Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 130 of 297
Found at i:44848055 original size:28 final size:27
Alignment explanation
Indices: 44847998--44848149 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
44847988 TAAATTGTGC
*
44847998 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
44848025 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
44848053 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
44848080 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
44848108 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
44848135 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
44848150 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:44848063 original size:55 final size:55
Alignment explanation
Indices: 44847998--44848149 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
44847988 TAAATTGTGC
*
44847998 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
44848053 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
44848108 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
44848150 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:44852403 original size:40 final size:40
Alignment explanation
Indices: 44852330--44852433 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
44852320 ATGTAAATTA
* * *
44852330 TACCC-TGATTGCACATACGTGACCTTATTTGTACTTCGG
1 TACCCTTGATTGCACATACGTGCCCCTATGTGTACTTCGG
* *
44852369 TA-CCTTCGATTACACATACGTGCCCCTGTGTGTACTTCGG
1 TACCCTT-GATTGCACATACGTGCCCCTATGTGTACTTCGG
*
44852409 TACCCTTGATTGCACTTACGTGCCC
1 TACCCTTGATTGCACATACGTGCCC
44852434 TTGTTTACAT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
38 2 0.04
39 3 0.05
40 46 0.84
41 4 0.07
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (40 bp):
TACCCTTGATTGCACATACGTGCCCCTATGTGTACTTCGG
Found at i:44853769 original size:17 final size:17
Alignment explanation
Indices: 44853744--44853776 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44853734 GTTCAAAAAT
*
44853744 ATTTTTTTAATTTAATA
1 ATTTATTTAATTTAATA
44853761 ATTTATTTAATTTAAT
1 ATTTATTTAATTTAAT
44853777 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATTTAATTTAATA
Found at i:44857207 original size:7 final size:7
Alignment explanation
Indices: 44857169--44857217 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
44857159 AAATAAGAAA
44857169 TAGGGTT
1 TAGGGTT
*
44857176 TAGTGTT
1 TAGGGTT
*
44857183 TAAGGTT
1 TAGGGTT
*
44857190 T-GGATT
1 TAGGGTT
44857196 T-GGGTT
1 TAGGGTT
44857202 TAGGGTT
1 TAGGGTT
44857209 TAGGGTT
1 TAGGGTT
44857216 TA
1 TA
44857218 TAGTTTGTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 9 0.26
7 26 0.74
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:44858765 original size:25 final size:24
Alignment explanation
Indices: 44858685--44858765 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 24
44858675 TTCGACTTAT
44858685 GTTTCAATTTAAGGTTTGGTTTGGGG
1 GTTTCAATTTAA-GTTTGGTTT-GGG
*
44858711 GTTT-AGATTT-AGTTTCGATTTGGG
1 GTTTCA-ATTTAAGTTT-GGTTTGGG
* *
44858735 GATTCAATTTCAAGTTTGGTTTGTG
1 GTTTCAATTT-AAGTTTGGTTTGGG
44858760 GTTTCA
1 GTTTCA
44858766 TTTCAAAGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
24 14 0.31
25 18 0.40
26 13 0.29
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.48
Consensus pattern (24 bp):
GTTTCAATTTAAGTTTGGTTTGGG
Found at i:44859544 original size:143 final size:143
Alignment explanation
Indices: 44859286--44859570 Score: 453
Period size: 143 Copynumber: 2.0 Consensus size: 143
44859276 CATCTTACGC
*
44859286 TTGACTACAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTG
1 TTGACTACAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTC
* *
44859351 AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTGGGGTCTGGTTTGGGGTTTTAGATTTG
66 AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTAGGGTCTGGTTTGGGGTTTTAGATTCG
*
44859416 TCTACGATTTGGG
131 TCCACGATTTGGG
* * * *
44859429 TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAATTTAGTTACCCAAATTTGTTC
1 TTGACTACAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTC
* * * * *
44859494 ACAGCTTTAATTTGGGATTTTGAGTTATGTTTAAATTTAGGGTCTGGTTTGGGGTTTTAGATTCG
66 AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTAGGGTCTGGTTTGGGGTTTTAGATTCG
44859559 TCCACGATTTGG
131 TCCACGATTTGG
44859571 TGATTTGATT
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
143 129 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (143 bp):
TTGACTACAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTC
AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTAGGGTCTGGTTTGGGGTTTTAGATTCG
TCCACGATTTGGG
Found at i:44862029 original size:704 final size:697
Alignment explanation
Indices: 44860156--44863871 Score: 3368
Period size: 692 Copynumber: 5.4 Consensus size: 697
44860146 TAAAAGGTTT
* * * * * * *
44860156 TTGAAATCCTTCAATTTGGGATTTTGATTTAGGTTTTAATTTAGGGTTTGGTTTGGGGTTTTAGA
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTAGGTTTTGGTTT-GGGTTTTAGA
* ** ** * * ** * * * * ** * *
44860221 TTCAATTTTGATTTGGGGATTTGATTTTATTTTTTATTTGAGGTCTCAATTTGAAG-GGTTTCGA
65 TTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTGG
* * * * * * * * *
44860285 TTGTTCGGTTACCTCTC-GAGTAACTGAGCTAGTGTGGTAATTTTTTAAGTTTTTAATATATATA
130 TTGTTCGGTAACCTC-CGGAGTAACTAAACAAGTGTTGCAATTCTATAAGTTTGTAATATATATA
* *
44860349 AATATATAAATTCAAC-AAAAAATATTCAAAATTAATTT-A-AT-ATGTTCACCTTAAT-AAA-A
194 AATATATAAATTCAACAAAAAAAT-TTAAAAATTAATTTAATATGATGTTTA-CTTAATAAAACA
* * ** * *
44860408 -AACTTGACCAACAAT--TA-TAAAAT---CT---AT---AATTTTTATATTCTATATTTCAAAA
257 TAATTTGACCAACAATAATATTAAAATGAAATAAAATCAAAAAATTTATATTATATATTTCAGAA
* * * **
44860460 CCTCAATTACTTTTTG-CTCATTTTAAGTTATCAAAACTCTATGGTCTTTCAAAAATTTGGTGGT
322 TCTCCATAACTTTTTGACTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAAATTTGGTGGT
* * * *
44860524 TTTAATAATACTAATTTAGAGCTGAAATTTAATTCTAAAATAAGAAATTTTGTTTGATCAAAAAG
387 TTTAATAATATTAATTTAGAGTTGAAATGTAATTCTAAAA-AA-ATATTTTGTTT-ATCAAAAAG
* * * *
44860589 AGTAACCAAAAGCTTAAGATTC-GAGGCTTAAAACATTCAAAATCGTCACAA-TTTGCTCAAAAT
449 AGTAACCAAAAGCCTAAGATTCAG-GGCTTAAAACTTTCAAAATCGTCACAACTTGGCTCAGAAT
* * * *
44860652 TTCAAAGTTTTCTATTTCAAGTAGGCTACTTTGGGAGCTTGGTTCTTTTAAGACACAACATAATT
513 TTCAAAGTTTTCTGTTTCAAGTAGGCTACTTT-GGAGCTTGGTTCTTTTAACACACAACACATTT
* * * * * *
44860717 TGGCTTGGAAAACATACTAATGGAAAGATCACAGTTAATACAATATAAATCATCTCACGTTCGAC
577 TGGCTTGGAAAACATACCAATGGAAAGATCGCATTTCATACAATAGAAATCATCTCACTTTCGAC
* ** * *
44860782 TAAAATGAAAAATAATAAAAGGTTTTTTAAAGCC-TTATATTTAGTTACCCAAATCTA
642 TAGAATGAGCAACAATAAAAGG-TTTTGAAAGCCTTTA-ATTTAGTTACCCAAATCTA
* * *
44860839 TTGAAAGCCTTAAATTAG-GAATTTTGA-TATAGGTTTCACTTTA-----------GGGTTTTAG
1 TTGAAAGCCTTAAATTTGAG-ATTTCGACT-TAGGTTTCAATTTAGGTTTTGGTTTGGGTTTTAG
* * * * *
44860891 ATTTGGTTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATCCAAAGCTCTTTTG
64 ATTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTG
* * * *
44860956 GTTGTTCGATAACCTCCAGAGGAACTAAACAAGTG-TGACAATTCTATAAGTTTGTAATATATAC
129 GTTGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTG-CAATTCTATAAGTTTGTAATATATAT
* *
44861020 AAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATAATGTTTACCTTAATAAAAAA
193 AAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATGTTTA-CTTAATAAAACA
** * * * * *** **
44861085 TTGTTTGACCAACAACAATAATAATATGGAATAAAATCTAAAGTTTTTATAACATATATTTCAGA
257 TAATTTGACCAACAATAATATTAAAATGAAATAAAATC-AAAAAATTTATATTATATATTTCAGA
* * * * *
44861150 ACCTCAATGACTTTTTCACTCATTTTAAGTTATCAAAACTCTATGA-TCTTTCAAAATTTTGGTG
321 ATCTCCATAACTTTTTGACTCATTTTAAGTTATCAAAACTCTAT-ACTCTTTCAAAAATTTGGTG
* * * *
44861214 GTTTTAATAATATTAATTTAGAGTTGGAATGTAATTCTAAAACAAAAAATTTTGCTTGATAAAAA
385 GTTTTAATAATATTAATTTAGAGTTGAAATGTAATTCT-AAA-AAAATATTTTG-TTTATCAAAA
* * * * *
44861279 AGAGTAACCGAAAGCCTAACACTCAGGGCTTAAAACATTCAAAATCGTCACAA-TTGGCTCAAAA
447 AGAGTAACCAAAAGCCTAAGATTCAGGGCTTAAAACTTTCAAAATCGTCACAACTTGGCTCAGAA
* * * * *
44861343 TGTCAAAGTTTTCTGTTCCAAGTAGGCTACTTTGAGAGCTTGGTTCTTTTAAGAAACAACACAAT
512 TTTCAAAGTTTTCTGTTTCAAGTAGGCTACTTTG-GAGCTTGGTTCTTTTAACACACAACACATT
* * * *
44861408 TTGGCTTGGAAAACATACTAATGGAAAGATCGCATTTCATACAATACAAATCCTCTCACTTTCAA
576 TTGGCTTGGAAAACATACCAATGGAAAGATCGCATTTCATACAATAGAAATCATCTCACTTTCGA
* * *
44861473 TTAGAATGAGAAAAAATAAAAGGTTTCTGAAAGCCTTTAATTTAGTTACCCAAATCTA
641 CTAGAATGAGCAACAATAAAAGGTTT-TGAAAGCCTTTAATTTAGTTACCCAAATCTA
* * *
44861531 ATGAAAGCCTTAAATTTGGGATTTCGACATAGGTTTCAATTTAGGTTTTTGGTTTGGGTTTTAGA
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTAGG-TTTTGGTTTGGGTTTTAGA
* ** * * *
44861596 TTTGGCTTCAATTTGGGGATTCAAGTTCAATTTTGGTTTGTGGTTGCAATTCGAAGCCCTTTTGG
65 TTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTGG
* * *
44861661 TTATTCGGTAACCTCCGGAGTAGCTAAACAAGTGTGGCAATTCTATAAGTTTGTAATATATATAA
130 TTGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTGCAATTCTATAAGTTTGTAATATATATAA
*
44861726 ATATATATATATTCAACAAAAAAATTTTAAAAATTAGTTTAATATGATGTTTATCTTAATAAAAC
195 ATATATA-A-ATTCAACAAAAAAA-TTTAAAAATTAATTTAATATGATGTTTA-CTTAATAAAAC
* * *** *
44861791 ATAATTTGACCAACAATAATATTAAAATCAAATCAAATCAAATTTTTTTTTGATTATATATTTCA
256 ATAATTTGACCAACAATAATATTAAAATGAAATAAAATCAAA-AAATTTAT-ATTATATATTTCA
*
44861856 GAATCTCCATAACTTTTTGACTCATTTTAAGCTATCAAAACTCTATACTCTTTCAAAAATTTGGT
319 GAATCTCCATAACTTTTTGACTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAAATTTGGT
* * *
44861921 TGTTTTAATAATATTAATTTAGAGTTCAAATGTAATTCTAAAACAATATTTT-TTTATCAAACAA
384 GGTTTTAATAATATTAATTTAGAGTTGAAATGTAATTCTAAAAAAATATTTTGTTTATCAAA-AA
* * * *
44861985 -AGTAACCAAAAGCCTAAGGTTCAAGGCTTAAAACTTTGAAAATCGTCACAACTT-GCCCAGAAT
448 GAGTAACCAAAAGCCTAAGATTCAGGGCTTAAAACTTTCAAAATCGTCACAACTTGGCTCAGAAT
* * * * *
44862048 TTTAAAG-TTTCTTGTTTCAAGTAGACTACTTTGGGAGCTTGGTTATTTTAACATAGAACACATT
513 TTCAAAGTTTTC-TGTTTCAAGTAGGCTACTTT-GGAGCTTGGTTCTTTTAACACACAACACATT
* * * * * * * *
44862112 TTGGCATGGAAAATAGACAAATGAAAAGAT-GACATTTTC-TACAATAGAAATAACCTCACGTTC
576 TTGGCTTGGAAAACATACCAATGGAAAGATCG-CA-TTTCATACAATAGAAATCATCTCACTTTC
44862175 GACTAGAATGAGCAACAAT---A------G-AAG-----------G--------AT-T-
639 GACTAGAATGAGCAACAATAAAAGGTTTTGAAAGCCTTTAATTTAGTTACCCAAATCTA
* * * * *
44862203 TAGAAAGCTTTAAATTTGAGATTTTGACTTAAGTTTTAATTTAGGGTTTTGGTTTGGGTTTTAGA
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTA-GGTTTTGGTTTGGGTTTTAGA
* * * * * ** * **
44862268 TTCAATTTCGATATGGGGAGT-AGATTT-ATGTTTTGGTCTTG-CCTTTTGATTCGAAGGTCTTT
65 TTCGATTTCAATTTGGGGATTCA-ATTTCA-ATTTTGGT-TTGTGGTTTCGATTCGAAGCCCTTT
* * * * *
44862330 TAGTTGTTCGGTAACCT-C--A-CAACTAAACAATTGTTGTAATTCTATAAGTTTGTAATATATT
127 TGGTTGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTGCAATTCTATAAGTTTGTAATATATA
* * * * *
44862391 TTAATATATAAATTCAACAAAAAATTTTAAAAATTAATTTAATATTATATTTACATGAATAAAAC
192 TAAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATGTTTAC-TTAATAAAAC
* * *
44862456 ATAATTTGGCCAACAATAATATTAAAATGAAATAAAATAAAAGAAATTTATATTCTATATTTCAG
256 ATAATTTGACCAACAATAATATTAAAATGAAATAAAATCAAA-AAATTTATATTATATATTTCAG
* *
44862521 AATCT-CATTGACTTTTT-AGCTCATTTTAAGTTACCAAAACTC--TACTCTTTCAAAAATTTGG
320 AATCTCCA-TAACTTTTTGA-CTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAAATTTGG
* * *
44862582 TGGTTTTAATAATAATAATAATTTATAGTTGAAATGTAATTTTAAAATAATAAAATTTTTGTTTA
383 TGGTTTTAATAAT-AT--TAATTTAGAGTTGAAATGTAATTCT-AAA-AA-AATA-TTTTGTTT-
* * * * ** * * *
44862647 ATCAAAAAGAGTAATCAAATGCCAAAAATTTGGGGGTAAAAAAATTT-AAAATCGTCACAACTTG
440 ATCAAAAAGAGTAACCAAAAGCCTAAGATTCAGGGCT-TAAAACTTTCAAAATCGTCACAACTTG
* * * * * *
44862711 CCT-AGAATTTCAAAGTTTTCTGTTTCAAGTACGCTAATTTCGGTGCTAGGTTCTTTTAACACAG
504 GCTCAGAATTTCAAAGTTTTCTGTTTCAAGTAGGCTACTTT-GGAGCTTGGTTCTTTTAACACAC
** * * *
44862775 AACTTATTTTGGCTTGCAAAACATACCAATGGAAAGATCGCATTTCATACAACAGATATCATCTC
568 AACACATTTTGGCTTGGAAAACATACCAATGGAAAGATCGCATTTCATACAATAGAAATCATCTC
* * * *
44862840 A-TGTTCGACTAGAATGACCAACAATAAAAGGTTTTAAAAAGCCTTAAATTTAGTTACCCAAACC
633 ACT-TTCGACTAGAATGAGCAACAATAAAAGGTTTT-GAAAGCCTTTAATTTAGTTACCCAAATC
*
44862904 TG
696 TA
* * ** * * *
44862906 TTGAAAGCCTTCAATTTGAGATTTCAACTTATATTTCAAATTAGGGTTTGGTTTGGGGTTTTATA
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTAGGTTTTGGTTT-GGGTTTTAGA
* * * * *
44862971 TTCGATTTCAATTTGGGGATTCAATTTCAAGTTTGGTATGTGGTTTCGATTCAAAGTCTTTTTGG
65 TTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTGG
*
44863036 TTGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTGAAATTCTATAAGTTTGTAACATATATAT
130 TTGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTGCAATTCTATAAGTTTG-------TA-AT
* * *
44863101 AAATATATAAATATATAAATTTAACAAAAAAATTTAAAAATTAATTTAGTATGATGTTTATATTA
187 --ATATATAAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATGTTTA-CTTA
* * * * * *
44863166 ATAAAACATAATTTGGA-AAACAATAATATTAAAATGAAATAATATAAAAAAAATTGTATTCTAT
249 ATAAAACATAATTT-GACCAACAATAATATTAAAATGAAATAAAATCAAAAAATTTATATTATAT
* ** * *
44863230 AGTTCAGAATCT-CATAGACTTTTTGGTTCATTTTAAGTTATCAAAACTTTATGCTCTTTCAAAA
313 ATTTCAGAATCTCCATA-ACTTTTTGACTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAA
* * * *
44863294 ATTTGATTGTTTTAATAGTATTAATTTAGAGTTGAAATGTAATTCTAAAAAAAATAATTTTTTTT
377 ATTTGGTGGTTTTAATAATATTAATTTAGAGTTGAAATGTAATTCT-AAAAAAAT-ATTTTGTTT
* * * *
44863359 ATCAAATAGAGTAACCAAAAGCCTAATATTC-GGTGCTTAAAACTTTAAAAATCATCACAACTTG
440 ATCAAAAAGAGTAACCAAAAGCCTAAGATTCAGG-GCTTAAAACTTTCAAAATCGTCACAACTTG
* * * * *
44863423 CCT-AGAATTTGAAAGTTTTCTATTTCAAGTAGACTACTTTCGGAGCATGGTTCTTTTAACACAC
504 GCTCAGAATTTCAAAGTTTTCTGTTTCAAGTAGGCTACTTT-GGAGCTTGGTTCTTTTAACACAC
*** * * * ** *
44863487 AGTTCATTTTGACTTGGAAAACATGCCAATGAAAAGATCGCATTTTGTACAATAGAAATAATCTC
568 AACACATTTTGGCTTGGAAAACATACCAATGGAAAGATCGCATTTCATACAATAGAAATCATCTC
* * *
44863552 A-TGTTCGACTAGAATGAGCAACAATAGAAGGTTTTAGAAAG-TTTTAAATTTATTTACCCAAAT
633 ACT-TTCGACTAGAATGAGCAACAATAAAAGGTTTT-GAAAGCCTTT-AATTTAGTTACCCAAAT
44863615 CTA
695 CTA
* * *
44863618 TTGAAAGCCTTAAATTTGATATTTTGACTTAGGTTTCAATTTAGGGTTTTTGTTTGGGGTTTTAG
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTA-GGTTTTGGTTT-GGGTTTTAG
* ** ** * * * * * * * *
44863683 ATTCAATTTTTATCAGGTGATTCAATTTTAGTTTTGATTTATGGTTTCGATTTGAAG-GCATTTG
64 ATTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTG
* * ** * *
44863747 GTTTTTCGATAACCTCTTGAGTAACTAAACAAGGGTTGTAATTCTATAAGTTTGTAATATATATA
129 GTTGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTGCAATTCTATAAGTTTGTAATATATATA
* * *
44863812 AATATATAAATTCAGC-AAAATATTT-AAAATTTATTTAATATGATGTTTACATTAATAAAA
194 AATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATGTTTAC-TTAATAAAA
44863872 TTGTTGGTTT
Statistics
Matches: 2494, Mismatches: 393, Indels: 275
0.79 0.12 0.09
Matches are distributed among these distances:
662 31 0.01
663 5 0.00
664 48 0.02
665 98 0.04
666 16 0.01
667 2 0.00
668 48 0.02
669 5 0.00
670 9 0.00
671 210 0.08
672 201 0.08
673 14 0.01
674 5 0.00
675 13 0.01
676 3 0.00
677 1 0.00
678 11 0.00
680 2 0.00
681 5 0.00
682 6 0.00
683 34 0.01
684 1 0.00
687 2 0.00
691 38 0.02
692 344 0.14
693 16 0.01
694 2 0.00
700 31 0.01
701 10 0.00
702 34 0.01
703 105 0.04
704 303 0.12
705 13 0.01
706 26 0.01
707 107 0.04
708 104 0.04
711 11 0.00
712 294 0.12
713 70 0.03
714 5 0.00
715 30 0.01
716 53 0.02
717 99 0.04
718 29 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (697 bp):
TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTAGGTTTTGGTTTGGGTTTTAGAT
TCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTGGT
TGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTGCAATTCTATAAGTTTGTAATATATATAAA
TATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATGTTTACTTAATAAAACATAAT
TTGACCAACAATAATATTAAAATGAAATAAAATCAAAAAATTTATATTATATATTTCAGAATCTC
CATAACTTTTTGACTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAAATTTGGTGGTTTTA
ATAATATTAATTTAGAGTTGAAATGTAATTCTAAAAAAATATTTTGTTTATCAAAAAGAGTAACC
AAAAGCCTAAGATTCAGGGCTTAAAACTTTCAAAATCGTCACAACTTGGCTCAGAATTTCAAAGT
TTTCTGTTTCAAGTAGGCTACTTTGGAGCTTGGTTCTTTTAACACACAACACATTTTGGCTTGGA
AAACATACCAATGGAAAGATCGCATTTCATACAATAGAAATCATCTCACTTTCGACTAGAATGAG
CAACAATAAAAGGTTTTGAAAGCCTTTAATTTAGTTACCCAAATCTA
Found at i:44863108 original size:8 final size:8
Alignment explanation
Indices: 44863095--44863120 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
44863085 TTTGTAACAT
44863095 ATATATAA
1 ATATATAA
44863103 ATATATAA
1 ATATATAA
44863111 ATATATAA
1 ATATATAA
44863119 AT
1 AT
44863121 TTAACAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAA
Found at i:44863576 original size:712 final size:711
Alignment explanation
Indices: 44862205--44863822 Score: 1994
Period size: 712 Copynumber: 2.3 Consensus size: 711
44862195 GAAGGATTTA
* *
44862205 GAAAGCTTTAAATTTGAGATTTTGACTTAAGTTTTAATTTAGGGTTTTGGTTT-GGGTTTTAGAT
1 GAAAGCCTTAAATTTGAGATTTTGACTTAA-TTTCAATTTAGGGTTTTGGTTTGGGGTTTTAGAT
* * * * * * * *
44862269 TCAATTTCGATATGGGGAGT-AGATTTATGTTTTGGTCTTGCCTTTTGATTCGAAGGTCTTTTAG
65 TCAATTTCAATATGGGGATTCA-ATTTAAGTTTTGGTATTG-GTTTCGATTC-AAAGTCTTTTGG
* *
44862333 TTGTTCGGTAACCT-C-A-CAACTAAACAATTGTTGTAATTCTATAAGTTTGT-A-ATATAT---
127 TTGTTCGGTAACCTCCGAGTAACTAAACAAGTGTTGTAATTCTATAAGTTTGTAATATATATAAA
* *
44862390 T-T-T-AATATATAAATTCAACAAAAAATTTTAAAAATTAATTTAATATTATATTTACATGAATA
192 TATATAAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATATTTACATGAATA
** * *
44862452 AAACATAATTTGGCCAACAATAATATTAAAATGAAATAAAATAAAAGAAATTTATATTCTATATT
257 AAACATAATTTGGAAAACAATAATATTAAAATGAAATAAAATAAAAGAAAATTATATTCTATAGT
* *
44862517 TCAGAATCTCATTGACTTTTTAGCTCATTTTAAGTTACCAAAACTCTACTCTTTCAAAAATTTGG
322 TCAGAATCTCATAGACTTTTTAGCTCATTTTAAGTTACCAAAACTCTACTCTTTCAAAAATTTGA
* *
44862582 TGGTTTTAATAATAATAATAATTTATAGTTGAAATGTAATTTTAAAATAATAAAATTTTTGTTTA
387 TGGTTTTAATAATAAT-ATAATTTAGAGTTGAAATGTAATTCTAAAATAATAAAATTTTTGTTTA
* * * * *
44862647 ATCAAAAAGAGTAATCAAATGCCAAAAATTTGGGGGTAAAAAAATTTAAAATCGTCACAACTTGC
451 ATCAAAAAGAGTAACCAAAAGCCAAAAATTCGGGGCTAAAAAAATTTAAAATCATCACAACTTGC
* *
44862712 CTAGAATTTCAAAGTTTTCTGTTTCAAGTACGCTAATTTCGGTGCTAGGTTCTTTTAACACAGAA
516 CTAGAATTTCAAAGTTTTCTATTTCAAGTACGCTAATTTCGGAGCTAGGTTCTTTTAACACAGAA
* * * *
44862777 CTTATTTTGGCTTGCAAAACATACCAATGGAAAGATCGCATTTCATACAACAGATATCATCTCAT
581 CTTATTTTGACTTGCAAAACATACCAATGAAAAGATCGCATTTCATACAACAGAAATAATCTCAT
*
44862842 GTTCGACTAGAATGACCAACAATAAAAGGTTTTAAAAAGCCTTAAATTTAGTTACCCAAACCTGT
646 GTTCGACTAGAATGACCAACAATAAAAGGTTTTAAAAAGCCTTAAATTTAGTTACCCAAACCTAT
44862907 T
711 T
* ** * *
44862908 GAAAGCCTTCAATTTGAGATTTCAACTTATATTTCAAATTAGGG-TTTGGTTTGGGGTTTTATAT
1 GAAAGCCTTAAATTTGAGATTTTGACTTA-ATTTCAATTTAGGGTTTTGGTTTGGGGTTTTAGAT
* *
44862972 TCGATTTCAATTTGGGGATTCAATTTCAAG-TTTGGTATGTGGTTTCGATTCAAAGTCTTTTTGG
65 TCAATTTCAATATGGGGATTCAATTT-AAGTTTTGGTAT-TGGTTTCGATTCAAAGTC-TTTTGG
*
44863036 TTGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTGAAATTCTATAAGTTTGTAACATATATAT
127 TTGTTCGGTAACCTCC-GAGTAACTAAACAAGTGTTGTAATTCTATAAGTTTGT-A-ATATATAT
* * * * *
44863101 AAATATATAAATATATAAATTTAACAAAAAAATTTAAAAATTAATTTAGTATGATGTTTATATTA
189 AAATATATAAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATATTTACATGA
* *
44863166 ATAAAACATAATTTGGAAAACAATAATATTAAAATGAAATAATATAAAA-AAAATTGTATTCTAT
254 ATAAAACATAATTTGGAAAACAATAATATTAAAATGAAATAAAATAAAAGAAAATTATATTCTAT
* * * *
44863230 AGTTCAGAATCTCATAGACTTTTTGGTTCATTTTAAGTTATCAAAACTTTATGCTCTTTCAAAAA
319 AGTTCAGAATCTCATAGACTTTTTAGCTCATTTTAAGTTACCAAAACTCTA--CTCTTTCAAAAA
* *
44863295 TTTGATTGTTTTAATAGT-AT-TAATTTAGAGTTGAAATGTAATTCTAAAA-AA-AATAATTTTT
382 TTTGATGGTTTTAATAATAATATAATTTAGAGTTGAAATGTAATTCTAAAATAATAA-AATTTTT
* * * * * *
44863356 -TTT-ATCAAATAGAGTAACCAAAAGCCTAATATTCGGTGCT-TAAAACTTTAAAAATCATCACA
446 GTTTAATCAAAAAGAGTAACCAAAAGCCAAAAATTCGGGGCTAAAAAAATTT-AAAATCATCACA
* *
44863418 ACTTGCCTAGAATTTGAAAGTTTTCTATTTCAAGTA-GACTACTTTCGGAGC-ATGGTTCTTTTA
510 ACTTGCCTAGAATTTCAAAGTTTTCTATTTCAAGTACG-CTAATTTCGGAGCTA-GGTTCTTTTA
* * * * ** *
44863481 ACACA-CAGTTCATTTTGACTTGGAAAACATGCCAATGAAAAGATCGCATTTTGTACAATAGAAA
573 ACACAGAACTT-ATTTTGACTTGCAAAACATACCAATGAAAAGATCGCATTTCATACAACAGAAA
* * * ** *
44863545 TAATCTCATGTTCGACTAGAATGAGCAACAATAGAAGGTTTTAGAAAGTTTTAAATTTATTTACC
637 TAATCTCATGTTCGACTAGAATGACCAACAATAAAAGGTTTTAAAAAGCCTTAAATTTAGTTACC
*
44863610 CAAATCTATT
702 CAAACCTATT
* * *
44863620 GAAAGCCTTAAATTTGATATTTTGACTTAGGTTTCAATTTAGGGTTTTTGTTTGGGGTTTTAGAT
1 GAAAGCCTTAAATTTGAGATTTTGACTTA-ATTTCAATTTAGGGTTTTGGTTTGGGGTTTTAGAT
** * * * * ** * *
44863685 TCAATTTTTATCA-GGTGATTCAATTTTAGTTTTGATTTATGGTTTCGATTTGAAGGCATTTGGT
65 TCAATTTCAAT-ATGGGGATTCAATTTAAGTTTTGGTAT-TGGTTTCGATTCAAAGTCTTTTGGT
* * * *
44863749 TTTTCGATAACCTCTTGAGTAACTAAACAAGGGTTGTAATTCTATAAGTTTGTAATATATATAAA
128 TGTTCGGTAACCTC-CGAGTAACTAAACAAGTGTTGTAATTCTATAAGTTTGTAATATATATAAA
44863814 TATATAAAT
192 TATATAAAT
44863823 TCAGCAAAAT
Statistics
Matches: 780, Mismatches: 104, Indels: 55
0.83 0.11 0.06
Matches are distributed among these distances:
702 13 0.02
703 100 0.13
704 7 0.01
706 1 0.00
707 31 0.04
710 21 0.03
711 19 0.02
712 303 0.39
713 64 0.08
714 10 0.01
715 28 0.04
716 59 0.08
717 97 0.12
718 27 0.03
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (711 bp):
GAAAGCCTTAAATTTGAGATTTTGACTTAATTTCAATTTAGGGTTTTGGTTTGGGGTTTTAGATT
CAATTTCAATATGGGGATTCAATTTAAGTTTTGGTATTGGTTTCGATTCAAAGTCTTTTGGTTGT
TCGGTAACCTCCGAGTAACTAAACAAGTGTTGTAATTCTATAAGTTTGTAATATATATAAATATA
TAAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATATTTACATGAATAAAAC
ATAATTTGGAAAACAATAATATTAAAATGAAATAAAATAAAAGAAAATTATATTCTATAGTTCAG
AATCTCATAGACTTTTTAGCTCATTTTAAGTTACCAAAACTCTACTCTTTCAAAAATTTGATGGT
TTTAATAATAATATAATTTAGAGTTGAAATGTAATTCTAAAATAATAAAATTTTTGTTTAATCAA
AAAGAGTAACCAAAAGCCAAAAATTCGGGGCTAAAAAAATTTAAAATCATCACAACTTGCCTAGA
ATTTCAAAGTTTTCTATTTCAAGTACGCTAATTTCGGAGCTAGGTTCTTTTAACACAGAACTTAT
TTTGACTTGCAAAACATACCAATGAAAAGATCGCATTTCATACAACAGAAATAATCTCATGTTCG
ACTAGAATGACCAACAATAAAAGGTTTTAAAAAGCCTTAAATTTAGTTACCCAAACCTATT
Found at i:44867714 original size:16 final size:18
Alignment explanation
Indices: 44867682--44867714 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
44867672 ATATATTATA
44867682 ATAATTAAAATGAAAGAT
1 ATAATTAAAATGAAAGAT
44867700 ATAA-TAAAA-GAAAGA
1 ATAATTAAAATGAAAGA
44867715 AAAAAAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
ATAATTAAAATGAAAGAT
Found at i:44868856 original size:25 final size:25
Alignment explanation
Indices: 44868828--44868875 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
44868818 TGTCATTGAC
*
44868828 ATTGAAATGGCAAAGATGAGAAAAT
1 ATTGAAATGACAAAGATGAGAAAAT
*
44868853 ATTGAAATGACAAATATGAGAAA
1 ATTGAAATGACAAAGATGAGAAA
44868876 TGAAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (25 bp):
ATTGAAATGACAAAGATGAGAAAAT
Found at i:44870172 original size:49 final size:49
Alignment explanation
Indices: 44870093--44870186 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
44870083 TCAAGAAGGG
* * *
44870093 ATAAATAGTGATAAGAGTGTGGATAATGGAAGACTAAATTTAGCAATGT
1 ATAAATAGTGATAAAAGTGTAGATAATGGAAGACCAAATTTAGCAATGT
* *
44870142 ATAAATAGTGATAAAAGTGTAGATAGTGGAAGACCAATTTTAGCA
1 ATAAATAGTGATAAAAGTGTAGATAATGGAAGACCAAATTTAGCA
44870187 TTGCATAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (49 bp):
ATAAATAGTGATAAAAGTGTAGATAATGGAAGACCAAATTTAGCAATGT
Found at i:44875249 original size:16 final size:18
Alignment explanation
Indices: 44875228--44875261 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
44875218 TGTAGCTAAT
44875228 TAAATTTT-TG-AATTAG
1 TAAATTTTGTGAAATTAG
44875244 TAAATTTTGTGAAATTAG
1 TAAATTTTGTGAAATTAG
44875262 GAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (18 bp):
TAAATTTTGTGAAATTAG
Found at i:44875487 original size:16 final size:18
Alignment explanation
Indices: 44875455--44875487 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
44875445 ATATATTATA
44875455 ATAATTAAAATGAAAGAT
1 ATAATTAAAATGAAAGAT
44875473 ATAA-TAAAA-GAAAGA
1 ATAATTAAAATGAAAGA
44875488 AAAAGAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
ATAATTAAAATGAAAGAT
Found at i:44875536 original size:13 final size:13
Alignment explanation
Indices: 44875518--44875548 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
44875508 CATGCAAATT
44875518 AGAAAAGAAAAAA
1 AGAAAAGAAAAAA
*
44875531 AGAAAAGAAAGAA
1 AGAAAAGAAAAAA
44875544 AGAAA
1 AGAAA
44875549 TGGAGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAAAA
Found at i:44876287 original size:25 final size:25
Alignment explanation
Indices: 44876239--44876287 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
44876229 CATAATTGAA
* * *
44876239 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
44876264 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
44876288 AGGTGTGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:44876693 original size:43 final size:43
Alignment explanation
Indices: 44876645--44876730 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
44876635 TATATGATTG
* *
44876645 ATATTGGAATGGAAAA-GATGATAAATGAAAACGAGATGAGAAA
1 ATATTGAAAT-GAAAATGATGAAAAATGAAAACGAGATGAGAAA
* ** *
44876688 ATATTGAAATGAAAATTATGAAAAATGATTATGAGATGAGAAA
1 ATATTGAAATGAAAATGATGAAAAATGAAAACGAGATGAGAAA
44876731 TGAAATATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
42 5 0.14
43 31 0.86
ACGTcount: A:0.53, C:0.01, G:0.22, T:0.23
Consensus pattern (43 bp):
ATATTGAAATGAAAATGATGAAAAATGAAAACGAGATGAGAAA
Found at i:44878970 original size:100 final size:99
Alignment explanation
Indices: 44878852--44879040 Score: 263
Period size: 100 Copynumber: 1.9 Consensus size: 99
44878842 TAAAATATTG
* * *
44878852 AATGTTTAAATGTTTAAATGTTTCCGATTGTATGGTAATGC-TCCATAACCCTAATCTAGCGACG
1 AATGTTAAAATGTTTAAATGTTTCCGATTGTACGGTAATGCAT-CATAACCCTAATCCAGCGACG
* * *
44878916 GAGACGGGTTAGGGGTGTTACATTTAGAAATTCTTC
65 AAGACAGGTTAGGGATGTTAC-TTTAGAAATTCTTC
* * * *
44878952 AATGTTAAAATGTTTAAATGTTTTCGATTGTACGGTAATGCATCGTAACCCTAATCCAGTGATGA
1 AATGTTAAAATGTTTAAATGTTTCCGATTGTACGGTAATGCATCATAACCCTAATCCAGCGACGA
44879017 AGACAGGTTAGGGATGTTACTTTA
66 AGACAGGTTAGGGATGTTACTTTA
44879041 TATGTAGGTA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
99 4 0.05
100 73 0.94
101 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (99 bp):
AATGTTAAAATGTTTAAATGTTTCCGATTGTACGGTAATGCATCATAACCCTAATCCAGCGACGA
AGACAGGTTAGGGATGTTACTTTAGAAATTCTTC
Found at i:44894187 original size:22 final size:23
Alignment explanation
Indices: 44894159--44894206 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
44894149 CACGGGAATG
44894159 GCAATTTATC-GCATTTTTACTA
1 GCAATTTATCTGCATTTTTACTA
* **
44894181 GCAATTTGTCTGTGTTTTTACTA
1 GCAATTTATCTGCATTTTTACTA
44894204 GCA
1 GCA
44894207 TAATTTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.46
Consensus pattern (23 bp):
GCAATTTATCTGCATTTTTACTA
Found at i:44895498 original size:29 final size:29
Alignment explanation
Indices: 44895445--44895502 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
44895435 CCAACTAGAT
*
44895445 GGCCTAGCACACGACCGTGTAGATCACAC
1 GGCCTAGCACACGACCATGTAGATCACAC
* * *
44895474 GGCCTGGCACACGGCCATGTGGATCACAC
1 GGCCTAGCACACGACCATGTAGATCACAC
44895503 AGCTTGGGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.34, G:0.28, T:0.14
Consensus pattern (29 bp):
GGCCTAGCACACGACCATGTAGATCACAC
Found at i:44896049 original size:15 final size:14
Alignment explanation
Indices: 44896030--44896074 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
44896020 TTTGAAGGAG
44896030 TAAAAAGAAGAAAA
1 TAAAAAGAAGAAAA
* *
44896044 GAAAAAGAACAAAAA
1 TAAAAAGAA-GAAAA
44896059 TAAAAAGAAAGAAAA
1 TAAAAAG-AAGAAAA
44896074 T
1 T
44896075 GGAAGAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 8 0.32
15 15 0.60
16 2 0.08
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (14 bp):
TAAAAAGAAGAAAA
Found at i:44898952 original size:11 final size:11
Alignment explanation
Indices: 44898936--44898961 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44898926 AGGTCCAAGG
44898936 TAAGTTGATTT
1 TAAGTTGATTT
44898947 TAAGTTGATTT
1 TAAGTTGATTT
44898958 TAAG
1 TAAG
44898962 GTTGTTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (11 bp):
TAAGTTGATTT
Found at i:44902827 original size:32 final size:32
Alignment explanation
Indices: 44902791--44902873 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
44902781 ACAATTATGG
* * *
44902791 AACCTAGTTTTGAGGTTTACTTATGATTTAA-A
1 AACCTAGTTGTGAGGCTTACTGATGA-TTAAGA
*
44902823 AACCTAGTTGTAAGGCTTACTGATGATTAAGA
1 AACCTAGTTGTGAGGCTTACTGATGATTAAGA
44902855 AACCTAGTTGTGAGGCTTA
1 AACCTAGTTGTGAGGCTTA
44902874 TTGAGGTTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
31 4 0.09
32 41 0.91
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (32 bp):
AACCTAGTTGTGAGGCTTACTGATGATTAAGA
Found at i:44903230 original size:31 final size:32
Alignment explanation
Indices: 44903195--44903259 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
44903185 AAGCCGAGCA
*
44903195 TTAAGGTCCATATTAA-TTTATAA-ACCTAGTT
1 TTAAGGCCCATATTAATTTTA-AAGACCTAGTT
* *
44903226 TTAAGGCCCATTTTTATTTTAAAGACCTAGTT
1 TTAAGGCCCATATTAATTTTAAAGACCTAGTT
44903258 TT
1 TT
44903260 GACATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (32 bp):
TTAAGGCCCATATTAATTTTAAAGACCTAGTT
Found at i:44909062 original size:29 final size:30
Alignment explanation
Indices: 44909023--44909083 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
44909013 CAAATTTTTT
44909023 TATATAAAATT-ACATAAAACCAAAATTTA
1 TATATAAAATTAACATAAAACCAAAATTTA
* * *
44909052 TATATACAATTACACATTAAACCATAATTTA
1 TATATAAAATTA-ACATAAAACCAAAATTTA
44909083 T
1 T
44909084 TTTGCCCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 10 0.37
31 17 0.63
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (30 bp):
TATATAAAATTAACATAAAACCAAAATTTA
Found at i:44913965 original size:18 final size:17
Alignment explanation
Indices: 44913920--44913971 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
44913910 GTAATAAAAT
**
44913920 AAAATAAAAACAAATGCA
1 AAAATAAAAA-AAATTAA
44913938 AAAATGAAAAAAAATTAA
1 AAAAT-AAAAAAAATTAA
*
44913956 GAAAATAAAATAAATT
1 -AAAATAAAAAAAATT
44913972 GGTAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 19 0.66
19 10 0.34
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATAAAAAAAATTAA
Found at i:44914819 original size:23 final size:23
Alignment explanation
Indices: 44914792--44914843 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
44914782 TAGATTTTTC
44914792 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
* *
44914815 CTAAATGTTATCATTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
44914838 CAAAAT
1 CTAAAT
44914844 TTAAAAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:44914870 original size:12 final size:12
Alignment explanation
Indices: 44914853--44914877 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44914843 TTTAAAAATT
44914853 GAATTTAAACTA
1 GAATTTAAACTA
44914865 GAATTTAAACTA
1 GAATTTAAACTA
44914877 G
1 G
44914878 TTACAGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (12 bp):
GAATTTAAACTA
Found at i:44916204 original size:11 final size:11
Alignment explanation
Indices: 44916188--44916213 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44916178 GTAGGAAGGG
44916188 GAAAGAAAAAA
1 GAAAGAAAAAA
44916199 GAAAGAAAAAA
1 GAAAGAAAAAA
44916210 GAAA
1 GAAA
44916214 TTATTAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAGAAAAAA
Found at i:44916339 original size:23 final size:23
Alignment explanation
Indices: 44916307--44916371 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
44916297 TAGATTTTTC
*
44916307 CTAAACATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
44916330 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
44916353 CTAAATATTATCACTAAAT
1 CTAAATATTATCACTAAAT
44916372 TTGAAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:44916348 original size:13 final size:13
Alignment explanation
Indices: 44916307--44916371 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
44916297 TAGATTTTTC
*
44916307 CTAAACATTATCA
1 CTAAATATTATCA
*
44916320 CTAAATA--AT-T
1 CTAAATATTATCA
44916330 CTAAATATTATCA
1 CTAAATATTATCA
*
44916343 CTAAATA--AT-T
1 CTAAATATTATCA
44916353 CTAAATATTATCA
1 CTAAATATTATCA
44916366 CTAAAT
1 CTAAAT
44916372 TTGAAATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
10 14 0.34
11 4 0.10
12 4 0.10
13 19 0.46
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:44917255 original size:4 final size:4
Alignment explanation
Indices: 44917246--44917287 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
44917236 TTAACCAAGC
44917246 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TA
44917288 AAAGAGTACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:44921681 original size:23 final size:23
Alignment explanation
Indices: 44921630--44921675 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
44921620 TAGATTTTTC
*
44921630 CTAAACATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
44921653 CTAAATATTATCATTAAATAATT
1 CTAAATATTATCACTAAATAATT
44921676 TGAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:44921708 original size:12 final size:12
Alignment explanation
Indices: 44921691--44921715 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44921681 TTTAAAAATT
44921691 GAATTTAAACTA
1 GAATTTAAACTA
44921703 GAATTTAAACTA
1 GAATTTAAACTA
44921715 G
1 G
44921716 TTACAGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (12 bp):
GAATTTAAACTA
Found at i:44922711 original size:9 final size:9
Alignment explanation
Indices: 44922697--44922727 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44922687 GTTAAACAAA
44922697 TCGAGTTAT
1 TCGAGTTAT
*
44922706 TCGAGTTAA
1 TCGAGTTAT
44922715 TCGAGTTAT
1 TCGAGTTAT
44922724 TCGA
1 TCGA
44922728 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:44924269 original size:20 final size:20
Alignment explanation
Indices: 44924244--44924290 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
44924234 ATATCTCGTT
44924244 TTGATTTGATTTTAATCAAA
1 TTGATTTGATTTTAATCAAA
*
44924264 TTGATTTGATTTTATTCAAA
1 TTGATTTGATTTTAATCAAA
44924284 TTGATTT
1 TTGATTT
44924291 AAAGGCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (20 bp):
TTGATTTGATTTTAATCAAA
Found at i:44924699 original size:6 final size:6
Alignment explanation
Indices: 44924672--44924713 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
44924662 ATTTGTTCAA
**
44924672 ATATTT -TATTT AATATAA ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT -ATATTT ATATTT ATATTT ATATTT ATATTT
44924714 GTTTGCTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 5 0.17
6 22 0.73
7 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
ATATTT
Found at i:44925665 original size:32 final size:31
Alignment explanation
Indices: 44925624--44925686 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 31
44925614 CATAGATGTT
44925624 TAATAATAATCTCTTAATGTTGCATTGTTCA
1 TAATAATAATCTCTTAATGTTGCATTGTTCA
44925655 NTAATAATAATCTCTTAATGTTGCATTGTTCA
1 -TAATAATAATCTCTTAATGTTGCATTGTTCA
44925687 ACGAGGGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (31 bp):
TAATAATAATCTCTTAATGTTGCATTGTTCA
Found at i:44926656 original size:76 final size:77
Alignment explanation
Indices: 44926530--44926683 Score: 267
Period size: 76 Copynumber: 2.0 Consensus size: 77
44926520 GTTTGGGTAA
44926530 TCCACGGGCAATTAGAAGACTCTAGCATGTGCTGAAGATGTATAATCCCCAGGTAGTC-TTTTTT
1 TCCACGGGCAATTAGAAGACTCTAGCATGTGCTGAAGATGTATAATCCCCAGGTAGTCTTTTTTT
44926594 GTGGAGACTAAG
66 GTGGAGACTAAG
* *
44926606 TCCACGGGCAGTTAGAAGACT-TCGGCATGTGCTGAAGATGTATAATCCCCAGGTAGTCTTTTTT
1 TCCACGGGCAATTAGAAGACTCT-AGCATGTGCTGAAGATGTATAATCCCCAGGTAGTCTTTTTT
44926670 TGTGGAGACTAAG
65 TGTGGAGACTAAG
44926683 T
1 T
44926684 TATGCAAGGT
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
75 1 0.01
76 54 0.73
77 19 0.26
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (77 bp):
TCCACGGGCAATTAGAAGACTCTAGCATGTGCTGAAGATGTATAATCCCCAGGTAGTCTTTTTTT
GTGGAGACTAAG
Found at i:44938518 original size:31 final size:31
Alignment explanation
Indices: 44938474--44938549 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
44938464 ATCACACTAG
* * *
44938474 TAGTCTTCTAACTATTAGCCAATTTCTTTTT
1 TAGTCATCTAACTATTAGCAAATTTATTTTT
* *
44938505 TAGTCATCCAACTATTAGTAAATTTATTTTT
1 TAGTCATCTAACTATTAGCAAATTTATTTTT
*
44938536 TGGTCATCTAACTA
1 TAGTCATCTAACTA
44938550 AGAAAAGTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (31 bp):
TAGTCATCTAACTATTAGCAAATTTATTTTT
Found at i:44939129 original size:18 final size:17
Alignment explanation
Indices: 44939101--44939134 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
44939091 TTAATCACTT
44939101 TAATATTAAATTTAATC
1 TAATATTAAATTTAATC
44939118 TAATATTTAAATTTAAT
1 TAATA-TTAAATTTAAT
44939135 ATTAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTAAATTTAATC
Found at i:44941220 original size:29 final size:29
Alignment explanation
Indices: 44941187--44941247 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
44941177 ACAAAATTGA
*
44941187 ATAATTAGGTGATCATTCTGTAACTTTTC
1 ATAATTAGGTGACCATTCTGTAACTTTTC
* *
44941216 ATAATTGGGTGACCATTTTGTAACTTTTC
1 ATAATTAGGTGACCATTCTGTAACTTTTC
44941245 ATA
1 ATA
44941248 TTTGAGTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (29 bp):
ATAATTAGGTGACCATTCTGTAACTTTTC
Found at i:44942708 original size:24 final size:24
Alignment explanation
Indices: 44942670--44942817 Score: 104
Period size: 24 Copynumber: 6.2 Consensus size: 24
44942660 CTAGCATGTA
* * *
44942670 ACCTGCAAACCCCTATCACCAAAT
1 ACCTGCGAACACCTATCACCAGAT
* * * *
44942694 ACCTACGAACACCTATTACTAGAC
1 ACCTGCGAACACCTATCACCAGAT
*
44942718 ACATGCGAAC-CCTATCACCAGAT
1 ACCTGCGAACACCTATCACCAGAT
* *
44942741 ACCTGTGAACACCTATCACCAGAC
1 ACCTGCGAACACCTATCACCAGAT
* * * * *
44942765 ACATGC-AAAACACTACCACTAGAC
1 ACCTGCGAACAC-CTATCACCAGAT
* *
44942789 ACATGCGAAC-CCATATCACCAGAC
1 ACCTGCGAACACC-TATCACCAGAT
44942813 ACCTG
1 ACCTG
44942818 TAAATCCCTA
Statistics
Matches: 96, Mismatches: 24, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
23 23 0.24
24 71 0.74
25 2 0.02
ACGTcount: A:0.37, C:0.36, G:0.10, T:0.16
Consensus pattern (24 bp):
ACCTGCGAACACCTATCACCAGAT
Found at i:44942751 original size:47 final size:47
Alignment explanation
Indices: 44942680--44942770 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
44942670 ACCTGCAAAC
* *
44942680 CCCTATCACCAAATACCTACGAACACCTATTACTAGACACATGCGAA
1 CCCTATCACCAAATACCTACGAACACCTATCACCAGACACATGCGAA
* **
44942727 CCCTATCACCAGATACCTGTGAACACCTATCACCAGACACATGC
1 CCCTATCACCAAATACCTACGAACACCTATCACCAGACACATGC
44942771 AAAACACTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.35, C:0.36, G:0.10, T:0.19
Consensus pattern (47 bp):
CCCTATCACCAAATACCTACGAACACCTATCACCAGACACATGCGAA
Found at i:44944863 original size:46 final size:46
Alignment explanation
Indices: 44944809--44944937 Score: 170
Period size: 46 Copynumber: 2.8 Consensus size: 46
44944799 AGTGTATTGA
* * *
44944809 ATCGGGCCTTGAGCCTAGCAGGTTTTATGCCGGTGTATTTTAATGT
1 ATCGGGCCTTGAGCCTAGCAGGTTTTATACCGGTGTACTGTAATGT
*
44944855 ATCGGGCCTTGTGCCTAGCAGGTTTTATACCGGTGTACTGTAATGT
1 ATCGGGCCTTGAGCCTAGCAGGTTTTATACCGGTGTACTGTAATGT
* * * *
44944901 ATCAGGCCTTGTA-CCTAGCAGGCTTCATATCGGTGTA
1 ATCGGGCCTTG-AGCCTAGCAGGTTTTATACCGGTGTA
44944938 TCTATTAGGC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (46 bp):
ATCGGGCCTTGAGCCTAGCAGGTTTTATACCGGTGTACTGTAATGT
Found at i:44946365 original size:23 final size:24
Alignment explanation
Indices: 44946338--44946416 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
44946328 GACACCTGCA
*
44946338 AACCCCTAT-ACCAGACACCTATG
1 AACCCCTATCACCAGACACATATG
* *
44946361 GACCCCTATCACTAGACACATATG
1 AACCCCTATCACCAGACACATATG
** * **
44946385 AACCCCTATTTCCAGATACATGCG
1 AACCCCTATCACCAGACACATATG
44946409 AACCCCTA
1 AACCCCTA
44946417 CAGTGAACCC
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 8 0.18
24 37 0.82
ACGTcount: A:0.33, C:0.37, G:0.10, T:0.20
Consensus pattern (24 bp):
AACCCCTATCACCAGACACATATG
Found at i:44948560 original size:17 final size:16
Alignment explanation
Indices: 44948540--44948579 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
44948530 ATGGAATTAG
44948540 AATTTACTTGAAAAAAT
1 AATTTAC-TGAAAAAAT
44948557 AATTTAACTGAAAAAAT
1 AATTT-ACTGAAAAAAT
*
44948574 TATTTA
1 AATTTA
44948580 AATTCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.86
18 2 0.10
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (16 bp):
AATTTACTGAAAAAAT
Found at i:44948580 original size:17 final size:17
Alignment explanation
Indices: 44948548--44948580 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44948538 AGAATTTACT
44948548 TGAAAAAATAATTTAAC
1 TGAAAAAATAATTTAAC
*
44948565 TGAAAAAATTATTTAA
1 TGAAAAAATAATTTAA
44948581 ATTCATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (17 bp):
TGAAAAAATAATTTAAC
Found at i:44951983 original size:24 final size:24
Alignment explanation
Indices: 44951927--44952002 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
44951917 CCGGATAATA
* *
44951927 TAACGGGAAGCTCACAAAGAGC-CT
1 TAACGGGTAGCTC-CAAAGAGCAAT
44951951 ATAAC-GGTAGCTCCAAAGAGCAAT
1 -TAACGGGTAGCTCCAAAGAGCAAT
44951975 TAACGGGTAGCTCCAAAGAGCAAT
1 TAACGGGTAGCTCCAAAGAGCAAT
44951999 TAAC
1 TAAC
44952003 AGGAAGCACC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.26
24 31 0.66
25 4 0.09
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (24 bp):
TAACGGGTAGCTCCAAAGAGCAAT
Found at i:44954358 original size:25 final size:24
Alignment explanation
Indices: 44954330--44954377 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
44954320 AGATACTTTT
*
44954330 TTTATTATAAAATATCACATTTTAG
1 TTTATTATAAAATAT-AAATTTTAG
44954355 TTTATTATAAAATATAAATTTTA
1 TTTATTATAAAATATAAATTTTA
44954378 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTATTATAAAATATAAATTTTAG
Found at i:44957076 original size:28 final size:27
Alignment explanation
Indices: 44957029--44957081 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
44957019 TTTTTATTAA
44957029 TTTTTATATTTAAAATTTTTAAAATGT
1 TTTTTATATTTAAAATTTTTAAAATGT
*
44957056 TTTTATATATTTTTAAA-TTTTAAAAT
1 TTTT-TATA-TTTAAAATTTTTAAAAT
44957082 AATAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 13 0.57
29 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTTATATTTAAAATTTTTAAAATGT
Found at i:44976283 original size:72 final size:72
Alignment explanation
Indices: 44976166--44976304 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 72
44976156 GATATACAAT
* * *
44976166 AATGATACATGGGAATAGGTTGATAAGTCAGTCCAGAAAATAATCATTAGTGTAACATGGGTATT
1 AATGATACATAGGAATAGGTTGATAAGTCAGTCCAGAAAAGAATCATTAGTGTAACATAGGTATT
44976231 CAGGACC
66 CAGGACC
* *
44976238 AATGATACATAGGAACT-GGTTGATAGGTCAGTCCAGAAAAGAATCATTGGTGTAACATAGGTAT
1 AATGATACATAGGAA-TAGGTTGATAAGTCAGTCCAGAAAAGAATCATTAGTGTAACATAGGTAT
44976302 TCA
65 TCA
44976305 ATACCAAGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 60 0.98
73 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (72 bp):
AATGATACATAGGAATAGGTTGATAAGTCAGTCCAGAAAAGAATCATTAGTGTAACATAGGTATT
CAGGACC
Found at i:44984044 original size:69 final size:69
Alignment explanation
Indices: 44983842--44984051 Score: 287
Period size: 69 Copynumber: 3.0 Consensus size: 69
44983832 TCATCTGTAA
* * * * *
44983842 CCTTAATATGATAGCTGAGAGTTTTGCTCTCACTAACTGTGTTGGAGGCTGTGGCTCTTCATCTA
1 CCTTAATATGATAGCTGAGAGCTTTGCTCTCACTAACTGTGTTAGAGGCTATGGCTCTTCACCTG
44983907 CGAG
66 CGAG
**
44983911 CCTTAATATGATAGCTGAGAGCTTTGCTCTCACTAACTGTGTTAGAGGCTACAGCTCTTCACCTG
1 CCTTAATATGATAGCTGAGAGCTTTGCTCTCACTAACTGTGTTAGAGGCTATGGCTCTTCACCTG
44983976 CGAG
66 CGAG
* * * **
44983980 CCTTAATATGACAGCTG-GGGACTTTGCTCTCGCTAACTGTGTTAGAGATTATGGCTCTTCACCT
1 CCTTAATATGATAGCTGAGAG-CTTTGCTCTCACTAACTGTGTTAGAGGCTATGGCTCTTCACCT
*
44984044 GTGAG
65 GCGAG
44984049 CCT
1 CCT
44984052 CTTCACCTGC
Statistics
Matches: 125, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
68 2 0.02
69 123 0.98
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (69 bp):
CCTTAATATGATAGCTGAGAGCTTTGCTCTCACTAACTGTGTTAGAGGCTATGGCTCTTCACCTG
CGAG
Found at i:44984066 original size:16 final size:16
Alignment explanation
Indices: 44984034--44984067 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44984024 GAGATTATGG
**
44984034 CTCTTCACCTGTGAGC
1 CTCTTCACCTGCAAGC
44984050 CTCTTCACCTGCAAGC
1 CTCTTCACCTGCAAGC
44984066 CT
1 CT
44984068 TAATAATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.29
Consensus pattern (16 bp):
CTCTTCACCTGCAAGC
Found at i:45004808 original size:44 final size:46
Alignment explanation
Indices: 45004721--45004808 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 46
45004711 TTTCTTTAGT
* *
45004721 TTATATATAATATAATATAATATAATTAAAACATAAAATATCTTTA
1 TTATATATAATATAATATAATATAACTAAAACATAAAAAATCTTTA
45004767 TTATATAATAATAT-A-ATAATAT-ACT-AAACATAAAAAAATCTT
1 TTATAT-ATAATATAATATAATATAACTAAAACAT-AAAAAATCTT
45004809 AGATTTTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
43 6 0.16
44 11 0.29
45 7 0.18
46 7 0.18
47 7 0.18
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (46 bp):
TTATATATAATATAATATAATATAACTAAAACATAAAAAATCTTTA
Found at i:45011829 original size:13 final size:13
Alignment explanation
Indices: 45011813--45011846 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
45011803 TTTTAAATCA
45011813 TACTTTTCAAAAG
1 TACTTTTCAAAAG
*
45011826 TACTTCTCAAAAG
1 TACTTTTCAAAAG
*
45011839 TATTTTTC
1 TACTTTTC
45011847 TATAGCACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (13 bp):
TACTTTTCAAAAG
Found at i:45011939 original size:33 final size:34
Alignment explanation
Indices: 45011901--45011970 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
45011891 TAAAATTGCT
*
45011901 ATTTAAATTCTT-AAATTTTTTTAAAAATTTTAA
1 ATTTAAATTCTTAAAATTTTTTTAAAAAATTTAA
45011934 ATTTAAATTCTTAAAATTTTTTTAAAAAATTTAA
1 ATTTAAATTCTTAAAATTTTTTTAAAAAATTTAA
45011968 ATT
1 ATT
45011971 AGTAAAGGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 12 0.34
34 23 0.66
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (34 bp):
ATTTAAATTCTTAAAATTTTTTTAAAAAATTTAA
Found at i:45013261 original size:32 final size:32
Alignment explanation
Indices: 45013219--45013283 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
45013209 ACAAATGATG
45013219 TCATTGGTGATAATCCATTCTCCATCATGGAA
1 TCATTGGTGATAATCCATTCTCCATCATGGAA
*
45013251 TCATTTGTGATAATCCATTCTCCATCATGGAA
1 TCATTGGTGATAATCCATTCTCCATCATGGAA
45013283 T
1 T
45013284 GCCAACCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (32 bp):
TCATTGGTGATAATCCATTCTCCATCATGGAA
Found at i:45016556 original size:12 final size:12
Alignment explanation
Indices: 45016526--45016558 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
45016516 TATATATTTT
45016526 AAAATT-ATATA
1 AAAATTAATATA
45016537 AAAA-TAATATA
1 AAAATTAATATA
45016548 AAAATTAATAT
1 AAAATTAATAT
45016559 GGACTGATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:45027739 original size:18 final size:17
Alignment explanation
Indices: 45027712--45027746 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
45027702 GAGATGGCAA
45027712 TTTTATTTATTGTTTAT
1 TTTTATTTATTGTTTAT
45027729 TTTTAATTTATTGTTTAT
1 TTTT-ATTTATTGTTTAT
45027747 AATTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTATTTATTGTTTAT
Found at i:45027755 original size:18 final size:17
Alignment explanation
Indices: 45027713--45027755 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
45027703 AGATGGCAAT
*
45027713 TTTATTTATTGTTTATT
1 TTTATTTATTGTTTATA
45027730 TTTAATTTATTGTTTATAA
1 TTT-ATTTATTGTTTAT-A
45027749 TTTATTT
1 TTTATTT
45027756 TTATTAGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
TTTATTTATTGTTTATA
Found at i:45027965 original size:21 final size:23
Alignment explanation
Indices: 45027937--45027989 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
45027927 TTTTCATATT
45027937 TTTA-TTTTATTT-ATTC-AAAA
1 TTTATTTTTATTTAATTCTAAAA
*
45027957 TTTATTTTTATTTAATTCTAATA
1 TTTATTTTTATTTAATTCTAAAA
*
45027980 TATATTTTTA
1 TTTATTTTTA
45027990 AAATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 8 0.29
22 4 0.14
23 12 0.43
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTATTTTTATTTAATTCTAAAA
Found at i:45028021 original size:15 final size:15
Alignment explanation
Indices: 45027984--45028028 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
45027974 CTAATATATA
45027984 TTTTTAAAATTTTAT
1 TTTTTAAAATTTTAT
45027999 TTTATTAAAACTTTT-T
1 TTT-TTAAAA-TTTTAT
45028015 TTTTTAAAATTTTA
1 TTTTTAAAATTTTA
45028029 AAATTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 10 0.37
17 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTAAAATTTTAT
Found at i:45034035 original size:28 final size:28
Alignment explanation
Indices: 45034003--45034072 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
45033993 TATGGTACTC
*
45034003 AGTGTACGAAATATTGAGAATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
* *
45034031 AGTGTGCGAGATATTGAGGATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
*
45034059 AGTGTGCAAAATAT
1 AGTGTGCGAAATAT
45034073 CGAATGATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (28 bp):
AGTGTGCGAAATATTGAGAATGACACTT
Found at i:45053432 original size:29 final size:29
Alignment explanation
Indices: 45053384--45053448 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
45053374 ACCGACCGAG
*
45053384 TTCGGTTAATCGGTCGGTTAACTGAAAAAA
1 TTCGG-TAATCGGTCGGTTAACCGAAAAAA
45053414 TTCGGTAATCGGTCGGTTAACCGAAAAAA
1 TTCGGTAATCGGTCGGTTAACCGAAAAAA
45053443 TTCGGT
1 TTCGGT
45053449 CGGGGTCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 29 0.85
30 5 0.15
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (29 bp):
TTCGGTAATCGGTCGGTTAACCGAAAAAA
Found at i:45053759 original size:9 final size:9
Alignment explanation
Indices: 45053745--45053770 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
45053735 TCTCCTCCCT
45053745 AATTTCACA
1 AATTTCACA
45053754 AATTTCACA
1 AATTTCACA
45053763 AATTTCAC
1 AATTTCAC
45053771 TTTCACACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
AATTTCACA
Found at i:45057611 original size:24 final size:24
Alignment explanation
Indices: 45057554--45057612 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
45057544 GGTTTAATGC
* *
45057554 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
*
45057578 AAATGAATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
45057602 AAATGGATATA
1 AAATGGATATA
45057613 AATGGAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:45057704 original size:20 final size:19
Alignment explanation
Indices: 45057678--45057742 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
45057668 AATATTTTTA
45057678 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
* ***
45057697 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCAAAG
45057715 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
45057734 ATTTATGTA
1 A-TTATGTA
45057743 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
ATTATGTAGTGATTCAAAG
Found at i:45057707 original size:37 final size:37
Alignment explanation
Indices: 45057653--45057765 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
45057643 TTATGTTTTA
*
45057653 ATTC-AAGACTTGTGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
45057689 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* *
45057726 ATTCAAAGATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
45057763 ATT
1 ATT
45057766 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:45057721 original size:17 final size:17
Alignment explanation
Indices: 45057665--45057759 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 17
45057655 TCAAGACTTG
45057665 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
45057682 TGTAGTGATTCAAAGACTTA
1 TGTAAT-ATTTTTA-A-TTA
45057702 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
45057719 TGTAGTGATTCAAAGATTTA
1 TGTAAT-ATTTTTA-A-TTA
*
45057739 TGTAATGTTTTTAATTA
1 TGTAATATTTTTAATTA
45057756 TGTA
1 TGTA
45057760 GTGATTTAAT
Statistics
Matches: 55, Mismatches: 17, Indels: 12
0.65 0.20 0.14
Matches are distributed among these distances:
17 20 0.36
18 10 0.18
19 9 0.16
20 16 0.29
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (17 bp):
TGTAATATTTTTAATTA
Found at i:45057780 original size:9 final size:9
Alignment explanation
Indices: 45057766--45057902 Score: 193
Period size: 9 Copynumber: 14.6 Consensus size: 9
45057756 TGTAGTGATT
45057766 TAATTCGGG
1 TAATTCGGG
45057775 TAATTCGGG
1 TAATTCGGG
45057784 TAATTTTCGGG
1 TAA--TTCGGG
45057795 TAATTTTCGGG
1 TAA--TTCGGG
*
45057806 TAATTTGGG
1 TAATTCGGG
45057815 TAATTTTCGGG
1 TAA--TTCGGG
45057826 TAATTCGGG
1 TAATTCGGG
45057835 TAATTCGGG
1 TAATTCGGG
45057844 TAATTCGGG
1 TAATTCGGG
*
45057853 TAAGTCGGG
1 TAATTCGGG
45057862 TAATTCGGG
1 TAATTCGGG
*
45057871 TAAGTCGGG
1 TAATTCGGG
45057880 TAATTCGGG
1 TAATTCGGG
45057889 TAATTCGGG
1 TAATTCGGG
45057898 TAATT
1 TAATT
45057903 TTTAACCAAA
Statistics
Matches: 118, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
9 90 0.76
11 28 0.24
ACGTcount: A:0.22, C:0.09, G:0.32, T:0.36
Consensus pattern (9 bp):
TAATTCGGG
Found at i:45058040 original size:28 final size:27
Alignment explanation
Indices: 45058008--45058073 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
45057998 AAAATTCGGT
45058008 TCGGTTAACGGTTA-AAAAATTTGAGAGG
1 TCGGTTAACGGTTACAAAAATTT-AG-GG
* *
45058036 TCGGTTAATTCGGTTACAAGAATTTCGGG
1 TCGGTTAA--CGGTTACAAAAATTTAGGG
45058065 TCGGTTAAC
1 TCGGTTAAC
45058074 CGACTGAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 8 0.24
29 10 0.30
30 7 0.21
31 7 0.21
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (27 bp):
TCGGTTAACGGTTACAAAAATTTAGGG
Found at i:45058922 original size:20 final size:20
Alignment explanation
Indices: 45058851--45058963 Score: 70
Period size: 20 Copynumber: 5.7 Consensus size: 20
45058841 TTGGCATACC
*
45058851 AAAATTTCTAA-GATTTTATT
1 AAAATTTCTAAGGA-TTTACT
* * * *
45058871 GAAGTTTATAAGG-TTATACC
1 AAAATTTCTAAGGATT-TACT
* *
45058891 AAAATATGTAAGGATTTACT
1 AAAATTTCTAAGGATTTACT
* *
45058911 AGAATTTTTAAGG-TTATACT
1 AAAATTTCTAAGGATT-TACT
*
45058931 AAAATTTCTAAGGATTTATT
1 AAAATTTCTAAGGATTTACT
* *
45058951 AATATATCTAAGG
1 AAAATTTCTAAGG
45058964 GTTTTTACCA
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
19 4 0.06
20 61 0.87
21 5 0.07
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (20 bp):
AAAATTTCTAAGGATTTACT
Found at i:45058963 original size:40 final size:39
Alignment explanation
Indices: 45058846--45058989 Score: 114
Period size: 40 Copynumber: 3.6 Consensus size: 39
45058836 ACATTTTGGC
45058846 ATACCAAAATTTCTAA-GATTTTATTGAAGT-TTATAAGGTT
1 ATACCAAAATTTCTAAGGA-TTTATT-AA-TATTATAAGGTT
* * * *
45058886 ATACCAAAATATGTAAGGATTTACTAGA-ATTTTTAAGGTT
1 ATACCAAAATTTCTAAGGATTTATTA-ATA-TTATAAGGTT
* *
45058926 ATACTAAAATTTCTAAGGATTTATTAATATATCTAAGGGTTT
1 ATACCAAAATTTCTAAGGATTTATTAATAT-TATAA-GG-TT
* * *
45058968 TTACCAAAATTTCAAAAGATTT
1 ATACCAAAATTTCTAAGGATTT
45058990 CCTTAGTGCC
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
39 3 0.04
40 56 0.67
41 4 0.05
42 20 0.24
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (39 bp):
ATACCAAAATTTCTAAGGATTTATTAATATTATAAGGTT
Found at i:45059056 original size:20 final size:21
Alignment explanation
Indices: 45059031--45059090 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
45059021 TCTTGGCATG
45059031 CTAAAATTTCCAAGGATTT-T
1 CTAAAATTTCCAAGGATTTAT
* *
45059051 CTAAAATTTCTAAAGATTTAT
1 CTAAAATTTCCAAGGATTTAT
* *
45059072 C-AAAATTTACGAGGATTTA
1 CTAAAATTTCCAAGGATTTA
45059091 CAAAACTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
CTAAAATTTCCAAGGATTTAT
Found at i:45059116 original size:40 final size:40
Alignment explanation
Indices: 45059033--45059117 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
45059023 TTGGCATGCT
* * *
45059033 AAAATTTCCAAGGATTTTCTAAAATTTCTAAAGATTTATC
1 AAAATTTACAAGGATTTACTAAAATTTCTAAAGATTTACC
* *
45059073 AAAATTTACGAGGATTTAC-AAAACTTTCTAACG-TTATACC
1 AAAATTTACAAGGATTTACTAAAA-TTTCTAAAGATT-TACC
45059113 AAAAT
1 AAAAT
45059118 ACCTAACGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 6 0.16
40 32 0.84
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.35
Consensus pattern (40 bp):
AAAATTTACAAGGATTTACTAAAATTTCTAAAGATTTACC
Found at i:45059125 original size:20 final size:20
Alignment explanation
Indices: 45059100--45059158 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
45059090 ACAAAACTTT
45059100 CTAACGTTATACCAAAATAC
1 CTAACGTTATACCAAAATAC
* **
45059120 CTAACGGTT-TACCCAAATTT
1 CTAAC-GTTATACCAAAATAC
* *
45059140 CTAAAGTTATATCAAAATA
1 CTAACGTTATACCAAAATA
45059159 TTTATAGATT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (20 bp):
CTAACGTTATACCAAAATAC
Found at i:45059178 original size:40 final size:40
Alignment explanation
Indices: 45059053--45059179 Score: 102
Period size: 40 Copynumber: 3.2 Consensus size: 40
45059043 AGGATTTTCT
*
45059053 AAAATTTCTAAAGATT-TATC-AAA-ATTTACGAGGATTT-AC
1 AAAATTTCTAAAG-TTATATCAAAATATTTA--ACGATTTAAC
* * ** * *
45059092 AAAACTTTCTAACGTTATACCAAAATACCTAACGGTTTACC
1 AAAA-TTTCTAAAGTTATATCAAAATATTTAACGATTTAAC
*
45059133 CAAATTTCTAAAGTTATATCAAAATATTTATA-GATTTAAC
1 AAAATTTCTAAAGTTATATCAAAATATTTA-ACGATTTAAC
45059173 AAAATTT
1 AAAATTT
45059180 AAATATCTAA
Statistics
Matches: 67, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
39 6 0.09
40 50 0.75
41 8 0.12
42 3 0.04
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (40 bp):
AAAATTTCTAAAGTTATATCAAAATATTTAACGATTTAAC
Found at i:45059290 original size:37 final size:37
Alignment explanation
Indices: 45059236--45059308 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
45059226 TGATAAGTCC
45059236 TTAGATTTTTTTGATTGGCCAAAATGTTGAGTTGATT
1 TTAGATTTTTTTGATTGGCCAAAATGTTGAGTTGATT
*
45059273 TTAGATTTTTTTTATTGGCCAAAATGTTGAGTTGAT
1 TTAGATTTTTTTGATTGGCCAAAATGTTGAGTTGAT
45059309 CGAGTCTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.25, C:0.05, G:0.21, T:0.49
Consensus pattern (37 bp):
TTAGATTTTTTTGATTGGCCAAAATGTTGAGTTGATT
Found at i:45059420 original size:20 final size:19
Alignment explanation
Indices: 45059397--45059459 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
45059387 CTTAGAAATA
45059397 TTGGTATAACCTTAAAATTT
1 TTGGTA-AACCTTAAAATTT
* *
45059417 TTGGTAACGCCTTAAAAATT
1 TTGGTAA-ACCTTAAAATTT
* *
45059437 TTAGTAAATCCTTATAATTT
1 TTGGTAAA-CCTTAAAATTT
45059457 TTG
1 TTG
45059460 AAATTTACCA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (19 bp):
TTGGTAAACCTTAAAATTT
Found at i:45059542 original size:20 final size:20
Alignment explanation
Indices: 45059479--45059558 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
45059469 ATTATGGCAG
* *
45059479 AACCTTATAAATTTTGATAA
1 AACCTTAGAAATTTTGGTAA
* * * * *
45059499 ATCCATGGATATTGTGGT-A
1 AACCTTAGAAATTTTGGTAA
45059518 AACCTTAGAAATTTTGGTAA
1 AACCTTAGAAATTTTGGTAA
* *
45059538 AACCTTAAAAATCTTGGTAA
1 AACCTTAGAAATTTTGGTAA
45059558 A
1 A
45059559 TATTGATATG
Statistics
Matches: 45, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
19 14 0.31
20 31 0.69
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (20 bp):
AACCTTAGAAATTTTGGTAA
Found at i:45062140 original size:108 final size:109
Alignment explanation
Indices: 45061984--45062265 Score: 345
Period size: 109 Copynumber: 2.6 Consensus size: 109
45061974 AAAAAATTTT
* * * *
45061984 AATTCTTTTAGGTGCTGGCCTTGTAATGGCTGGCACCAAGTACAAAAAAAATT-AATTTTTTTTA
1 AATT-TTTTA-GTTCTGGCCTTCTAATGGCCGGCACCAGGTACAAAAAAAATTCAATTTTTTTTA
* * *
45062048 AATGTTAGCCTTCTAATGGTCAGTACCAGACTACCAGTATTTA-AAA
64 AATGTTAGCCTTCTAATGGCCAGCACCA-ACTACCAATATTTACAAA
* *
45062094 AATTTTTTAGTTCTGGCCTTCTAATGGCCGGCACCAGGTACGAAAAAAATTCAAATTTTTTTTAG
1 AATTTTTTAGTTCTGGCCTTCTAATGGCCGGCACCAGGTACAAAAAAAATTC-AATTTTTTTTAA
* * * *
45062159 CTGTTGGCCTTCTAATGGCCTGCACCAAGTACCAATATTTACAAA
65 ATGTTAGCCTTCTAATGGCCAGCACCAACTACCAATATTTACAAA
*** * *
45062204 AAAAATTTA-TTCTGGCCTTCTAATGGCCGGCACCTGGTACAAAAAAAATTCAAATTTTTTTA
1 AATTTTTTAGTTCTGGCCTTCTAATGGCCGGCACCAGGTACAAAAAAAATTCAATTTTTTTTA
45062266 GGTGCTGACC
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
108 47 0.31
109 57 0.38
110 46 0.31
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (109 bp):
AATTTTTTAGTTCTGGCCTTCTAATGGCCGGCACCAGGTACAAAAAAAATTCAATTTTTTTTAAA
TGTTAGCCTTCTAATGGCCAGCACCAACTACCAATATTTACAAA
Found at i:45062221 original size:109 final size:109
Alignment explanation
Indices: 45061998--45062297 Score: 356
Period size: 108 Copynumber: 2.8 Consensus size: 109
45061988 CTTTTAGGTG
* * * * *
45061998 CTGGCCTTGTAATGGCTGGCACCAAGTACAAAAAAAATT--AATTTTTTTTAAATGTTAGCCTTC
1 CTGGCCTTCTAATGGCCGGCACCAGGTACAAAAAAAATTCAAATTTTTTTTAGATGTTGGCCTTC
* * * * ***
45062061 TAATGGTCAGTACCAGACTACCAGTATTTAAAAAATTTTTTAGTT
66 TAATGGCCAGCACCA-AGTACCAATATTTAAAAAAAAATTTAGTT
* *
45062106 CTGGCCTTCTAATGGCCGGCACCAGGTACGAAAAAAATTCAAATTTTTTTTAGCTGTTGGCCTTC
1 CTGGCCTTCTAATGGCCGGCACCAGGTACAAAAAAAATTCAAATTTTTTTTAGATGTTGGCCTTC
*
45062171 TAATGGCCTGCACCAAGTACCAATATTTACAAAAAAAATTTA-TT
66 TAATGGCCAGCACCAAGTACCAATATTTA-AAAAAAAATTTAGTT
* * * *
45062215 CTGGCCTTCTAATGGCCGGCACCTGGTACAAAAAAAATTCAAA-TTTTTTTAGGTGCTGACCTTC
1 CTGGCCTTCTAATGGCCGGCACCAGGTACAAAAAAAATTCAAATTTTTTTTAGATGTTGGCCTTC
* * *
45062279 TACTTGCCGGCACCAAGTA
66 TAATGGCCAGCACCAAGTA
45062298 TGAAAAAAAA
Statistics
Matches: 166, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
108 69 0.42
109 55 0.33
110 42 0.25
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (109 bp):
CTGGCCTTCTAATGGCCGGCACCAGGTACAAAAAAAATTCAAATTTTTTTTAGATGTTGGCCTTC
TAATGGCCAGCACCAAGTACCAATATTTAAAAAAAAATTTAGTT
Found at i:45080879 original size:20 final size:20
Alignment explanation
Indices: 45080851--45080891 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
45080841 AGTTAGTAGA
*
45080851 AATTGGGTTAGTAAACTAAG
1 AATTAGGTTAGTAAACTAAG
*
45080871 AATTAGGTTAGTGAACTAAG
1 AATTAGGTTAGTAAACTAAG
45080891 A
1 A
45080892 GTTGTAACGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.29
Consensus pattern (20 bp):
AATTAGGTTAGTAAACTAAG
Found at i:45082070 original size:41 final size:41
Alignment explanation
Indices: 45082025--45082103 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
45082015 GACCACGTGG
* *
45082025 GTCACACGACCGTGTGGTAGGCCATGTGACAGACTGTGTAA
1 GTCACACGACCGTATGGCAGGCCATGTGACAGACTGTGTAA
*
45082066 GTCACACGACCGTATGGCAGGCCGTGTGACAGACTGTG
1 GTCACACGACCGTATGGCAGGCCATGTGACAGACTGTG
45082104 CGGATTACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.20
Consensus pattern (41 bp):
GTCACACGACCGTATGGCAGGCCATGTGACAGACTGTGTAA
Found at i:45082299 original size:82 final size:81
Alignment explanation
Indices: 45082183--45082338 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
45082173 GTAGCAGATC
* * *
45082183 GTGTAGGTCATACAACTATGTGGTAGGTTGTGTGGTAGACCGTGCCGGTCACAGGACCATATGGT
1 GTGTAGGTCATACAACTATGTAGTAGGCTATGTGGTAGACCGTG-CGGTCACAGGACCATATGGT
*
45082248 AATCCATGTGACAGACT
65 AAGCCATGTGACAGACT
* * *
45082265 GTGTAGGTCATACGAAC-ATGTAGTAGGCTATGTGGTAGACCGTGTGGTCACATGACCATGTGGT
1 GTGTAGGTCATAC-AACTATGTAGTAGGCTATGTGGTAGACCGTGCGGTCACAGGACCATATGGT
*
45082329 AGGCCATGTG
65 AAGCCATGTG
45082339 GCGATTATGT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 25 0.38
82 37 0.57
83 3 0.05
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (81 bp):
GTGTAGGTCATACAACTATGTAGTAGGCTATGTGGTAGACCGTGCGGTCACAGGACCATATGGTA
AGCCATGTGACAGACT
Found at i:45087462 original size:26 final size:22
Alignment explanation
Indices: 45087411--45087470 Score: 61
Period size: 26 Copynumber: 2.6 Consensus size: 22
45087401 TTTCCACTAT
45087411 TACTT-TTATTTTCTTTATTTA
1 TACTTGTTATTTTCTTTATTTA
45087432 T-CTTGTTATTTTGCTTTAATCGTTA
1 TACTTGTTATTTT-CTTT-AT--TTA
*
45087457 TACTTGCTATTTTC
1 TACTTGTTATTTTC
45087471 ATGCTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
20 3 0.09
21 8 0.25
22 4 0.12
23 2 0.06
25 5 0.16
26 10 0.31
ACGTcount: A:0.17, C:0.13, G:0.07, T:0.63
Consensus pattern (22 bp):
TACTTGTTATTTTCTTTATTTA
Found at i:45090284 original size:31 final size:31
Alignment explanation
Indices: 45090249--45090309 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
45090239 ACAACCCAAC
45090249 GACTTAAATAAAAACTATTGAATAATTCAAT
1 GACTTAAATAAAAACTATTGAATAATTCAAT
* * * *
45090280 GACTTAAATGAGAACTTTTGAATAGTTCAA
1 GACTTAAATAAAAACTATTGAATAATTCAA
45090310 AGACCAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (31 bp):
GACTTAAATAAAAACTATTGAATAATTCAAT
Found at i:45094974 original size:30 final size:30
Alignment explanation
Indices: 45094940--45095026 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 30
45094930 AATTTTAAAA
45094940 TTTTAAAATAATAAAGATAAAATTATAT-T
1 TTTTAAAATAATAAAGATAAAATTATATGT
* * * **
45094969 TTTTTAAATTATAAAAATATTATT-TAATGT
1 TTTTAAAATAATAAAGATAAAATTAT-ATGT
* *
45094999 TTTAAAAATGATAAAGATAAAAATTATA
1 TTTTAAAATAATAAAGAT-AAAATTATA
45095027 AAAAATTAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
28 1 0.02
29 21 0.49
30 15 0.35
31 5 0.12
32 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.43
Consensus pattern (30 bp):
TTTTAAAATAATAAAGATAAAATTATATGT
Found at i:45096501 original size:8 final size:8
Alignment explanation
Indices: 45096475--45096592 Score: 58
Period size: 8 Copynumber: 13.6 Consensus size: 8
45096465 TTCCTCATAA
*
45096475 AAAAATTT
1 AAAAATAT
*
45096483 AAAATTCAT
1 AAAAAT-AT
45096492 AAAAATAT
1 AAAAATAT
45096500 AAAAA-ATT
1 AAAAATA-T
*
45096508 AAAATTTAT
1 AAAA-ATAT
45096517 AAAAATAT
1 AAAAATAT
45096525 AAAAATTATT
1 AAAAA-TA-T
** *
45096535 AAACTTAA
1 AAAAATAT
45096543 AAAAATATT
1 AAAAATA-T
45096552 AAAATTGATAT
1 AAAA---ATAT
**
45096563 AAACTTAT
1 AAAAATAT
45096571 AAAAATTAT
1 AAAAA-TAT
*
45096580 AAAAACAT
1 AAAAATAT
45096588 AAAAA
1 AAAAA
45096593 AATCTAATAA
Statistics
Matches: 83, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
7 1 0.01
8 43 0.52
9 27 0.33
10 5 0.06
11 4 0.05
12 3 0.04
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (8 bp):
AAAAATAT
Found at i:45096505 original size:19 final size:19
Alignment explanation
Indices: 45096469--45096507 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
45096459 AAATATTTCC
**
45096469 TCATAAAAAAATTTAAAAT
1 TCATAAAAAAATAAAAAAT
*
45096488 TCATAAAAATATAAAAAAT
1 TCATAAAAAAATAAAAAAT
45096507 T
1 T
45096508 AAAATTTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
TCATAAAAAAATAAAAAAT
Found at i:45096517 original size:17 final size:18
Alignment explanation
Indices: 45096483--45096592 Score: 59
Period size: 17 Copynumber: 6.2 Consensus size: 18
45096473 AAAAAAATTT
*
45096483 AAAATTCATAAAAATATA
1 AAAATTTATAAAAATATA
* **
45096501 AAAAATTA-AAATTTATA
1 AAAATTTATAAAAATATA
45096518 AAAA--TATAAAAAT-TA
1 AAAATTTATAAAAATATA
* * * *
45096533 TTAAACTTAAAAAAATATT
1 -AAAATTTATAAAAATATA
**
45096552 AAAATTGATATAAACTTATA
1 AAAATT--TATAAAAATATA
*
45096572 AAAA-TTATAAAAACATA
1 AAAATTTATAAAAATATA
45096589 AAAA
1 AAAA
45096593 AATCTAATAA
Statistics
Matches: 67, Mismatches: 18, Indels: 15
0.67 0.18 0.15
Matches are distributed among these distances:
15 4 0.06
16 7 0.10
17 24 0.36
18 18 0.27
19 2 0.03
20 12 0.18
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (18 bp):
AAAATTTATAAAAATATA
Found at i:45096521 original size:26 final size:26
Alignment explanation
Indices: 45096474--45096584 Score: 111
Period size: 26 Copynumber: 4.2 Consensus size: 26
45096464 TTTCCTCATA
*
45096474 AAAAAATT-TAAAATTCATAAAAATAT
1 AAAAAATTATAAACTT-ATAAAAATAT
*
45096500 AAAAAATTA-AAATTTATAAAAATAT
1 AAAAAATTATAAACTTATAAAAATAT
*
45096525 -AAAAATTATTAAACTTAAAAAAATAT
1 AAAAAATTA-TAAACTTATAAAAATAT
* *
45096551 TAAAATTGATATAAACTTATAAAAATTAT
1 AAAAAAT--TATAAACTTATAAAAA-TAT
45096580 AAAAA
1 AAAAA
45096585 CATAAAAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
24 8 0.11
25 10 0.14
26 27 0.38
27 5 0.07
28 13 0.18
29 9 0.12
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.32
Consensus pattern (26 bp):
AAAAAATTATAAACTTATAAAAATAT
Found at i:45096640 original size:22 final size:20
Alignment explanation
Indices: 45096615--45096673 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
45096605 TATGAAGAAT
45096615 TTTATAAAATTAATAAAACTTA
1 TTTA-AAAATT-ATAAAACTTA
*
45096637 TTTAAAATTTTATAAAAACTTA
1 TTTAAAA-ATTAT-AAAACTTA
*
45096659 -ATAAAAATTATAAAA
1 TTTAAAAATTATAAAA
45096674 AAAATCATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 10 0.31
22 14 0.44
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTAAAAATTATAAAACTTA
Found at i:45096674 original size:9 final size:9
Alignment explanation
Indices: 45096475--45096674 Score: 99
Period size: 9 Copynumber: 21.6 Consensus size: 9
45096465 TTCCTCATAA
45096475 AAAAATT-T
1 AAAAATTAT
45096483 -AAAATTCAT
1 AAAAATT-AT
45096492 AAAAA-TAT
1 AAAAATTAT
*
45096500 AAAAAAT-T
1 AAAAATTAT
*
45096508 AAAATTTAT
1 AAAAATTAT
45096517 AAAAA-TAT
1 AAAAATTAT
45096525 AAAAATTAT
1 AAAAATTAT
* *
45096534 TAAACTTA-
1 AAAAATTAT
*
45096542 AAAAAATAT
1 AAAAATTAT
*
45096551 TAAAATTGAT
1 AAAAATT-AT
*
45096561 ATAAACTTAT
1 A-AAAATTAT
45096571 AAAAATTAT
1 AAAAATTAT
* *
45096580 AAAAACATAA
1 AAAAA-TTAT
45096590 AAAAATCTA-
1 AAAAAT-TAT
* *
45096599 ATAATTTAT
1 AAAAATTAT
* *
45096608 GAAGAATTTT
1 -AAAAATTAT
45096618 ATAAAATTAAT
1 A-AAAATT-AT
*
45096629 AAAACTTATTT
1 AAAAATTA--T
*
45096640 AAAATTTTAT
1 AAAA-ATTAT
45096650 AAAAACTTAAT
1 AAAAA-TT-AT
45096661 AAAAATTAT
1 AAAAATTAT
45096670 AAAAA
1 AAAAA
45096675 AAATCATAAA
Statistics
Matches: 145, Mismatches: 27, Indels: 39
0.69 0.13 0.18
Matches are distributed among these distances:
7 6 0.04
8 28 0.19
9 47 0.32
10 42 0.29
11 19 0.13
12 3 0.02
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:45096675 original size:22 final size:22
Alignment explanation
Indices: 45096629--45096676 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
45096619 TAAAATTAAT
* * * *
45096629 AAAACTTATTTAAAATTTTATA
1 AAAACTTAATAAAAATTATAAA
45096651 AAAACTTAATAAAAATTATAAA
1 AAAACTTAATAAAAATTATAAA
45096673 AAAA
1 AAAA
45096677 ATCATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAACTTAATAAAAATTATAAA
Found at i:45100056 original size:21 final size:21
Alignment explanation
Indices: 45100011--45100060 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
45100001 CTAAGATGTG
* *
45100011 AATTGGATTAAATTGAATTTG
1 AATTGTATTAAATTGAATTTA
45100032 AATTGTATTAAATTG-ATGTTA
1 AATTGTATTAAATTGAAT-TTA
45100053 AATT-TATT
1 AATTGTATT
45100061 CATATATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (21 bp):
AATTGTATTAAATTGAATTTA
Found at i:45100668 original size:24 final size:24
Alignment explanation
Indices: 45100636--45100752 Score: 69
Period size: 25 Copynumber: 4.7 Consensus size: 24
45100626 ACCTTTCCGA
45100636 TATTGGCTCGTATGAGCTTCCCGT
1 TATTGGCTCGTATGAGCTTCCCGT
* *
45100660 TATTGGCTC-TCCA-GAGTTTTCCGT
1 TATTGGCTCGT--ATGAGCTTCCCGT
* **
45100684 TACATGGCTCACATGAGCTTCCCGT
1 TA-TTGGCTCGTATGAGCTTCCCGT
* * *
45100709 TATATGGCTAGAGAGAGAGCTTCCCGT
1 TAT-TGGCTCG-TA-TGAGCTTCCCGT
45100736 T-TATGTGCTCGTATGAG
1 TAT-TG-GCTCGTATGAG
45100753 TATTCCCGAA
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
23 1 0.01
24 21 0.30
25 26 0.37
26 6 0.09
27 16 0.23
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (24 bp):
TATTGGCTCGTATGAGCTTCCCGT
Found at i:45100708 original size:25 final size:25
Alignment explanation
Indices: 45100647--45100717 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
45100637 ATTGGCTCGT
* *
45100647 ATGAGCTTCCCGTTATTGGCTCTCC
1 ATGAGCTTCCCGTTAATGGCTCTAC
* *
45100672 A-GAGTTTTCCGTTACATGGCTC-AC
1 ATGAGCTTCCCGTTA-ATGGCTCTAC
45100696 ATGAGCTTCCCGTTATATGGCT
1 ATGAGCTTCCCGTTA-ATGGCT
45100718 AGAGAGAGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 13 0.35
25 24 0.65
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (25 bp):
ATGAGCTTCCCGTTAATGGCTCTAC
Found at i:45103066 original size:31 final size:31
Alignment explanation
Indices: 45103028--45103093 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
45103018 TCAACTGAAC
45103028 TTTTTTATAATATTT-ATAAGTTTTTAAGATT
1 TTTTTTATAAT-TTTGATAAGTTTTTAAGATT
* *
45103059 TTTTTTATGATTTTGATAAGTTTTTATGATT
1 TTTTTTATAATTTTGATAAGTTTTTAAGATT
45103090 TTTT
1 TTTT
45103094 ATAAGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (31 bp):
TTTTTTATAATTTTGATAAGTTTTTAAGATT
Found at i:45103082 original size:20 final size:21
Alignment explanation
Indices: 45103059--45103103 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
45103049 TTTTAAGATT
45103059 TTTTTTATGA-TTTTGATAAG
1 TTTTTTATGATTTTTGATAAG
*
45103079 -TTTTTATGATTTTTTATAAG
1 TTTTTTATGATTTTTGATAAG
45103099 TTTTT
1 TTTTT
45103104 ATAAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 9 0.41
21 4 0.18
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (21 bp):
TTTTTTATGATTTTTGATAAG
Found at i:45103083 original size:11 final size:10
Alignment explanation
Indices: 45103029--45103191 Score: 70
Period size: 10 Copynumber: 16.3 Consensus size: 10
45103019 CAACTGAACT
45103029 TTTTTATAA-
1 TTTTTATAAG
*
45103038 TATTTATAAG
1 TTTTTATAAG
*
45103048 TTTTTA-AGAT
1 TTTTTATA-AG
* *
45103058 TTTTTTTATG
1 TTTTTATAAG
*
45103068 ATTTTGATAAG
1 -TTTTTATAAG
* *
45103079 TTTTTATGAT
1 TTTTTATAAG
45103089 TTTTTATAAG
1 TTTTTATAAG
*
45103099 TTTTTATAAA
1 TTTTTATAAG
* *
45103109 ATTTTA-AATA
1 TTTTTATAA-G
45103119 TGTTTTATTAA-
1 T-TTTTA-TAAG
*
45103130 -TTTTATTAAA
1 TTTTTA-TAAG
*
45103140 CTTTTATAA-
1 TTTTTATAAG
* *
45103149 TATTTATAAA
1 TTTTTATAAG
* *
45103159 TTTTTATTAT
1 TTTTTATAAG
45103169 TTTATTATAA-
1 TTT-TTATAAG
45103179 TTTTTATAAG
1 TTTTTATAAG
45103189 TTT
1 TTT
45103192 ATATCAATTT
Statistics
Matches: 118, Mismatches: 23, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
9 33 0.28
10 60 0.51
11 23 0.19
13 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.61
Consensus pattern (10 bp):
TTTTTATAAG
Found at i:45103113 original size:20 final size:20
Alignment explanation
Indices: 45103030--45103187 Score: 89
Period size: 20 Copynumber: 7.9 Consensus size: 20
45103020 AACTGAACTT
*
45103030 TTTTAT-AATATTTATAAGT-
1 TTTTATAAATTTTTATAA-TA
* * *
45103049 TTTTA-AGATTTTTTTTATGA
1 TTTTATAAATTTTTATAAT-A
* * *
45103069 TTTTGATAAGTTTTTATGATT
1 TTTT-ATAAATTTTTATAATA
* *
45103090 TTTTATAAGTTTTTATAAAA
1 TTTTATAAATTTTTATAATA
*
45103110 TTTTA-AATATGTTTTATTA-A
1 TTTTATAA-AT-TTTTATAATA
*
45103130 TTTTATTAAACTTTTATAATA
1 TTTTA-TAAATTTTTATAATA
45103151 -TTTATAAATTTTTAT--TA
1 TTTTATAAATTTTTATAATA
45103168 TTTTATTATAATTTTTATAA
1 TTTTA-TA-AATTTTTATAA
45103188 GTTTATATCA
Statistics
Matches: 107, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
17 2 0.02
18 5 0.05
19 26 0.24
20 49 0.46
21 14 0.13
22 11 0.10
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTATAAATTTTTATAATA
Found at i:45103192 original size:20 final size:21
Alignment explanation
Indices: 45103074--45103212 Score: 80
Period size: 20 Copynumber: 6.9 Consensus size: 21
45103064 TATGATTTTG
* *
45103074 ATAAGTTTTTATGATTTT-TT
1 ATAAATTTTTATAATTTTATT
* **
45103094 ATAAGTTTTTATAAAATT-TT
1 ATAAATTTTTATAATTTTATT
45103114 A-AATATGTTTTATTAATTTTA-T
1 ATAA-AT-TTTTA-TAATTTTATT
* *
45103136 -TAAACTTTTATAA-TAT-TT
1 ATAAATTTTTATAATTTTATT
*
45103154 ATAAATTTTTATTATTTTATT
1 ATAAATTTTTATAATTTTATT
*
45103175 AT-AATTTTTATAAGTTTA-T
1 ATAAATTTTTATAATTTTATT
* * *
45103194 ATCAATTTTAATATTTTTA
1 ATAAATTTTTATAATTTTA
45103213 AATTTAATAA
Statistics
Matches: 93, Mismatches: 16, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.03
19 19 0.20
20 53 0.57
21 10 0.11
22 8 0.09
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (21 bp):
ATAAATTTTTATAATTTTATT
Found at i:45103203 original size:39 final size:38
Alignment explanation
Indices: 45103061--45103187 Score: 107
Period size: 39 Copynumber: 3.2 Consensus size: 38
45103051 TTAAGATTTT
* * * *
45103061 TTTTATGAT-TTTGATAAGTTTTTATGATTTT-TTATAAGT
1 TTTTATAATATTT-ATAAATTTTTATTATTTTATTA-AA-C
*
45103100 TTTTATAAAATTT-TAAATATGTTTTATTAATTTTATTAAAC
1 TTTTATAATATTTAT-AA-AT-TTTTATT-ATTTTATTAAAC
*
45103141 TTTTATAATATTTATAAATTTTTATTATTTTATTATAAT
1 TTTTATAATATTTATAAATTTTTATTATTTTATTA-AAC
45103180 TTTTATAA
1 TTTTATAA
45103188 GTTTATATCA
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
38 10 0.14
39 26 0.36
40 6 0.08
41 20 0.27
42 8 0.11
43 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.61
Consensus pattern (38 bp):
TTTTATAATATTTATAAATTTTTATTATTTTATTAAAC
Found at i:45112446 original size:50 final size:50
Alignment explanation
Indices: 45112371--45112547 Score: 273
Period size: 50 Copynumber: 3.5 Consensus size: 50
45112361 CCATGGCAGC
* *
45112371 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
45112421 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTAATCAAGGACAAGTGA
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
45112471 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
45112521 CAAGTGAAAAGTAGTAGCTTCGGCTAC
1 -AAGTGATAAGTAATAGCTTCGGCTAC
45112548 CTGATCAGTG
Statistics
Matches: 114, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 92 0.81
51 22 0.19
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:45112561 original size:31 final size:31
Alignment explanation
Indices: 45112523--45112671 Score: 199
Period size: 31 Copynumber: 4.8 Consensus size: 31
45112513 ACAAATGACA
*
45112523 AGTGAAAAGTAGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
45112554 AGTGAAAAGTGGTAGCTTCTGCTACTTGATT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
45112585 AGTGAAAAGTGGTAGCTCCGACTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
45112616 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
45112647 AGTGAATAGTGGTAGCTTTGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
45112672 AAGTGACAAG
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:45112842 original size:49 final size:48
Alignment explanation
Indices: 45112771--45112902 Score: 186
Period size: 49 Copynumber: 2.9 Consensus size: 48
45112761 GCACCAGTGA
* * *
45112771 GATATGTGATTCGTGTAAGACCATAGCTGGGCTACGGCATTGATATGT
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
45112819 GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
1 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
45112868 GA-A--T-A-T-GTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATC
45112903 ATTATGTGAA
Statistics
Matches: 80, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
42 29 0.36
44 1 0.01
45 1 0.01
46 1 0.01
48 12 0.15
49 36 0.45
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (48 bp):
GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
Found at i:45112878 original size:42 final size:43
Alignment explanation
Indices: 45112783--45112946 Score: 172
Period size: 42 Copynumber: 3.7 Consensus size: 43
45112773 TATGTGATTC
* * *
45112783 GTGTAAGACCATAGCTGGGCTACGGCATTGATATGTGATATG-TGATT
1 GTGTAAGACCATAGCTGGGCTATGGCATCG--AT-T-ATATGAAGA-T
*
45112830 ACGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 --GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
45112874 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
45112916 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
45112947 GAAAACGAAG
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.01
42 64 0.62
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
49 28 0.27
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:45118044 original size:30 final size:30
Alignment explanation
Indices: 45118010--45118068 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
45118000 TTCAAGAGAT
*
45118010 AGGCTATTATGAGCTTAACCAAGAAGCTGG
1 AGGCTATAATGAGCTTAACCAAGAAGCTGG
*
45118040 AGGCTATAATGAGCTTAGCCAAGAAGCTG
1 AGGCTATAATGAGCTTAACCAAGAAGCTG
45118069 AAGACATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (30 bp):
AGGCTATAATGAGCTTAACCAAGAAGCTGG
Found at i:45124215 original size:10 final size:10
Alignment explanation
Indices: 45124200--45124224 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
45124190 TTGGCATTTG
45124200 TGGCACTTCC
1 TGGCACTTCC
45124210 TGGCACTTCC
1 TGGCACTTCC
45124220 TGGCA
1 TGGCA
45124225 TGATCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.36, G:0.24, T:0.28
Consensus pattern (10 bp):
TGGCACTTCC
Found at i:45131041 original size:23 final size:23
Alignment explanation
Indices: 45131011--45131054 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
45131001 GACTCTTTCT
45131011 CAATGCGACTTCTCGAGCCCGCC
1 CAATGCGACTTCTCGAGCCCGCC
45131034 CAATGCGACTTCTCGAGCCCG
1 CAATGCGACTTCTCGAGCCCG
45131055 AGTATCCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (23 bp):
CAATGCGACTTCTCGAGCCCGCC
Found at i:45135590 original size:20 final size:20
Alignment explanation
Indices: 45135550--45135590 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
45135540 TGGTGGTTGC
*
45135550 GGCGGTGGCAGGGAGTTGGT
1 GGCGGTGGCAGGGAGTAGGT
45135570 GGCGGTGGCAGAGGA-TAGGT
1 GGCGGTGGCAG-GGAGTAGGT
45135590 G
1 G
45135591 ATGGGTGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.15, C:0.10, G:0.59, T:0.17
Consensus pattern (20 bp):
GGCGGTGGCAGGGAGTAGGT
Found at i:45135675 original size:46 final size:46
Alignment explanation
Indices: 45135620--45135709 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
45135610 TTAGGGGCTA
45135620 GGTCTGTTTTGGGTCTTGGGTTTGGGCTGGTTCAGATTGGGCTTTG
1 GGTCTGTTTTGGGTCTTGGGTTTGGGCTGGTTCAGATTGGGCTTTG
45135666 GGTCTGTTTTGGGTCTTGGGTTTGGGCTGGTTCAGATTGGGCTT
1 GGTCTGTTTTGGGTCTTGGGTTTGGGCTGGTTCAGATTGGGCTT
45135710 GTACATTCGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.04, C:0.11, G:0.41, T:0.43
Consensus pattern (46 bp):
GGTCTGTTTTGGGTCTTGGGTTTGGGCTGGTTCAGATTGGGCTTTG
Found at i:45137479 original size:21 final size:21
Alignment explanation
Indices: 45137450--45137489 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
45137440 ATGATAATTC
45137450 AAAAATATATATA-ATATAAA
1 AAAAATATATATATATATAAA
45137470 AAAAAGTATATATATATATA
1 AAAAA-TATATATATATATA
45137490 TATAGAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAAATATATATATATATAAA
Found at i:45137682 original size:3 final size:3
Alignment explanation
Indices: 45137674--45137711 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
45137664 AATATATAGG
*
45137674 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
45137712 AATTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:45138299 original size:15 final size:14
Alignment explanation
Indices: 45138266--45138312 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
45138256 TTTAAGTGAA
45138266 AAAAATAAATAAAAC
1 AAAAATAAA-AAAAC
*
45138281 -AAAATGAAAAAAAT
1 AAAAAT-AAAAAAAC
45138295 AAAAATAAAAAAAC
1 AAAAATAAAAAAAC
45138309 AAAA
1 AAAA
45138313 CTAAGAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.11
Consensus pattern (14 bp):
AAAAATAAAAAAAC
Found at i:45138307 original size:23 final size:23
Alignment explanation
Indices: 45138262--45138307 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
45138252 GTTTTTTAAG
*
45138262 TGAAAAAAATAAATAAAACAAAA
1 TGAAAAAAATAAATAAAAAAAAA
45138285 TGAAAAAAATAAA-AATAAAAAAA
1 TGAAAAAAATAAATAA-AAAAAAA
45138308 CAAAACTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (23 bp):
TGAAAAAAATAAATAAAAAAAAA
Found at i:45140536 original size:22 final size:20
Alignment explanation
Indices: 45140502--45140542 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
45140492 ATGAAAATAA
*
45140502 AATAAAAATAAAAAGAATCG
1 AATAAAAATAAAAAAAATCG
45140522 AATAAGAAAGTAAAAAAAATC
1 AATAA-AAA-TAAAAAAAATC
45140543 ACCTCTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.15
Consensus pattern (20 bp):
AATAAAAATAAAAAAAATCG
Done.