
66 GCTG
*
33886477 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
33886542 GCTG
66 GCTG
33886546 A
1 A
33886547 TAGAGTCTTG
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 138 1.00
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.28
Consensus pattern (69 bp):
ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
GCTG
Found at i:33897243 original size:3 final size:3
Alignment explanation
Indices: 33897235--33897263 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
33897225 CTCTCGTGTT
33897235 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
33897264 TAATTTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33898265 original size:7 final size:7
Alignment explanation
Indices: 33898253--33898278 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
33898243 GCATAACTCA
33898253 AAAATTT
1 AAAATTT
33898260 AAAATTT
1 AAAATTT
33898267 AAAATTT
1 AAAATTT
33898274 AAAAT
1 AAAAT
33898279 ATATAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:33899507 original size:23 final size:23
Alignment explanation
Indices: 33899480--33899535 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
33899470 AAAAAAGAGG
* * * *
33899480 GAAAGAAATGAGAGGAAGGAGAA
1 GAAAGAAAGGAAAAGAAGAAGAA
33899503 GAAAGAAAGGAAAAGAAGAAGAA
1 GAAAGAAAGGAAAAGAAGAAGAA
*
33899526 GAAAGGAAGG
1 GAAAGAAAGG
33899536 TACGTATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.38, T:0.02
Consensus pattern (23 bp):
GAAAGAAAGGAAAAGAAGAAGAA
Found at i:33902183 original size:37 final size:38
Alignment explanation
Indices: 33902114--33902189 Score: 136
Period size: 37 Copynumber: 2.0 Consensus size: 38
33902104 ATTCGATAGT
33902114 TTTCCCTACATTAGAGGGAGAGAAATAATAACTTGTAA
1 TTTCCCTACATTAGAGGGAGAGAAATAATAACTTGTAA
*
33902152 TTTCCCTACATTAG-GGGGGAGAAATAATAACTTGTAA
1 TTTCCCTACATTAGAGGGAGAGAAATAATAACTTGTAA
33902189 T
1 T
33902190 GAGTTAGGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 23 0.62
38 14 0.38
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (38 bp):
TTTCCCTACATTAGAGGGAGAGAAATAATAACTTGTAA
Found at i:33903998 original size:112 final size:112
Alignment explanation
Indices: 33903844--33904356 Score: 495
Period size: 112 Copynumber: 4.7 Consensus size: 112
33903834 ATAAAAGTGA
* * * *
33903844 TTTTTTTT--AATTATTTTAAAGTTTTTTTGTTAGTGATATATGATTAGGTTATAAATTGTGTGT
1 TTTTTTTTAAAATTATCTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTGTGT
* * *
33903907 GTTGAATTTAGTG-TT-TTGTGAATTT-TTATTAATGTAAATTTTTTGT
66 GTTTAGTTTAGTGTTTATTGTG-ATTTCTTATGAATGTAAATTTTTT-T
* * * * * *
33903953 TTTTTTTTAAAAATTATTTTATACTTATTTTGTTAGTAATTTATGATTATGTTATAAATTGTTTC
1 TTTTTTTT-AAAATTATCTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTGTG
33904018 TGTTTAGTTTAGTG-TT-TTGTGATTTCTTATGAATGTAAATTTTTTTT
65 TGTTTAGTTTAGTGTTTATTGTGATTTCTTATGAATGTAAA-TTTTTTT
* *
33904065 TTGTATTTTTAAAATTATCTTAAAGTCATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTT
1 TT-T-TTTTTAAAATTATCTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG--T
* *
33904130 GTGTGTGCTTTGTTTAATGTTTATTGTGACTTT-TTATGAATGTAAA-------
62 GTGTGT--TTAGTTTAGTGTTTATTGTGA-TTTCTTATGAATGTAAATTTTTTT
* * * *
33904176 TTTTTTTT--AATTATCTGAAAGTTATTTTATTAGCAATTTATGATTAGGTTATAAATTGTTTGT
1 TTTTTTTTAAAATTATCTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTGTGT
*
33904239 GTTTAGTTTAGTGTTTATTGTGATTTGTTATGAATGTAAA-------
66 GTTTAGTTTAGTGTTTATTGTGATTTCTTATGAATGTAAATTTTTTT
* * * * *
33904279 --TTTTTT-AAATTATTTTAAAGTTATTTTATTAGTAATTTATGATTAGCTTATAAATTATTTGT
1 TTTTTTTTAAAATTATCTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTGTGT
33904341 GTTTAGTTTAGTGTTT
66 GTTTAGTTTAGTGTTT
33904357 TAAAATTATT
Statistics
Matches: 354, Mismatches: 34, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
101 6 0.02
102 69 0.19
103 32 0.09
105 6 0.02
107 45 0.13
109 13 0.04
110 1 0.00
111 6 0.02
112 80 0.23
113 53 0.15
114 5 0.01
115 5 0.01
117 9 0.03
118 2 0.01
119 19 0.05
120 3 0.01
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (112 bp):
TTTTTTTTAAAATTATCTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTGTGT
GTTTAGTTTAGTGTTTATTGTGATTTCTTATGAATGTAAATTTTTTT
Found at i:33904316 original size:102 final size:102
Alignment explanation
Indices: 33904069--33904356 Score: 407
Period size: 102 Copynumber: 2.8 Consensus size: 102
33904059 TTTTTTTTGT
* * *
33904069 ATTTTTAAAATTATCTTAAAGTCATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGT
1 ATTTTTTAAATTATCTTAAAGTTATTTTATTAGTAATTTATGATTAGATTATAAATTG-TT-TGT
* *
33904134 GTGCTTTGTTTAATGTTTATTGTGACTTTTTATGAATGTAA
64 GT--TTAGTTTAGTGTTTATTGTGACTTTTTATGAATGTAA
* * * *
33904175 ATTTTTTTTAATTATCTGAAAGTTATTTTATTAGCAATTTATGATTAGGTTATAAATTGTTTGTG
1 A-TTTTTTAAATTATCTTAAAGTTATTTTATTAGTAATTTATGATTAGATTATAAATTGTTTGTG
33904240 TTTAGTTTAGTGTTTATTGTGA-TTTGTTATGAATGTAA
65 TTTAGTTTAGTGTTTATTGTGACTTT-TTATGAATGTAA
* * *
33904278 ATTTTTTAAATTATTTTAAAGTTATTTTATTAGTAATTTATGATTAGCTTATAAATTATTTGTGT
1 ATTTTTTAAATTATCTTAAAGTTATTTTATTAGTAATTTATGATTAGATTATAAATTGTTTGTGT
33904343 TTAGTTTAGTGTTT
66 TTAGTTTAGTGTTT
33904357 TAAAATTATT
Statistics
Matches: 165, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
102 75 0.45
103 32 0.19
105 5 0.03
106 3 0.02
107 50 0.30
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (102 bp):
ATTTTTTAAATTATCTTAAAGTTATTTTATTAGTAATTTATGATTAGATTATAAATTGTTTGTGT
TTAGTTTAGTGTTTATTGTGACTTTTTATGAATGTAA
Found at i:33904707 original size:11 final size:12
Alignment explanation
Indices: 33904680--33904709 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33904670 TTATGAGATA
*
33904680 TTTTTTATTGTG
1 TTTTTTACTGTG
33904692 TTTTTTACTGTG
1 TTTTTTACTGTG
33904704 TTTTTT
1 TTTTTT
33904710 GTTACTTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.03, G:0.13, T:0.77
Consensus pattern (12 bp):
TTTTTTACTGTG
Found at i:33904718 original size:19 final size:19
Alignment explanation
Indices: 33904696--33904746 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
33904686 ATTGTGTTTT
*
33904696 TTACTGTGTTTTTTGTTAC
1 TTACTGTGTTTTTTATTAC
* * **
33904715 TTAC-GTATTTATTATTTT
1 TTACTGTGTTTTTTATTAC
33904733 TTACTGTGTTTTTT
1 TTACTGTGTTTTTT
33904747 TGTTTCTCAA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.14, C:0.08, G:0.12, T:0.67
Consensus pattern (19 bp):
TTACTGTGTTTTTTATTAC
Found at i:33915563 original size:128 final size:126
Alignment explanation
Indices: 33915282--33915712 Score: 520
Period size: 126 Copynumber: 3.5 Consensus size: 126
33915272 GCCAAACGGT
* * * * * * *
33915282 AAATCGCAACCCAGCACGATTGGGCACGATTTATCGAATTTTCAAATACGAAATATTGCCTCATT
1 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGCCTCATT
* * ** * *
33915347 TTAATTTAAGAAAATATGGATGAAATGTCGAAAGGATATTTCGTATCTTAGTCGAATGAAA
66 TTAATTTAAGAAAACATGGATGAAATTTTAAAAGGATATTCCGTATTTTAGTCGAATGAAA
*
33915408 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGCCTCGTT
1 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGCCTCATT
* * *
33915473 TTAGTTTAAGAAAACGTGGATGAAATTTTAAAAAAGGATATTCCATATTTTAGTCGAATGAAAA
66 TTAATTTAAGAAAACATGGATGAAATTTT--AAAAGGATATTCCGTATTTTAGTCGAATG-AAA
*
33915537 AAAT-GAAACCCAGCACGATTGGGCACGATCTCTCAAAC-T-C---C-CGAAATGTTGCCTCATT
1 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGCCTCATT
* * *
33915595 TTAATTTTAAAAAAACATGGACGAAATTTTTAAAGGATATTCCGTATTTTAG-CTGAATG-AA
66 TTAA-TTTAAGAAAACATGGATGAAATTTTAAAAGGATATTCCGTATTTTAGTC-GAATGAAA
* * * * *
33915656 AAATCGAAACCCAGCACAATTGGGCACGACCCCTCGAACTCCCAAACACGAAATATT
1 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATT
33915713 TCCTAATATT
Statistics
Matches: 262, Mismatches: 31, Indels: 24
0.83 0.10 0.08
Matches are distributed among these distances:
119 6 0.02
120 31 0.12
121 25 0.10
122 19 0.07
123 23 0.09
125 1 0.00
126 90 0.34
127 1 0.00
128 59 0.23
129 7 0.03
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (126 bp):
AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGCCTCATT
TTAATTTAAGAAAACATGGATGAAATTTTAAAAGGATATTCCGTATTTTAGTCGAATGAAA
Found at i:33916404 original size:16 final size:16
Alignment explanation
Indices: 33916357--33916404 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
33916347 TGTATATAAG
*
33916357 AAAATTTAAAATAAAC
1 AAAATTTAAAAAAAAC
*
33916373 -AAATTACAAAATAAAAC
1 AAAATT-TAAAA-AAAAC
33916390 AAAATTTAAAAAAAA
1 AAAATTTAAAAAAAA
33916405 TACAAGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.19
16 8 0.31
17 8 0.31
18 5 0.19
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATTTAAAAAAAAC
Found at i:33916442 original size:19 final size:18
Alignment explanation
Indices: 33916417--33916460 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
33916407 CAAGTAAAAT
*
33916417 ATTAAAATAGA-TAAATAA
1 ATTAAAA-AGAGTAAAGAA
*
33916435 ATTAAAAAGAGTAAAGGA
1 ATTAAAAAGAGTAAAGAA
33916453 ATTAAAAA
1 ATTAAAAA
33916461 AAACTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (18 bp):
ATTAAAAAGAGTAAAGAA
Found at i:33917053 original size:46 final size:46
Alignment explanation
Indices: 33916986--33917077 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
33916976 CAGGTATGTC
33916986 TCTTTCCCTTAAGTTTTTATTCTAAATCAATTTGTAAAAAACACAA
1 TCTTTCCCTTAAGTTTTTATTCTAAATCAATTTGTAAAAAACACAA
*
33917032 TCTTTCCCTTCAGTTTTTATTCTAAATCAATTTGTAAAAAACACAA
1 TCTTTCCCTTAAGTTTTTATTCTAAATCAATTTGTAAAAAACACAA
33917078 AAAAATAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.41
Consensus pattern (46 bp):
TCTTTCCCTTAAGTTTTTATTCTAAATCAATTTGTAAAAAACACAA
Found at i:33917883 original size:84 final size:83
Alignment explanation
Indices: 33917776--33918084 Score: 377
Period size: 84 Copynumber: 3.7 Consensus size: 83
33917766 TTTTGGGATA
* * * * * * * *
33917776 AGATCTGTATTTTTCAGCTTGTTACACTACTGCTTAGGGGATTACGGTTTGCTGTCTTTGATTTG
1 AGATCTGTATTTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTTGATCTG
* *
33917841 CTCCCCTACTATTTAGGGG
66 CTCCACTACTGTTTA-GGG
* *
33917860 AGATCTGTATTTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTCCTGTCTTCGATCTG
1 AGATCTGTATTTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTTGATCTG
33917925 CTCCACTACTGTTTATGGG
66 CTCCACTACTGTTTA-GGG
* * *
33917944 AGATCTGTATTTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACTAT-TTTCGATCT
1 AGATCTGTATTTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTT-GATCT
*
33918008 GCTCCACTATTGTTTAGGG
65 GCTCCACTACTGTTTAGGG
* * * * * * *
33918027 AGATCTGTATTTTCTAGCCTGTCACCTTATTGCTTTGGGGGTTAAAGCTTGCTGTCTT
1 AGATCTGTATTTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTT
33918085 GACCGATGCC
Statistics
Matches: 197, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
83 52 0.26
84 145 0.74
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (83 bp):
AGATCTGTATTTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTTGATCTG
CTCCACTACTGTTTAGGG
Found at i:33918084 original size:167 final size:168
Alignment explanation
Indices: 33917776--33918084 Score: 408
Period size: 167 Copynumber: 1.8 Consensus size: 168
33917766 TTTTGGGATA
* * * ** * *
33917776 AGATCTGTATTTTTCAGCTTGTTACACTACTGCTTAGGGGATTACGGTTTGCTGTCTTTGATTTG
1 AGATCTGTATTTTTCAGCCTGTTACACTACTGCTTAGGGGATTAAGGCTCACTATCTTTGATCTG
* * *
33917841 CTCCCCTACTATTTAGGGGAGATCTGTATTTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
66 CTCCACTACTATTTAGGGGAGATCTGTATTTTCCAGCCTGTCACCCTACTGCTTAGGGGGTTAAA
33917906 GCTTCCTGTCTTCGATCTGCTCCACTACTGTTTATGGG
131 GCTTCCTGTCTTCGATCTGCTCCACTACTGTTTATGGG
* *
33917944 AGATCTGTA-TTTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACTAT-TTTCGATC
1 AGATCTGTATTTTTC-AGCCTGTTACACTACTGCTTAGGGGATTAAGGCTCACTATCTTT-GATC
* * * * * *
33918007 TGCTCCACTATTGTTTA-GGGAGATCTGTATTTTCTAGCCTGTCACCTTATTGCTTTGGGGGTTA
64 TGCTCCACTACTATTTAGGGGAGATCTGTATTTTCCAGCCTGTCACCCTACTGCTTAGGGGGTTA
*
33918071 AAGCTTGCTGTCTT
129 AAGCTTCCTGTCTT
33918085 GACCGATGCC
Statistics
Matches: 120, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
167 62 0.52
168 58 0.48
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (168 bp):
AGATCTGTATTTTTCAGCCTGTTACACTACTGCTTAGGGGATTAAGGCTCACTATCTTTGATCTG
CTCCACTACTATTTAGGGGAGATCTGTATTTTCCAGCCTGTCACCCTACTGCTTAGGGGGTTAAA
GCTTCCTGTCTTCGATCTGCTCCACTACTGTTTATGGG
Found at i:33929674 original size:128 final size:126
Alignment explanation
Indices: 33929393--33929802 Score: 518
Period size: 128 Copynumber: 3.2 Consensus size: 126
33929383 GCCAAACGGT
* * * ** * *
33929393 AAATCGCAACCCAGCACGATTGGGCACGATTTATTGAATTTCCAAATACAAAATATTGTCTCATT
1 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAATACGAAATATTGTCTCATT
* * * *
33929458 TTAATTTAAGAAAACATGGATGAAATGTCGAAAGGATATTTCGTATCTTAGTCGAATGAAA
66 TTAATTTAAGAAAACATGGATGAAATTTCAAAAGGATATTCCGTATTTTAGTCGAATGAAA
* * *
33929519 AAATCGAAACCCATCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGTCTCGTT
1 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAATACGAAATATTGTCTCATT
** * *
33929584 TTAGCTTAAGAAAACGTGGATGAAATTTCAAAAAAGGATATTCCATATTTTAGTCGAATGAAA
66 TTAATTTAAGAAAACATGGATGAAATTTC--AAAAGGATATTCCGTATTTTAGTCGAATGAAA
* * * *
33929647 AAAACGAAACCCAGCATGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCAT
1 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACT-TCCAAATACGAAATATTGTCTCAT
* * * *
33929712 TTTAATTTTAAAAAAACATGGACGAAATTTCTAAAGGATATTCCGTATTTTAG-CTGAACG-AA
65 TTTAA-TTTAAGAAAACATGGATGAAATTTCAAAAGGATATTCCGTATTTTAGTC-GAATGAAA
*
33929774 AAATCGAAACCCAGCACAATTGGGCACGA
1 AAATCGAAACCCAGCACGATTGGGCACGA
33929803 CCCCCCGAAC
Statistics
Matches: 243, Mismatches: 36, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
126 80 0.33
127 29 0.12
128 89 0.37
129 24 0.10
130 21 0.09
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (126 bp):
AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAATACGAAATATTGTCTCATT
TTAATTTAAGAAAACATGGATGAAATTTCAAAAGGATATTCCGTATTTTAGTCGAATGAAA
Found at i:33930563 original size:19 final size:18
Alignment explanation
Indices: 33930536--33930583 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
33930526 AATACACGTA
* *
33930536 AAATATTAAAATAGATAAAT
1 AAAT-TTAAAAGAG-TAAAG
33930556 AAATTTAAAAGAGTAAAG
1 AAATTTAAAAGAGTAAAG
*
33930574 GAATTTAAAA
1 AAATTTAAAA
33930584 AAAACTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 13 0.52
19 8 0.32
20 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.27
Consensus pattern (18 bp):
AAATTTAAAAGAGTAAAG
Found at i:33930721 original size:15 final size:15
Alignment explanation
Indices: 33930701--33930731 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33930691 CAATCAGGAA
33930701 CTAAAAATGCAAATT
1 CTAAAAATGCAAATT
33930716 CTAAAAATGCAAATT
1 CTAAAAATGCAAATT
33930731 C
1 C
33930732 CCCAAGTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (15 bp):
CTAAAAATGCAAATT
Found at i:33930981 original size:21 final size:21
Alignment explanation
Indices: 33930955--33930997 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
33930945 GGTTCGCTGT
*
33930955 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
33930976 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
33930997 A
1 A
33930998 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:33930997 original size:16 final size:16
Alignment explanation
Indices: 33930978--33931010 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33930968 TGTATTGGAT
*
33930978 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
33930994 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
33931010 T
1 T
33931011 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:33931055 original size:45 final size:44
Alignment explanation
Indices: 33930989--33931083 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
33930979 GGATTAGAGG
* *
33930989 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
33931034 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
33931078 TGTAAT
1 TGTAAT
33931084 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:33931266 original size:18 final size:17
Alignment explanation
Indices: 33931245--33931279 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
33931235 TTATTATTTA
*
33931245 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
33931263 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
33931280 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:33931273 original size:28 final size:27
Alignment explanation
Indices: 33931203--33931275 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
33931193 TTTATTATCA
*
33931203 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
33931231 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
33931258 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
33931276 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:33939783 original size:20 final size:20
Alignment explanation
Indices: 33939739--33939785 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
33939729 TATTGGTTAT
**
33939739 ATTTTA-ATATTTAAAATTT
1 ATTTTATATATTTAAAATAA
*
33939758 AGTTTATATATTTAAAATAA
1 ATTTTATATATTTAAAATAA
33939778 ATTTTATA
1 ATTTTATA
33939786 AATAATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTATATATTTAAAATAA
Found at i:33941457 original size:3 final size:3
Alignment explanation
Indices: 33941449--33941488 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
33941439 TCATTATTTT
33941449 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
33941489 CAAAATTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:33945636 original size:47 final size:48
Alignment explanation
Indices: 33945555--33945645 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
33945545 CAATGCTTTT
*
33945555 TTTCTATAAACCTCCCCCATGCATCTAGGAGCAGGGCCACTTTACCAC
1 TTTCTATAAACCTCCCCCATGCATCGAGGAGCAGGGCCACTTTACCAC
* * *
33945603 TTTCTATAAGCCTCTCCTATG-ATCGAGGAGCAGGGCCACTTTA
1 TTTCTATAAACCTCCCCCATGCATCGAGGAGCAGGGCCACTTTA
33945646 TCACCTCCCG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 21 0.54
48 18 0.46
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (48 bp):
TTTCTATAAACCTCCCCCATGCATCGAGGAGCAGGGCCACTTTACCAC
Found at i:33946008 original size:33 final size:33
Alignment explanation
Indices: 33945956--33946021 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
33945946 AAAAGCTATA
**
33945956 TTCAAACAGTAAGTGTACTTGTTTGCAAACATG
1 TTCAAACAGTAAGCATACTTGTTTGCAAACATG
* *
33945989 TTCAAACATTAAGCATACTTGTTTGCGAACATG
1 TTCAAACAGTAAGCATACTTGTTTGCAAACATG
33946022 ATTGAACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (33 bp):
TTCAAACAGTAAGCATACTTGTTTGCAAACATG
Found at i:33948669 original size:23 final size:24
Alignment explanation
Indices: 33948643--33948700 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
33948633 TTATTTCCTA
33948643 TAATATAATATCT-TAA-TTTTAAT
1 TAATATAATAT-TATAAGTTTTAAT
33948666 TAATATAAT-TTATAATGTTTTAAT
1 TAATATAATATTATAA-GTTTTAAT
33948690 TAA-ATAATATT
1 TAATATAATATT
33948701 TTTATAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 1 0.03
22 4 0.13
23 14 0.45
24 12 0.39
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TAATATAATATTATAAGTTTTAAT
Found at i:33951747 original size:21 final size:23
Alignment explanation
Indices: 33951723--33951766 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
33951713 AATACTACAT
*
33951723 AAATATATACATA-T-ATATTAA
1 AAATAAATACATATTAATATTAA
33951744 AAATAAATACATATTAATATTAA
1 AAATAAATACATATTAATATTAA
33951767 GATGATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATAAATACATATTAATATTAA
Found at i:33953751 original size:88 final size:88
Alignment explanation
Indices: 33953571--33953960 Score: 428
Period size: 88 Copynumber: 4.4 Consensus size: 88
33953561 GACTCTGGGT
** * * *
33953571 TCAACTCACCTCTCGCGCTATGAGTTGACTTTTTGAAAAAAAGACATTAAAAAAACCAGA-ATGT
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAACAGAAATT-GAAAAA-CAGATA-GT
* **
33953635 GAAAATAACTTGGCATGTGACCCGAGGC
61 GAAAATACCTCAGCATGTGACCCGAGGC
* *
33953663 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGAAAAACAGATCGTGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAAACAGATAGTGAAAA
33953728 TACCTCAGCATGTGACCCGAGGC
66 TACCTCAGCATGTGACCCGAGGC
* * * * * *
33953751 TCAAGTCACCTCTCGCAATATGAGCTGATTTTTTTG-AAACATAAATTGAAGAACAGA-AATTAA
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAAAACAGATAGTGAA
* *
33953814 AATTACCTCAGCGTGTGAGCCGAGGC
64 AA-TACCTCAGCATGTGACCCGAGGC
* * * *
33953840 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTGACGAACAGAAATTGAAAAATAGAAATTGAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTGAAAAACAGATAGTGAAA
* * *
33953904 ATACCTCAGCATTTGAACTGAGGC
65 ATACCTCAGCATGTGACCCGAGGC
* *
33953928 TGAACTCACCTCTCACAATATGAGTTGATTTTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTT
33953961 TTGATGAACA
Statistics
Matches: 256, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
86 5 0.02
88 124 0.48
89 80 0.31
90 15 0.06
91 6 0.02
92 26 0.10
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (88 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAAACAGATAGTGAAAA
TACCTCAGCATGTGACCCGAGGC
Found at i:33961217 original size:22 final size:22
Alignment explanation
Indices: 33961191--33961235 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
33961181 AATGGATGAA
33961191 TGAATAAATGACAAATAAATGT
1 TGAATAAATGACAAATAAATGT
* *
33961213 TGAATAAATGACGAATGAATGT
1 TGAATAAATGACAAATAAATGT
33961235 T
1 T
33961236 AGTCATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (22 bp):
TGAATAAATGACAAATAAATGT
Found at i:33969201 original size:25 final size:23
Alignment explanation
Indices: 33969133--33969220 Score: 85
Period size: 22 Copynumber: 3.9 Consensus size: 23
33969123 TACATATTAG
*
33969133 AAATA-ATAATAATATTAAAAAC
1 AAATACATAATAATATTAAAAAT
* * *
33969155 AACTA-TTAATAATACTACATAAAT
1 AAATACATAATAATATTA-A-AAAT
*
33969179 ATATACAT-AT-ATATTAAAAAT
1 AAATACATAATAATATTAAAAAT
33969200 AAATACATAATAATATTAAAA
1 AAATACATAATAATATTAAAA
33969221 TGATGATAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
21 11 0.21
22 17 0.33
23 15 0.29
24 8 0.15
25 1 0.02
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATACATAATAATATTAAAAAT
Found at i:33981451 original size:3 final size:3
Alignment explanation
Indices: 33981443--33981687 Score: 57
Period size: 3 Copynumber: 78.3 Consensus size: 3
33981433 NNNNNNNAAA
*
33981443 AAT AAT AAT AAT AGT GAA- AAT AAT AA- ATAT AAT AAT AA- ATAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT
* * * *
33981488 AAT AGA- AAA AGAT AAT ACT ATGT AAA AAGT ATAT ATAT ACAT ATAT AAT
1 AAT A-AT AAT A-AT AAT AAT A-AT AAT AA-T A-AT A-AT A-AT A-AT AAT
* * *
33981537 AA- AAT ATAT ACT AAT ATT AAT AAT AAT TAT AAT AGAGGT AA- AAGT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-A--T AAT AA-T
* *
33981582 AGAT -AT AAT AAT -AT AAAT AAT ACGT ACAT GAAA AAT AAT AAT AAAT
1 A-AT AAT AAT AAT AAT -AAT AAT A-AT A-AT -AAT AAT AAT AAT -AAT
* * * * *
33981628 AAT AAT -AT AAA AAG AA- AAT -AT GAT AA- AAT AAT AGT GTAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
33981669 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
33981688 TTTACAATAA
Statistics
Matches: 183, Mismatches: 27, Indels: 64
0.67 0.10 0.23
Matches are distributed among these distances:
2 23 0.13
3 116 0.63
4 38 0.21
5 4 0.02
6 2 0.01
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:33981553 original size:20 final size:21
Alignment explanation
Indices: 33981520--33981567 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
33981510 TAAAAAGTAT
33981520 ATATATACATATA-TAATAAA
1 ATATATACATATATTAATAAA
33981540 ATATATAC-TAATATTAATAATA
1 ATATATACAT-ATATTAATAA-A
33981562 AT-TATA
1 ATATATA
33981568 ATAGAGGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 11 0.44
21 10 0.40
22 3 0.12
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATATACATATATTAATAAA
Found at i:33981770 original size:3 final size:3
Alignment explanation
Indices: 33981762--33981872 Score: 90
Period size: 3 Copynumber: 38.7 Consensus size: 3
33981752 TATTAAAAAT
* *
33981762 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA T-A TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
33981809 CT-A TAG TAA TAA T-A TAT TGA TAA -AA TAA -AA -AA TAA TAG TGA
1 -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
33981850 TAA TAA GAA TAT TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
33981873 GTCATAAGGA
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
2 11 0.13
3 72 0.86
4 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:33981887 original size:27 final size:27
Alignment explanation
Indices: 33981833--33981896 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
33981823 TATTGATAAA
* * *
33981833 ATAAAAAATAATAGTGATAATAAGAAT
1 ATAAATAATAATAGTCATAAGAAGAAT
* * *
33981860 ATTAATAATAATAGTCATAAGGATAAT
1 ATAAATAATAATAGTCATAAGAAGAAT
33981887 ATAAATAATA
1 ATAAATAATA
33981897 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (27 bp):
ATAAATAATAATAGTCATAAGAAGAAT
Found at i:33984458 original size:41 final size:41
Alignment explanation
Indices: 33984397--33984821 Score: 636
Period size: 41 Copynumber: 10.4 Consensus size: 41
33984387 GTTTTATTAA
* *
33984397 AAAACGCCGCT-AAAACCAGAGCATTAGCGGCGCTTTTCCT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
* * * * *
33984437 AAAACGCTGCAAAAAATCAGAGCATTAGCGGCGCTTTTCCT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
* *
33984478 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
* *
33984519 AAAATGCCGCTAAACACCAGAGCATCAGCGGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
* *
33984560 AAAACGCCGCTAAATACCAGAGCATCAGCAGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
* *
33984601 AAAACACCGCTAAACACCAGAGCATCAGCGGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
* *
33984642 AAAACGCCGCTAAATACCAGAGCATCAGCAGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
* *
33984683 AAAACACCGCTAAACACCAGAGCATCAGCGGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
* *
33984724 AAAACGCCGCTAAATACCAGAGCATCAGCAGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
* *
33984765 AAAACACCGCTAAACACCAGAGCATCAGCGGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
33984806 AAAACGCCGCTAAAAA
1 AAAACGCCGCTAAAAA
33984822 TCTCATAACC
Statistics
Matches: 354, Mismatches: 30, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
40 9 0.03
41 345 0.97
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATCAGCGGCGCTTTTCGT
Found at i:33985000 original size:14 final size:14
Alignment explanation
Indices: 33984978--33985016 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
33984968 TTAATTATCA
* *
33984978 TTATAGTTTAAGGT
1 TTATGGTTTAAGAT
33984992 TTATGGTTTAAGAT
1 TTATGGTTTAAGAT
*
33985006 ATATGGTTTAA
1 TTATGGTTTAA
33985017 ACATGTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (14 bp):
TTATGGTTTAAGAT
Found at i:33985953 original size:24 final size:24
Alignment explanation
Indices: 33985903--33985953 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
33985893 TATATGAGAT
* * *
33985903 AAATATATATAAAATATTATTTTA
1 AAATATATATAAAATATCATATGA
33985927 AAATATATAT-AAATATACATATGA
1 AAATATATATAAAATAT-CATATGA
33985951 AAA
1 AAA
33985954 GTGGTTAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATATAAAATATCATATGA
Found at i:33987459 original size:61 final size:62
Alignment explanation
Indices: 33987346--33987465 Score: 224
Period size: 62 Copynumber: 2.0 Consensus size: 62
33987336 CCAAAATTTG
*
33987346 ATTTCTTTTTTGTCATTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
33987408 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGAT-TTTTTGTTCTGAAATGGAAAA
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAA
33987466 ACTAGTTTGT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 21 0.37
62 36 0.63
ACGTcount: A:0.19, C:0.07, G:0.17, T:0.56
Consensus pattern (62 bp):
ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
Found at i:33988176 original size:15 final size:15
Alignment explanation
Indices: 33988156--33988187 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
33988146 AAACATATAA
33988156 TCCAAATATTCACTG
1 TCCAAATATTCACTG
33988171 TCCAAATATTCACTG
1 TCCAAATATTCACTG
33988186 TC
1 TC
33988188 AAAACATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.34
Consensus pattern (15 bp):
TCCAAATATTCACTG
Found at i:33989861 original size:289 final size:289
Alignment explanation
Indices: 33989342--33990347 Score: 1967
Period size: 289 Copynumber: 3.5 Consensus size: 289
33989332 CCAACCTTAT
33989342 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGATTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGATTGCCTTATATCGAGCT
33989407 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
33989472 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
33989537 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATTACTATT
196 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATTACTATT
33989602 TTTTATATTAATAATGTTTGATTTTAATA
261 TTTTATATTAATAATGTTTGATTTTAATA
33989631 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGATTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGATTGCCTTATATCGAGCT
33989696 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
33989761 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
33989826 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATTACTATT
196 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATTACTATT
33989891 TTTTATATTAATAATGTTTGATTTTAATA
261 TTTTATATTAATAATGTTTGATTTTAATA
*
33989920 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGATTGCCTTATATCGAGCT
33989985 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
33990050 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
33990115 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATTACTATT
196 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATTACTA-T
33990180 TTTTTATATTAATAATGTTTGATTTTAATA
260 TTTTTATATTAATAATGTTTGATTTTAATA
* * *
33990210 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGATGGGTTGCCTTATATCAAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGATTGCCTTATATCGAGCT
33990275 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
33990340 AAAGACTT
131 AAAGACTT
33990348 TTTATCACAA
Statistics
Matches: 713, Mismatches: 3, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
289 546 0.77
290 167 0.23
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (289 bp):
TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGATTGCCTTATATCGAGCT
GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATTACTATT
TTTTATATTAATAATGTTTGATTTTAATA
Found at i:33990596 original size:15 final size:15
Alignment explanation
Indices: 33990552--33990607 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
33990542 AACGACATGT
*
33990552 ATATTACTTAATTAAA
1 ATATTATTTAATT-AA
33990568 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
33990581 ATATTATTTAATTAA
1 ATATTATTTAATTAA
33990596 ATATTATTTAAT
1 ATATTATTTAAT
33990608 CCCGCTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.09
13 7 0.20
14 2 0.06
15 16 0.46
16 4 0.11
17 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:33990752 original size:9 final size:9
Alignment explanation
Indices: 33990712--33990845 Score: 153
Period size: 9 Copynumber: 15.0 Consensus size: 9
33990702 TATTTGATAT
*
33990712 CATAATTTA
1 CATAACTTA
*
33990721 TATAACTTA
1 CATAACTTA
* *
33990730 CAAAACGTA
1 CATAACTTA
33990739 CATAACTTA
1 CATAACTTA
*
33990748 TATAACTTA
1 CATAACTTA
* *
33990757 GATAA-ATA
1 CATAACTTA
*
33990765 TATAACTTA
1 CATAACTTA
*
33990774 TATAACTTA
1 CATAACTTA
33990783 CATAACTTA
1 CATAACTTA
* *
33990792 TATAACATA
1 CATAACTTA
33990801 CATAACTTA
1 CATAACTTA
33990810 CATAACTTA
1 CATAACTTA
*
33990819 TATAACTTA
1 CATAACTTA
33990828 CATAACTTA
1 CATAACTTA
33990837 CATAACTTA
1 CATAACTTA
33990846 TATGTTGTCA
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
8 6 0.06
9 99 0.94
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (9 bp):
CATAACTTA
Found at i:33996631 original size:31 final size:31
Alignment explanation
Indices: 33996585--33996651 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
33996575 TGATTGTATT
* *
33996585 TTTTATGTTAAATTTGCTGTTTTTGGCTGCA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
* * * *
33996616 TTTTATATTATATTTGTTGTATTTGGTTGGA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
33996647 TTTTA
1 TTTTA
33996652 ATGCAGGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTTATATTAAATTTGCTGTATTTGGCTGCA
Found at i:33997092 original size:48 final size:47
Alignment explanation
Indices: 33997000--33997092 Score: 107
Period size: 48 Copynumber: 1.9 Consensus size: 47
33996990 CTAATAAGAG
* * * * *
33997000 TGTAGTAAGGTTGAAATACCTTATTCTAATCAATACATATAGAAGAAT
1 TGTAATAAGGTTGAAAAACCATATTCTAA-CAATAAATAAAGAAGAAT
33997048 TGTAATAAGGTTGAAAAACCATATTCTAA-AATAAAATAAAAGAAG
1 TGTAATAAGGTTGAAAAACCATATTCTAACAAT-AAAT-AAAGAAG
33997093 TGTAGTTCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
46 3 0.08
47 3 0.08
48 32 0.84
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (47 bp):
TGTAATAAGGTTGAAAAACCATATTCTAACAATAAATAAAGAAGAAT
Found at i:33997312 original size:21 final size:20
Alignment explanation
Indices: 33997288--33997327 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33997278 TAGCATATAA
33997288 TTAGATATTTAATTTATACAG
1 TTAG-TATTTAATTTATACAG
**
33997309 TTAGTATTTTTTTTATACA
1 TTAGTATTTAATTTATACA
33997328 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (20 bp):
TTAGTATTTAATTTATACAG
Found at i:34008517 original size:275 final size:272
Alignment explanation
Indices: 34008015--34008532 Score: 829
Period size: 275 Copynumber: 1.9 Consensus size: 272
34008005 AATGAGCTAC
* * * *
34008015 TTACAGCATCACGTCTACCTAAAGAAGGAACACAACATACTTTTGATAATGTTGACCTTGCCAAG
1 TTACAGAATCACGCCTACCTAAAGAAGCAACACAACATACTTTTGATAATGTTGACATTGCCAAG
* * * * *
34008080 CATGATGCGGGTGAGTTCCATGATGCCAATTCTGATCAGCAATGGCGACAAGTATTTGAACCCTT
66 CATGATACAGGTAAGTTCAATGATGCCAATTCTGATCAGCAATGGCGACAAGTATTTGAACCATT
**
34008145 CTACAATGGTGAAGATGGTGAGTTATCAAAGCTTGAAGAAAACTCATCATGGTTCTCCGGATATG
131 CTACAATGGTGAAGATCATGAGTTATCAAAGCTTGAAGAAAACTCATCATGGTTCTCCGGATATG
34008210 ATCGTTGCAATATTTAGATCACACTTAACTGCAGAATCATGTATGTATTATTAGTAACAGTTTCT
196 ATCGTTGCAATATTTAGATCACACTTAACTGCAGAATCATGTATGTATTATTAGTAACAGTTTCT
34008275 CTCACGTTTAAT
261 CTCACGTTTAAT
* * **
34008287 TTACAGAATCATGCCTACCTAAAGAAGCAATACAACATACTTTTGATAATGTTGACATTGCTGAG
1 TTACAGAATCACGCCTACCTAAAGAAGCAACACAACATACTTTTGATAATGTTGACATTGCCAAG
34008352 CATGATACAGGTAAGTTCAATGATGCCAATGATACTGATCAGCAATGGCGACAAGTATTTGAACC
66 CATGATACAGGTAAGTTCAATGATGCCAAT--T-CTGATCAGCAATGGCGACAAGTATTTGAACC
** *
34008417 ATTCTGTAATGGTGAAGATCATGAGTTATCAAAGCTTGAAGAAAACTCGTCATGGTTCTCCGGAT
128 ATTCTACAATGGTGAAGATCATGAGTTATCAAAGCTTGAAGAAAACTCATCATGGTTCTCCGGAT
**
34008482 ATGATCGTTGCAATATTTAGATCACGTTTAACTGCAGAATCATGTATGTAT
193 ATGATCGTTGCAATATTTAGATCACACTTAACTGCAGAATCATGTATGTAT
34008533 ACTAACAATT
Statistics
Matches: 223, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
272 83 0.37
274 1 0.00
275 139 0.62
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (272 bp):
TTACAGAATCACGCCTACCTAAAGAAGCAACACAACATACTTTTGATAATGTTGACATTGCCAAG
CATGATACAGGTAAGTTCAATGATGCCAATTCTGATCAGCAATGGCGACAAGTATTTGAACCATT
CTACAATGGTGAAGATCATGAGTTATCAAAGCTTGAAGAAAACTCATCATGGTTCTCCGGATATG
ATCGTTGCAATATTTAGATCACACTTAACTGCAGAATCATGTATGTATTATTAGTAACAGTTTCT
CTCACGTTTAAT
Found at i:34014093 original size:179 final size:179
Alignment explanation
Indices: 34013781--34014116 Score: 485
Period size: 179 Copynumber: 1.9 Consensus size: 179
34013771 ATAACAATCT
*
34013781 GTAATATTCAATCACCAAAATCAACCTAAATGACTTGCACAAAACTTCCAAAAGAACATCCACAC
1 GTAATATTCAATCACCAAAATCAACCCAAATGACTTGCACAAAACTTCCAAAAGAACATCCACAC
* * * ** * *
34013846 GCTTACCTCTTATGAACAGCCACCACATGAGTTCTACATCGTTAGAGGCTTACCAATCGCATCTT
66 ACTTACCTCTTACGAACAGCCACCACATGAGTTCTACATCGCTAGAGGCGCACCAACCGCAGCTT
*
34013911 GGACCTCTCCTAAGCATAACGAACCAACTCACCAAATTAGTAACAGTTC
131 GGACCTCTCCTAAGCATAACAAACCAACTCACCAAATTAGTAACAGTTC
* * *
34013960 GTAATATTCAATCACCAAAATCAACCCAAATGACTTGCACAACACTTCCAAAAGAACATCCATAT
1 GTAATATTCAATCACCAAAATCAACCCAAATGACTTGCACAAAACTTCCAAAAGAACATCCACAC
* * * * **
34014025 ACTTACCTCTTGCGAACAGCCACCACACT-AGTTCTACGTCGCTGGAGGCGCACCAGCCGTGGCT
66 ACTTACCTCTTACGAACAGCCACCACA-TGAGTTCTACATCGCTAGAGGCGCACCAACCGCAGCT
*
34014089 TGGACCTCTCCTAAGCATAGCAAACCAA
130 TGGACCTCTCCTAAGCATAACAAACCAA
34014117 TTAGATAGCA
Statistics
Matches: 137, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
179 136 0.99
180 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (179 bp):
GTAATATTCAATCACCAAAATCAACCCAAATGACTTGCACAAAACTTCCAAAAGAACATCCACAC
ACTTACCTCTTACGAACAGCCACCACATGAGTTCTACATCGCTAGAGGCGCACCAACCGCAGCTT
GGACCTCTCCTAAGCATAACAAACCAACTCACCAAATTAGTAACAGTTC
Found at i:34028465 original size:20 final size:19
Alignment explanation
Indices: 34028440--34028481 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
34028430 AAAAAGAATT
34028440 GAAGAAAAGAAAGAAACAGA
1 GAAGAAAAGAAAGAAA-AGA
*
34028460 GAAGAAAATAAAGAAAAGA
1 GAAGAAAAGAAAGAAAAGA
34028479 GAA
1 GAA
34028482 ATACCATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (19 bp):
GAAGAAAAGAAAGAAAAGA
Found at i:34028865 original size:56 final size:53
Alignment explanation
Indices: 34028795--34028904 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 53
34028785 GGGGCATTAC
* *
34028795 AGGTTAGCTATAAGGAATATCAACAAGTAAGCTTTTTAAGTAAGATTTACTTTTTA
1 AGGTTAGCTATAAGGAATATCAAAAAGTAAGC---TTAAGTAAGATTCACTTTTTA
34028851 AGGTTAGCTATAAGGAATATCAAAAAGTAAGCTTAAGTAAGATTCACTTTTTA
1 AGGTTAGCTATAAGGAATATCAAAAAGTAAGCTTAAGTAAGATTCACTTTTTA
34028904 A
1 A
34028905 ACTAACTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
53 21 0.40
56 31 0.60
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (53 bp):
AGGTTAGCTATAAGGAATATCAAAAAGTAAGCTTAAGTAAGATTCACTTTTTA
Found at i:34029201 original size:3 final size:3
Alignment explanation
Indices: 34029193--34029228 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
34029183 ACAATAGTAG
34029193 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
34029229 AAGAGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:34035642 original size:30 final size:30
Alignment explanation
Indices: 34035608--34035675 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
34035598 AAGCCCACAC
* *
34035608 ATTTCATTTA-TTTCACATTTTAGTCCCTCA
1 ATTTCATTTATTTTCACAATTTAATCCCT-A
*
34035638 ATTTC--TCATTTTCACAATTTAATCCCTA
1 ATTTCATTTATTTTCACAATTTAATCCCTA
34035666 ATATTCATTT
1 AT-TTCATTT
34035676 TTACTCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
28 5 0.17
29 19 0.63
30 5 0.17
31 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.01, T:0.50
Consensus pattern (30 bp):
ATTTCATTTATTTTCACAATTTAATCCCTA
Found at i:34035652 original size:29 final size:27
Alignment explanation
Indices: 34035618--34035676 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
34035608 ATTTCATTTA
* * *
34035618 TTTCACATTTTAGTCCCTCAATTTCTCAT
1 TTTCACAATTTAATCCCT-AATAT-TCAT
34035647 TTTCACAATTTAATCCCTAATATTCAT
1 TTTCACAATTTAATCCCTAATATTCAT
34035674 TTT
1 TTT
34035677 TACTCAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.25, C:0.24, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTCACAATTTAATCCCTAATATTCAT
Found at i:34062899 original size:25 final size:25
Alignment explanation
Indices: 34062860--34062917 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
34062850 CCATGTACAT
* *
34062860 GTATGCTCATACGAGCTGTGAATCA
1 GTATGCTCATACGAGATGTAAATCA
*
34062885 GTATGCTCACT-CGAGATGTAAATCG
1 GTATGCTCA-TACGAGATGTAAATCA
34062910 GTATGCTC
1 GTATGCTC
34062918 TCACTAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (25 bp):
GTATGCTCATACGAGATGTAAATCA
Found at i:34062954 original size:25 final size:25
Alignment explanation
Indices: 34062880--34062954 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
34062870 ACGAGCTGTG
* *
34062880 AATCAGTATGCTCAC-TCGAGATGTA
1 AATCGGTATGCTCACAT-GAGATATA
* *
34062905 AATCGGTATGCTCTCACT-AGTTATA
1 AATCGGTATGCTCACA-TGAGATATA
* *
34062930 AATTGGTATGCTCACATGAGCTATA
1 AATCGGTATGCTCACATGAGATATA
34062955 GATTAGAACG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
24 1 0.03
25 38 0.95
27 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (25 bp):
AATCGGTATGCTCACATGAGATATA
Found at i:34064702 original size:25 final size:25
Alignment explanation
Indices: 34064674--34064790 Score: 83
Period size: 25 Copynumber: 4.7 Consensus size: 25
34064664 TCCCACCCAC
*
34064674 AGCTCGTGTAAGCATACCGATTTGT
1 AGCTCGTGTAAGCATACCGATTTAT
* * *
34064699 AGCTTGTG-AGAGCATACCAATCTAT
1 AGCTCGTGTA-AGCATACCGATTTAT
* * * *
34064724 AGCTCGAGTGAGCATACCGATTCAC
1 AGCTCGTGTAAGCATACCGATTTAT
* * * * *
34064749 AGCTCGAGTGAGCATATCGATTCAC
1 AGCTCGTGTAAGCATACCGATTTAT
* *
34064774 AGCTCGTTTGAGCATAC
1 AGCTCGTGTAAGCATAC
34064791 ATGTACATGA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
24 1 0.01
25 74 0.99
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (25 bp):
AGCTCGTGTAAGCATACCGATTTAT
Found at i:34066988 original size:21 final size:21
Alignment explanation
Indices: 34066948--34066991 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34066938 ATTTTAGATA
*
34066948 TTTATGTATTTTTGTTTTTAT
1 TTTATGTATTTTTGTATTTAT
34066969 TTTATGTATTTATT-TATTTAT
1 TTTATGTATTT-TTGTATTTAT
34066990 TT
1 TT
34066992 ATCTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTATGTATTTTTGTATTTAT
Found at i:34067838 original size:21 final size:21
Alignment explanation
Indices: 34067814--34067859 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
34067804 GTGCCCCCTC
34067814 CACACGGCCATGTGTGGCCTT
1 CACACGGCCATGTGTGGCCTT
***
34067835 CACACGGGTGTGTGTGGCCTT
1 CACACGGCCATGTGTGGCCTT
34067856 CACA
1 CACA
34067860 TAGGCGTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (21 bp):
CACACGGCCATGTGTGGCCTT
Found at i:34067873 original size:21 final size:21
Alignment explanation
Indices: 34067849--34067888 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34067839 CGGGTGTGTG
34067849 TGGCCTTCACATAGGCGTGCA
1 TGGCCTTCACATAGGCGTGCA
* *
34067870 TGGCCTTTACATGGGCGTG
1 TGGCCTTCACATAGGCGTG
34067889 TAGACTCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.28
Consensus pattern (21 bp):
TGGCCTTCACATAGGCGTGCA
Found at i:34074038 original size:19 final size:19
Alignment explanation
Indices: 34074016--34074082 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
34074006 AATAATTATC
34074016 TTAATATTATTTTATTAAT
1 TTAATATTATTTTATTAAT
34074035 TTAATATTATTTTATTAAT
1 TTAATATTATTTTATTAAT
* * *
34074054 TTAATATTAATGTGATTATT
1 TTAATATT-ATTTTATTAAT
34074074 TTAATATTA
1 TTAATATTA
34074083 AATTTAATCT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
TTAATATTATTTTATTAAT
Found at i:34077072 original size:20 final size:19
Alignment explanation
Indices: 34077028--34077072 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
34077018 TGGTGAGATC
*
34077028 TAAAATAAATCAAACTAAT
1 TAAAATAAATAAAACTAAT
* *
34077047 TGAAATATATAAAACTTAAT
1 TAAAATAAATAAAAC-TAAT
34077067 TAAAAT
1 TAAAAT
34077073 CGACTCTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAATAAATAAAACTAAT
Found at i:34096526 original size:29 final size:29
Alignment explanation
Indices: 34096462--34096527 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
34096452 ATTTCATTTA
* * *
34096462 TTTCACAATTTAACCCCTAAATTTACACT
1 TTTCTCAATTTAACCCCTAAATATACAAT
* *
34096491 TTTCTCAATTTAATCCCT-AATATGCAAT
1 TTTCTCAATTTAACCCCTAAATATACAAT
34096519 TTTACTCAA
1 TTT-CTCAA
34096528 AATCACTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (29 bp):
TTTCTCAATTTAACCCCTAAATATACAAT
Found at i:34102889 original size:24 final size:24
Alignment explanation
Indices: 34102862--34102918 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
34102852 AATAGTTGAC
*
34102862 ATTTGACTATTAGGTAAATTTTAA
1 ATTTGAATATTAGGTAAATTTTAA
*
34102886 ATTTGAATATTGGGTAAATTTTAA
1 ATTTGAATATTAGGTAAATTTTAA
34102910 ATTTGAATA
1 ATTTGAATA
34102919 ATGATATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.46
Consensus pattern (24 bp):
ATTTGAATATTAGGTAAATTTTAA
Found at i:34103903 original size:47 final size:47
Alignment explanation
Indices: 34103849--34103942 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
34103839 ATAACGTCTA
34103849 ATCCCTAGATTGAATAATTGAGACTTTTCTCTAATTAACACCCTAGG
1 ATCCCTAGATTGAATAATTGAGACTTTTCTCTAATTAACACCCTAGG
*
34103896 ATCCCTAGATTGAATAATTGAGACTTTTCTCTAATTAACACTCTAGG
1 ATCCCTAGATTGAATAATTGAGACTTTTCTCTAATTAACACCCTAGG
34103943 GTTGCATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (47 bp):
ATCCCTAGATTGAATAATTGAGACTTTTCTCTAATTAACACCCTAGG
Found at i:34104531 original size:13 final size:13
Alignment explanation
Indices: 34104513--34104549 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
34104503 GCTCGGCAGG
34104513 GACACGCCCGTAT
1 GACACGCCCGTAT
*
34104526 GACACGCCTGTAT
1 GACACGCCCGTAT
34104539 GACACGCCCGT
1 GACACGCCCGT
34104550 CTGAGTCGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (13 bp):
GACACGCCCGTAT
Found at i:34113071 original size:25 final size:25
Alignment explanation
Indices: 34113033--34113082 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
34113023 GAGATTGTAA
34113033 GACTGCATAAGGTCCCTGTCTCTAT
1 GACTGCATAAGGTCCCTGTCTCTAT
**
34113058 GACTGCATGGGGTCCCTGTCTCTAT
1 GACTGCATAAGGTCCCTGTCTCTAT
34113083 CATTTTCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (25 bp):
GACTGCATAAGGTCCCTGTCTCTAT
Found at i:34115004 original size:43 final size:43
Alignment explanation
Indices: 34114916--34115026 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 43
34114906 TACCGAAATG
* * *
34114916 TGATTACATGTCAGACCATGTCTGGGACATTGACATTGTATTA
1 TGATTACATGTAAGACCATGTCTGGAACATTGACATCGTATTA
*
34114959 TGATTACATGTAAGACCATGTCTGGAATATTGGA-ATCGT-TATA
1 TGATTACATGTAAGACCATGTCTGGAACATT-GACATCGTAT-TA
* * * *
34115002 TGATTTCATATAAAACCCTGTCTGG
1 TGATTACATGTAAGACCATGTCTGG
34115027 GATAGTGGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.02
43 55 0.95
44 2 0.03
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (43 bp):
TGATTACATGTAAGACCATGTCTGGAACATTGACATCGTATTA
Found at i:34130312 original size:20 final size:20
Alignment explanation
Indices: 34130284--34130322 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34130274 ATCACATATT
*
34130284 TCATGAGCTCAGACCACAAC
1 TCATAAGCTCAGACCACAAC
*
34130304 TCATAAGCTCAGATCACAA
1 TCATAAGCTCAGACCACAA
34130323 AGTACCTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.31, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATAAGCTCAGACCACAAC
Found at i:34135516 original size:40 final size:40
Alignment explanation
Indices: 34135422--34135566 Score: 166
Period size: 40 Copynumber: 3.6 Consensus size: 40
34135412 CTCGCACAAG
* * * * * *
34135422 GCCTTCGGGTCTTAACCCCGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
34135462 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * * * *
34135502 GCCTTC-GGATCTTAGTCCGGATGTACTCGCTTAGAACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
34135543 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
34135567 CATTCGAGTA
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.03
40 57 0.64
41 26 0.29
42 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:34135557 original size:41 final size:40
Alignment explanation
Indices: 34135462--34135566 Score: 140
Period size: 41 Copynumber: 2.6 Consensus size: 40
34135452 TAGCATAAAT
* * *
34135462 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATACTCGCTAGAACAAAA
* *
34135502 GCCTTC-GGATCTTAGTCCGGATGTACTCGCTTAGAACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATACTCGC-TAGAACAAAA
34135543 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
34135567 CATTCGAGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
39 3 0.05
40 23 0.42
41 26 0.47
42 3 0.05
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATACTCGCTAGAACAAAA
Found at i:34136795 original size:38 final size:38
Alignment explanation
Indices: 34136753--34136964 Score: 424
Period size: 38 Copynumber: 5.6 Consensus size: 38
34136743 CAAGAACTCC
34136753 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
34136791 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
34136829 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
34136867 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
34136905 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
34136943 TTCCTCCTTCCTTAGAATTTTC
1 TTCCTCCTTCCTTAGAATTTTC
34136965 CTCCTTATTT
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 174 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:34142228 original size:42 final size:43
Alignment explanation
Indices: 34142169--34142264 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 43
34142159 TCTGTTTTGT
* *
34142169 GTGTAAGACCATGTCTGGGACA-TCGGCATC-ATATATGATTTC
1 GTGTAAGACCATATCTGGGACAGT-GGCATCGATATATGATTAC
* * *
34142211 GTGTAAGACCTTATCTGGGACAGTGGCATCGATGTTTGATTAC
1 GTGTAAGACCATATCTGGGACAGTGGCATCGATATATGATTAC
*
34142254 ATGTAAGACCA
1 GTGTAAGACCA
34142265 CGTCTGAGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 26 0.58
43 19 0.42
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATATCTGGGACAGTGGCATCGATATATGATTAC
Found at i:34143546 original size:20 final size:20
Alignment explanation
Indices: 34143521--34143558 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34143511 CCTATACATG
*
34143521 GTAAAAATTTTCTAAGTTTT
1 GTAAAAATTTCCTAAGTTTT
34143541 GTAAAAATTTCCTAAGTT
1 GTAAAAATTTCCTAAGTT
34143559 CTTGGTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (20 bp):
GTAAAAATTTCCTAAGTTTT
Found at i:34146393 original size:22 final size:23
Alignment explanation
Indices: 34146351--34146393 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
34146341 AAAACTACCG
*
34146351 GTAAAAATGCAGACAAGTTGCTA
1 GTAAAAATGCAGACAAATTGCTA
*
34146374 GTAAAAATG-AGATAAATTGC
1 GTAAAAATGCAGACAAATTGC
34146394 CTAATCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (23 bp):
GTAAAAATGCAGACAAATTGCTA
Found at i:34157177 original size:15 final size:15
Alignment explanation
Indices: 34157138--34157196 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
34157128 TAAAGGTAAC
*
34157138 AAGAAACCCGA-ATA
1 AAGAAACCCAAGATA
* *
34157152 AAGAAATCCAAGATT
1 AAGAAACCCAAGATA
* *
34157167 GAGAAACCCAAAATA
1 AAGAAACCCAAGATA
34157182 AAGAAACCCAAGATA
1 AAGAAACCCAAGATA
34157197 CGATACTATG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
14 9 0.26
15 26 0.74
ACGTcount: A:0.58, C:0.19, G:0.14, T:0.10
Consensus pattern (15 bp):
AAGAAACCCAAGATA
Found at i:34157184 original size:30 final size:29
Alignment explanation
Indices: 34157139--34157195 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
34157129 AAAGGTAACA
* *
34157139 AGAAACCCGAATAAAGAAATCCAAGATTG
1 AGAAACCCAAATAAAGAAACCCAAGATTG
34157168 AGAAACCCAAAATAAAGAAACCCAAGAT
1 AGAAACCC-AAATAAAGAAACCCAAGAT
34157196 ACGATACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.56, C:0.19, G:0.14, T:0.11
Consensus pattern (29 bp):
AGAAACCCAAATAAAGAAACCCAAGATTG
Found at i:34162440 original size:16 final size:16
Alignment explanation
Indices: 34162414--34162454 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
34162404 TGAATATTTC
34162414 TTCTTTA-TTCTTTAAT
1 TTCTTTATTTC-TTAAT
*
34162430 TTC-TTATTTCTTATT
1 TTCTTTATTTCTTAAT
34162445 TTCTTTATTT
1 TTCTTTATTT
34162455 TCTTGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCTTTATTTCTTAAT
Found at i:34173356 original size:13 final size:13
Alignment explanation
Indices: 34173340--34173379 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
34173330 GGGGGTAGGA
34173340 TTCTGTATATCTG
1 TTCTGTATATCTG
*
34173353 TTCTGCATATCTG
1 TTCTGTATATCTG
34173366 ATTCTGT-TATCTG
1 -TTCTGTATATCTG
34173379 T
1 T
34173380 ATTTGAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 1 0.04
13 18 0.75
14 5 0.21
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.53
Consensus pattern (13 bp):
TTCTGTATATCTG
Found at i:34176603 original size:48 final size:47
Alignment explanation
Indices: 34176516--34176612 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 47
34176506 TTTATGCTAC
** *
34176516 TTTAAGGACTGCTATTTGGTGTATTAATGCAGCTGAAAAATATGTTGT
1 TTTAAGGACTGCTATTTGGTGTATTAATGCAGCAAAAAAAT-TATTGT
* * *
34176564 TTTAAGGACTGTTGTTTGGTGTATTCATGCAGCAAAAAAATTATTGT
1 TTTAAGGACTGCTATTTGGTGTATTAATGCAGCAAAAAAATTATTGT
34176611 TT
1 TT
34176613 AGGCATCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
47 7 0.16
48 36 0.84
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (47 bp):
TTTAAGGACTGCTATTTGGTGTATTAATGCAGCAAAAAAATTATTGT
Found at i:34176712 original size:91 final size:91
Alignment explanation
Indices: 34176556--34177109 Score: 928
Period size: 91 Copynumber: 6.1 Consensus size: 91
34176546 AGCTGAAAAA
* * * * * *
34176556 TATGTTGTTTTAAGGACTGTTGTTTGGTGTATTCATGCAGCAAAAAAATTATTGTTTAGGCATCA
1 TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
34176621 ATTAATGTTGTCTAAGTGACTGTATT
66 ATTAATGTTGTCTAAGTGACTGTATT
* * * * * *
34176647 TATGTTATTTTAAGGACTGTTGTTTGGTGTATTAATACAGCAAAAAAATTGTTGTTTAGATATCA
1 TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
* *
34176712 ATTAATGTTTTCTAAGTGACTGCATT
66 ATTAATGTTGTCTAAGTGACTGTATT
* * * *
34176738 TATGATGTTTTAAGGACTGTTGTTTGATGTATTAATGCAGTAGAAAAATTGTTGTTTAGACATCA
1 TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
34176803 ATTAATGTTGTCTAAGTGACTGTATT
66 ATTAATGTTGTCTAAGTGACTGTATT
34176829 TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
1 TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
34176894 ATTAATGTTGTCTAAGTGACTGTATT
66 ATTAATGTTGTCTAAGTGACTGTATT
34176920 TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
1 TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
34176985 ATTAATGTTGTCTAAGTGACTGTATT
66 ATTAATGTTGTCTAAGTGACTGTATT
34177011 TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
1 TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
34177076 ATTAATGTTGTCTAAGTGACTGTAAATT
66 ATTAATGTTGTCTAAGTGACTGT--ATT
34177104 TATGTT
1 TATGTT
34177110 AATAATGGTT
Statistics
Matches: 440, Mismatches: 21, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
91 431 0.98
93 9 0.02
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (91 bp):
TATGTTGTTCTAAGGACTGTTGTTTGTTGTATTAATGCAGCAGAAAAATTGTTGTTTAGACATCA
ATTAATGTTGTCTAAGTGACTGTATT
Found at i:34183572 original size:48 final size:48
Alignment explanation
Indices: 34183501--34184366 Score: 1678
Period size: 48 Copynumber: 18.0 Consensus size: 48
34183491 CAAGATAAAT
* *
34183501 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183549 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183597 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183645 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183693 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183741 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183789 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183837 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183885 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183933 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34183981 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34184029 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34184077 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34184125 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34184173 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
34184221 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
34184269 ATATGTATATGTTGTAAAGCCGAATGGCTAGTGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
34184317 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
34184365 AT
1 AT
34184367 GTGTGTATAT
Statistics
Matches: 811, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 811 1.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:34184557 original size:37 final size:37
Alignment explanation
Indices: 34184507--34184609 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
34184497 GGAAATATAT
*
34184507 TCCGGGTAAGACCCGATGACTACGTGTGGAGCTTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
34184544 TCCGGGTAAGACCCGATGACTACATATGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
34184581 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
34184610 GGACTATTCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:34196207 original size:45 final size:44
Alignment explanation
Indices: 34196091--34196224 Score: 184
Period size: 43 Copynumber: 3.1 Consensus size: 44
34196081 TATCGAAATG
* *
34196091 TGATATTCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
1 TGATATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
* * *
34196135 TGATA-TCGGGCTTTGAGCTTAGTAGGCTATGATGCCGGTGAAA
1 TGATATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
34196178 T-ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGT-AAA
1 TGA-TATTCGGG-CTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
34196222 TGA
1 TGA
34196225 AATGTTATGT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
42 1 0.01
43 36 0.46
44 14 0.18
45 27 0.35
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (44 bp):
TGATATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
Done.