Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold13
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: 2744999
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.26
Warning! 506982 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1675859 original size:18 final size:15
Alignment explanation
Indices: 1675837--1675884 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 15
1675827 TATACTATAT
1675837 ATATATATTAGTATTA
1 ATATATATTA-TATTA
1675853 AGTTATATATATATATTA
1 A--TATATAT-TATATTA
*
1675871 ATATATATTTTATT
1 ATATATATTATATT
1675885 TCTTTTGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.18
16 8 0.29
18 13 0.46
19 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
ATATATATTATATTA
Found at i:1681560 original size:28 final size:28
Alignment explanation
Indices: 1681520--1681598 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
1681510 ATTACATAAA
* *
1681520 ATAAATTAT-TAATATATTAAAATTTAT
1 ATAAAATATATAATATATTAAAATTAAT
*
1681547 ATAAAATATATAATATTTTAAACA-TAAT
1 ATAAAATATATAATATATTAAA-ATTAAT
*
1681575 -TAAAATATATAAATATATAAAAAT
1 ATAAAATATAT-AATATATTAAAAT
1681599 ATAAAAAAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 19 0.44
28 23 0.53
29 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAAAATATATAATATATTAAAATTAAT
Found at i:1682785 original size:9 final size:9
Alignment explanation
Indices: 1682759--1682796 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1682749 CATCGGTAAT
1682759 TTTTATTT-
1 TTTTATTTA
*
1682767 TGTT-TTTA
1 TTTTATTTA
1682775 TTTTATTTA
1 TTTTATTTA
1682784 TTTTATTTA
1 TTTTATTTA
1682793 TTTT
1 TTTT
1682797 TTGTTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 3 0.12
8 6 0.23
9 17 0.65
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1683196 original size:20 final size:20
Alignment explanation
Indices: 1683149--1683199 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1683139 CATGATTATT
*
1683149 AATATATCAA-ATTTTATATA
1 AATATAT-AATATTTTAAATA
1683169 AATATATAATATTTTAAATA
1 AATATATAATATTTTAAATA
1683189 TAAT-TATAATA
1 -AATATATAATA
1683200 CTTAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATATAATATTTTAAATA
Found at i:1685792 original size:275 final size:275
Alignment explanation
Indices: 1684756--1686825 Score: 2204
Period size: 275 Copynumber: 7.6 Consensus size: 275
1684746 TACTTTTTTA
** * * * *
1684756 AATAATTTATTTACAATTAGAAAGATTGTGGTTAATTTTTTATTTGTATCATCAAAATCTACCAT
1 AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
* * * *
1684821 CTAGCCCCTAAAATCAAATATAATTACTCAAGACTTGTATCACAAGTTATAGTTTGGAATAAATT
66 CTAGCCTCTAAAATCAAGT-T--TAACTCAAGACTTGTATCACAAGTTATAGCTTGGAATAAATT
* * * *
1684886 TATTTATTCCAC-TTTC--ATTCTCATTGGATTCTAAGACATCATTTAAAAAGCAAAGCAAGAAA
128 TATTTATTCC-CTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAAAGCAAAGCAAGAAA
* ** **
1684948 CACGTTTATGAGACCAAAACTCAAAAGCAAAATAAATAAA-T-------TA--ACTTTAGTACAA
192 CACGTTTATGAGACCAAGACTTGAAAGCAAAATAAATAAATTAGCCACATATGACTTTAGTATTA
** * * *
1685003 AAGGTAAAACACTTTCCTA
257 AAGACAAAACATTTTCTTG
* * * * *
1685022 AATAATTTATTTACAATTTGGAAAGATTGTAATTTGCTTTTGACTTTTATCATCAAAATCCACCA
1 AATAATTTATTTACAA-TTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCA
* * * * * *
1685087 TTTAGCC-CT----TTAA---TCACTCAAGACTTATATCACAAGTTATAGTTTGAAATAAATTTA
65 TCTAGCCTCTAAAATCAAGTTTAACTCAAGACTTGTATCACAAGTTATAGCTTGGAATAAATTTA
* * * * *
1685144 TTTATTCCCTTTTATTTTTATCCTTAGATTCTAAGACATAA-TTAAAATGAAAAGCAAGAAATAC
130 TTTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAAAGCAAAGCAAGAAACAC
* *
1685208 GTTTATGAGACCAAGACTTGAATGCAAAATAAATAAATTAGCTACATATGACTTTCA-TATTAAA
195 GTTTATGAGACCAAGACTTGAAAGCAAAATAAATAAATTAGCCACATATGACTTT-AGTATT-AA
1685272 AGACAAAACATTTTCTTG
258 AGACAAAACATTTTCTTG
1685290 AATAATTTATTTACAATCT-GAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCA
1 AATAATTTATTTACAAT-TAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCA
* * * * * ** *
1685354 TTTAACCTTTAAAATCAAATATAATTACTCAAGAC-T-TATCACAAGTTGCATCTTGGAATAAAT
65 TCTAGCCTCTAAAATCAAGT-T--TAACTCAAGACTTGTATCACAAGTTATAGCTTGGAATAAAT
* * *
1685417 TTATTTATTCTCTTTTCTTTTTCTCCTTGGATTCTAAGACATAATTTAAAAAACAAAGCAAGAAA
127 TTATTTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAAAGCAAAGCAAGAAA
* **
1685482 CACGTTTATGAGACCAAGACTTAAAAGCAAAATAAATAAATTAGCCATGTATGACTTTAGTATTA
192 CACGTTTATGAGACCAAGACTTGAAAGCAAAATAAATAAATTAGCCACATATGACTTTAGTATTA
*
1685547 AAGACAAAACATTTTCCTG
257 AAGACAAAACATTTTCTTG
* *
1685566 AATAATTTATTTACAATTAGAAAGATTATCATTTACTTTTGACTTGTATCATCAAAATCTATCAT
1 AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
* * * * * *
1685631 CTAACCTCAAAAAGT-AAGTTTAACTCAAGATTTGTATTACGAGTTATAGCTTAGAATAAATTTA
66 CTAGCCTCTAAAA-TCAAGTTTAACTCAAGACTTGTATCACAAGTTATAGCTTGGAATAAATTTA
* * * * * *
1685695 TTTATTCCATTTTCTTTTTCTTCTCAGATTCTAAGATATAATTTAAAAAGCAAACCAGGAAACAC
130 TTTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAAAGCAAAGCAAGAAACAC
* * *
1685760 GTTTATGAGACCAATACTCGAAAGCGAAATAAATAAATTAGCCACATATGACTTTAGTATTAAAG
195 GTTTATGAGACCAAGACTTGAAAGCAAAATAAATAAATTAGCCACATATGACTTTAGTATTAAAG
* **
1685825 ACAAAATATTTTCCAG
260 ACAAAACATTTTCTTG
* * *
1685841 AATAATTTATTTACAATTAGAAAGATTATAATTTGCTTTTGACTTGTATCATCAAAATCTACCAT
1 AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
* * * * * * * *
1685906 CTAGCCTTTAAAATCAAGTTTAATCACTCAATACTTATATCATAAGTTGTAACTTGAAAAAAATT
66 CTAGCCTCTAAAATCAAGTTT-A--ACTCAAGACTTGTATCACAAGTTATAGCTTGGAATAAATT
** * *
1685971 TATTTATTCCCTTTTAATTTTCTCCTTAGATTCTAAGACATAATTTAAAAAAACAAAGCATGAAA
128 TATTTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTT-AAAAAGCAAAGCAAGAAA
* * * *
1686036 CACG----T-AGATCAAGACTTGAAAGTAAAATAAATAAATTAGCCACA-AGTGCCTTTAATATT
192 CACGTTTATGAGACCAAGACTTGAAAGCAAAATAAATAAATTAGCCACATA-TGACTTTAGTA-T
* * *
1686095 TAAAGACAAAATACTTTCTTA
255 TAAAGACAAAACATTTTCTTG
** * ** * *
1686116 AATAATTTATTTACAATCGGAGAGATTGTTGTTTACTTTTGACTTATATCATCAAAATTTACCAT
1 AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
* * * ** *
1686181 CTAGCCCCTAAAATCAAGTATAATTACTCAAGACTTG-ATCACAAATTGCATCTTGGAATAAATT
66 CTAGCCTCTAAAATCAAGT-T--TAACTCAAGACTTGTATCACAAGTTATAGCTTGGAATAAATT
* * * *
1686245 TATTTATTCCCTTTTCTTTTTCTCCTTAGATTTTAAGACATAATTTAAAAAACAAAGTAGGAAAC
128 TATTTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAAAGCAAAGCAAGAAAC
* * * *
1686310 ACGTTAATG-GACGAAGACTTAAAAGCAATATAAATAAATTAGCCACATATGACTTTAGTATTAA
193 ACGTTTATGAGACCAAGACTTGAAAGCAAAATAAATAAATTAGCCACATATGACTTTAGTATTAA
* *
1686374 AGGCAAAACATTTTTTTG
258 AGACAAAACATTTTCTTG
* * **
1686392 AATAATTTATTTACAATTAGAAAGATTGTCGTTTACTTTTGACTTATATCATCAAAATCTATTAT
1 AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
* * * *
1686457 CTAGCCTCAAAAACCAAGTTTAATTACTCAAGACTTGTATTACAAGTTATAGCTTAGAATAAATT
66 CTAGCCTCTAAAATCAAGTTT-A--ACTCAAGACTTGTATCACAAGTTATAGCTTGGAATAAATT
* * * * *
1686522 TATTTATTTCTTTTTCTTTTTCT-CTTCAAATTCTAAGACATAATTTAAAAAGCAAAACAGGAAA
128 TATTTATTCCCTTTTCTTTTTCTCCTT-AGATTCTAAGACATAATTTAAAAAGCAAAGCAAGAAA
* * *
1686586 CACGTTTATGAGACTAAGACTCGAAAGCAAAATAAATAAATTAACCACATATGACTTTAGTATTA
192 CACGTTTATGAGACCAAGACTTGAAAGCAAAATAAATAAATTAGCCACATATGACTTTAGTATTA
* ** *
1686651 AAAACAAATTAGTTTCTTG
257 AAGACAAAACATTTTCTTG
* * * *
1686670 AATAATTTATTTACAATTAGAAAGACTATCATTTACTTTTAACTTGTATCATCAAAATCTACGAT
1 AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
* * * * * * * *
1686735 TTAGCCCCAAAAAGT-AAATTTAATTACTCAAAATTTGTATCACAAGTTGTAACTTGGAATAAAT
66 CTAGCCTCTAAAA-TCAAGTTT-A--ACTCAAGACTTGTATCACAAGTTATAGCTTGGAATAAAT
*
1686799 TTATTTA--CTCTTTT-TTTTTCTCCTTAG
127 TTATTTATTCCCTTTTCTTTTTCTCCTTAG
1686826 CTTTCATCTT
Statistics
Matches: 1522, Mismatches: 224, Indels: 107
0.82 0.12 0.06
Matches are distributed among these distances:
255 1 0.00
256 52 0.03
257 53 0.03
258 21 0.01
262 3 0.00
265 2 0.00
266 18 0.01
267 99 0.07
268 34 0.02
272 3 0.00
273 31 0.02
274 109 0.07
275 344 0.23
276 271 0.18
277 201 0.13
278 261 0.17
279 19 0.01
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (275 bp):
AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
CTAGCCTCTAAAATCAAGTTTAACTCAAGACTTGTATCACAAGTTATAGCTTGGAATAAATTTAT
TTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAAAGCAAAGCAAGAAACACG
TTTATGAGACCAAGACTTGAAAGCAAAATAAATAAATTAGCCACATATGACTTTAGTATTAAAGA
CAAAACATTTTCTTG
Found at i:1685897 original size:551 final size:552
Alignment explanation
Indices: 1684756--1686825 Score: 2305
Period size: 551 Copynumber: 3.8 Consensus size: 552
1684746 TACTTTTTTA
** * * * *
1684756 AATAATTTATTTACAATTAGAAAGATTGTGGTTAATTTTTTATTTGTATCATCAAAATCTACCAT
1 AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
*
1684821 CTAGCCCCTAAAATCAAATATAATTACTCAAGACTTGTATCACAAGTTATAGT-TTGGAATAAAT
66 CTAGCCTCTAAAATCAAATATAATTACTCAAGACTTGTATCACAAGTTATA-TCTTGGAATAAAT
* * * * * *
1684885 TTATTTATTC-CACTTTC--ATTCTCATTGGATTCTAAGACATCATTTAAAAAGCAAAGCAAGAA
130 TTATTTATTCTCATTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAAAACAAAGCAAGAA
* **
1684947 ACACGTTTATGAGACCAAAACTCAAAAGCAAAATAAAT--A--A---ATTA--ACTTTAGTACAA
195 ACACGTTTATGAGACCAAGACTCAAAAGCAAAATAAATAAATTAGCCATTATGACTTTAGTATTA
** * * * *
1685003 AAGGTAAAACACTTTCCTAAATAATTTATTTACAATTTGGAAAGATTGTAATTTGCTTTTGACTT
260 AAGACAAAACACTTTCCTAAATAATTTATTTACAA-TTAGAAAGATTATCATTTACTTTTGACTT
* * * ** * *
1685068 TTATCATCAAAATCCACCATTTAG-CCC----TTTAA---TCACTCAAGACTTATATCACAAGTT
324 GTATCATCAAAATCTACCATCTAGCCCCAAAAAGTAAGTTTAACTCAAGACTTGTATCACAAGTT
* * * *
1685125 ATAGTTTGAAATAAATTTATTTATTCCCTTTTATTTTTATCCTTAGATTCTAAGACATAA-TTAA
389 ATAGCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAA
* * * * * *
1685189 AATGAAAAGCAAGAAATACGTTTATGAGACCAAGACTTGAATGCAAAATAAATAAATTAGCTACA
454 AAAGCAAAGCAGGAAACACGTTTATGAGACCAAGACTTGAAAGC-AAATAAATAAATTAGCCACA
1685254 TATGACTTTCA-TATTAAAAGACAAAACATTTTCTTG
518 TATGACTTT-AGTATT-AAAGACAAAACATTTTCTTG
1685290 AATAATTTATTTACAATCT-GAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCA
1 AATAATTTATTTACAAT-TAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCA
* * * **
1685354 TTTAACCTTTAAAATCAAATATAATTACTCAAGAC-T-TATCACAAGTTGCATCTTGGAATAAAT
65 TCTAGCCTCTAAAATCAAATATAATTACTCAAGACTTGTATCACAAGTTATATCTTGGAATAAAT
*
1685417 TTATTTATTCTC-TTTTCTTTTTCTCCTTGGATTCTAAGACATAATTTAAAAAACAAAGCAAGAA
130 TTATTTATTCTCATTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAAAACAAAGCAAGAA
*
1685481 ACACGTTTATGAGACCAAGACTTAAAAGCAAAATAAATAAATTAGCCATGTATGACTTTAGTATT
195 ACACGTTTATGAGACCAAGACTCAAAAGCAAAATAAATAAATTAGCCAT-TATGACTTTAGTATT
* *
1685546 AAAGACAAAACATTTTCCTGAATAATTTATTTACAATTAGAAAGATTATCATTTACTTTTGACTT
259 AAAGACAAAACACTTTCCTAAATAATTTATTTACAATTAGAAAGATTATCATTTACTTTTGACTT
* * * * * *
1685611 GTATCATCAAAATCTATCATCTAACCTCAAAAAGTAAGTTTAACTCAAGATTTGTATTACGAGTT
324 GTATCATCAAAATCTACCATCTAGCCCCAAAAAGTAAGTTTAACTCAAGACTTGTATCACAAGTT
* * * * *
1685676 ATAGCTTAGAATAAATTTATTTATTCCATTTTCTTTTTCTTCTCAGATTCTAAGATATAATTTAA
389 ATAGCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAA
* * *
1685741 AAAGCAAACCAGGAAACACGTTTATGAGACCAATACTCGAAAGCGAAATAAATAAATTAGCCACA
454 AAAGCAAAGCAGGAAACACGTTTATGAGACCAAGACTTGAAAGC-AAATAAATAAATTAGCCACA
* **
1685806 TATGACTTTAGTATTAAAGACAAAATATTTTCCAG
518 TATGACTTTAGTATTAAAGACAAAACATTTTCTTG
* * *
1685841 AATAATTTATTTACAATTAGAAAGATTATAATTTGCTTTTGACTTGTATCATCAAAATCTACCAT
1 AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
* * * * * * * * * * *
1685906 CTAGCCTTTAAAATCAAGTTTAATCACTCAATACTTATATCATAAGTTGTAACTTGAAAAAAATT
66 CTAGCCTCTAAAATCAAATATAATTACTCAAGACTTGTATCACAAGTTATATCTTGGAATAAATT
* ** *
1685971 TATTTATTC-CCTTTTAATTTTCTCCTTAGATTCTAAGACATAATTTAAAAAAACAAAGCATGAA
131 TATTTATTCTCATTTTCTTTTTCTCCTTAGATTCTAAGACATAATTT-AAAAAACAAAGCAAGAA
* ** * ** * *
1686035 ACACG----T-AGATCAAGACTTGAAAGTAAAATAAATAAATTAGCCACAAGTGCCTTTAATATT
195 ACACGTTTATGAGACCAAGACTCAAAAGCAAAATAAATAAATTAGCCATTA-TGACTTTAGTA-T
* * ** * * **
1686095 TAAAGACAAAATACTTTCTTAAATAATTTATTTACAATCGGAGAGATTGTTGTTTACTTTTGACT
258 TAAAGACAAAACACTTTCCTAAATAATTTATTTACAATTAGAAAGATTATCATTTACTTTTGACT
* * * *
1686160 TATATCATCAAAATTTACCATCTAGCCCCTAAAA-TCAAGTATAATTACTCAAGACTTG-ATCAC
323 TGTATCATCAAAATCTACCATCTAGCCCCAAAAAGT-AAGT-T--TAACTCAAGACTTGTATCAC
* ** * *
1686223 AAATTGCATCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTCTCCTTAGATTTTAAGACATAA
384 AAGTTATAGCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAA
* * * * *
1686288 TTTAAAAAACAAAGTAGGAAACACGTTAATG-GACGAAGACTTAAAAGCAATATAAATAAATTAG
449 TTTAAAAAGCAAAGCAGGAAACACGTTTATGAGACCAAGACTTGAAAGCAA-ATAAATAAATTAG
* *
1686352 CCACATATGACTTTAGTATTAAAGGCAAAACATTTTTTTG
513 CCACATATGACTTTAGTATTAAAGACAAAACATTTTCTTG
* * **
1686392 AATAATTTATTTACAATTAGAAAGATTGTCGTTTACTTTTGACTTATATCATCAAAATCTATTAT
1 AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
* * * * * * *
1686457 CTAGCCTCAAAAACCAAGTTTAATTACTCAAGACTTGTATTACAAGTTATAGCTTAGAATAAATT
66 CTAGCCTCTAAAATCAAATATAATTACTCAAGACTTGTATCACAAGTTATATCTTGGAATAAATT
* * * * *
1686522 TATTTATT-TCTTTTTCTTTTTCT-CTTCAAATTCTAAGACATAATTTAAAAAGCAAAACAGGAA
131 TATTTATTCTCATTTTCTTTTTCTCCTT-AGATTCTAAGACATAATTTAAAAAACAAAGCAAGAA
* * * *
1686585 ACACGTTTATGAGACTAAGACTCGAAAGCAAAATAAATAAATTAACCACATATGACTTTAGTATT
195 ACACGTTTATGAGACCAAGACTCAAAAGCAAAATAAATAAATTAGCCA-TTATGACTTTAGTATT
* ** * * * * *
1686650 AAAAACAAATTAGTTTCTTGAATAATTTATTTACAATTAGAAAGACTATCATTTACTTTTAACTT
259 AAAGACAAAACACTTTCCTAAATAATTTATTTACAATTAGAAAGATTATCATTTACTTTTGACTT
* * * * *
1686715 GTATCATCAAAATCTACGATTTAGCCCCAAAAAGTAAATTTAATTACTCAAAATTTGTATCACAA
324 GTATCATCAAAATCTACCATCTAGCCCCAAAAAGTAAGTTT-A--ACTCAAGACTTGTATCACAA
* * *
1686780 GTTGTAACTTGGAATAAATTTATTTA--CTCTTTT-TTTTTCTCCTTAG
386 GTTATAGCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTCTCCTTAG
1686826 CTTTCATCTT
Statistics
Matches: 1293, Mismatches: 193, Indels: 82
0.82 0.12 0.05
Matches are distributed among these distances:
531 1 0.00
532 37 0.03
533 2 0.00
534 164 0.13
535 1 0.00
536 1 0.00
538 1 0.00
541 2 0.00
542 2 0.00
543 44 0.03
544 43 0.03
548 4 0.00
549 44 0.03
550 114 0.09
551 387 0.30
552 172 0.13
553 83 0.06
554 118 0.09
555 72 0.06
556 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (552 bp):
AATAATTTATTTACAATTAGAAAGATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCAT
CTAGCCTCTAAAATCAAATATAATTACTCAAGACTTGTATCACAAGTTATATCTTGGAATAAATT
TATTTATTCTCATTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAAAACAAAGCAAGAAA
CACGTTTATGAGACCAAGACTCAAAAGCAAAATAAATAAATTAGCCATTATGACTTTAGTATTAA
AGACAAAACACTTTCCTAAATAATTTATTTACAATTAGAAAGATTATCATTTACTTTTGACTTGT
ATCATCAAAATCTACCATCTAGCCCCAAAAAGTAAGTTTAACTCAAGACTTGTATCACAAGTTAT
AGCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTCTCCTTAGATTCTAAGACATAATTTAAAA
AGCAAAGCAGGAAACACGTTTATGAGACCAAGACTTGAAAGCAAATAAATAAATTAGCCACATAT
GACTTTAGTATTAAAGACAAAACATTTTCTTG
Found at i:1686718 original size:829 final size:824
Alignment explanation
Indices: 1684749--1686825 Score: 2713
Period size: 829 Copynumber: 2.5 Consensus size: 824
1684739 TAACAAATAC
* * * * * *
1684749 TTTTTTAAATAATTTATTTACAATTAGAAAGATTGTGGTTAATTTTTTATTTGTATCATCAAAAT
1 TTTTTTGAATAATTTATTTACAATTAGAAAGATTGTCGTTTACTTTTGACTTGTATCATCAAAAT
* * * * * * * * *
1684814 CTACCATCTAGCCCCTAAAATCAAATATAATTACTCAAGACTTGTATCACAAGTTATAGTTTGGA
66 CTATCATCTAGCCTCAAAAACCAAGTTTAATTACTCAAGACTTGTATTACAAGTTATAGCTTAGA
* * * * *
1684879 ATAAATTTATTTATTCCACTTTC--ATTCTCATT-GGATTCTAAGACATCATTTAAAAAGCAAAG
131 ATAAATTTATTTATTCCATTTTCTTTTTCTC-TTCAGATTCTAAGACATAATTTAAAAAGCAAAA
* *
1684941 CAAGAAACACGTTTATGAGACCAAAACTCAAAAGCAAAATAAATAAA-T------TA--ACTTTA
195 CAGGAAACACGTTTATGAGACCAAAACTCGAAAGCAAAATAAATAAATTACCACATATGACTTTA
* ** * * * *
1684997 GTA-CAAAAGGTAAAACACTTTCCTAAATAATTTATTTACAATTTGGAAAGATTGTAATTTGCTT
260 GTATTAAAA-ACAAAATACTTTCCTGAATAATTTATTTACAA-TTAGAAAGATTATAATTTGCTT
* * *
1685061 TTGACTTTTATCATCAAAATCCACCATTTAGCC-----C--TTTAATCACTCAAGACTTATATCA
323 TTGACTTGTATCATCAAAATCTACCATTTAGCCAAAATCAATTTAATCACTCAAAACTTATATCA
* ** *
1685119 CAAGTTATAGTTTGAAATAAATTTATTTATTCCCTTTTATTTTTATCCTTAGATTCTAAGACATA
388 CAAGTTGTAACTTGAAATAAATTTATTTATTCCCTTTTATTTTTCTCCTTAGATTCTAAGACATA
** * *
1685184 ATTAAAATGAAAAGCAAGAAATACGTTTATGAGACCAAGACTTGAATGCAAAATAAATAAATTAG
453 ATTAAAAAAAAAAGCAAGAAACACG--T-TGAGACCAAGACTTGAAAGCAAAATAAATAAATTAG
* * * * *
1685249 CTACATATGACTTTCATATTAAAAGACAAAACATTTTCTTGAATAATTTATTTACAATCTGAAAG
515 CCACATATGACTTTAATATTAAAAGACAAAACACTTTCTTAAATAATTTATTTACAATCGGAAAG
* * **
1685314 ATTGTCATTTACTTTTGACTTGTATCATCAAAATCTACCATTTAACCTTTAAAATCAAATATAAT
580 ATTGTCATTTACTTTTGACTTATATCATCAAAATCTACCATCTAACCCCTAAAATCAAATATAAT
* *
1685379 TACTCAAGACTTATCACAAGTTGCATCTTGGAATAAATTTATTTATTCTCTTTTCTTTTTCTCCT
645 TACTCAAGACTTATCACAAATTGCATCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTCTCCT
* *
1685444 TGGATTCTAAGACATAATTTAAAAAACAAAGCAAGAAACACGTTTATGAGACCAAGACTTAAAAG
710 TAGATTCTAAGACATAATTTAAAAAACAAAGCAAGAAACACGTTAATGAGACCAAGACTTAAAAG
**
1685509 CAAAATAAATAAATTAGCCATGTATGACTTTAGTATTAAAGACAAAACAT
775 CAAAATAAATAAATTAGCCACATATGACTTTAGTATTAAAGACAAAACAT
** * *
1685559 TTTCCTGAATAATTTATTTACAATTAGAAAGATTATCATTTACTTTTGACTTGTATCATCAAAAT
1 TTTTTTGAATAATTTATTTACAATTAGAAAGATTGTCGTTTACTTTTGACTTGTATCATCAAAAT
* ** * *
1685624 CTATCATCTAACCTCAAAAAGTAAGTTT-A--ACTCAAGATTTGTATTACGAGTTATAGCTTAGA
66 CTATCATCTAGCCTCAAAAACCAAGTTTAATTACTCAAGACTTGTATTACAAGTTATAGCTTAGA
* *
1685686 ATAAATTTATTTATTCCATTTTCTTTTTCT-TCTCAGATTCTAAGATATAATTTAAAAAGCAAAC
131 ATAAATTTATTTATTCCATTTTCTTTTTCTCT-TCAGATTCTAAGACATAATTTAAAAAGCAAAA
* *
1685750 CAGGAAACACGTTTATGAGACCAATACTCGAAAGCGAAATAAATAAATTAGCCACATATGACTTT
195 CAGGAAACACGTTTATGAGACCAAAACTCGAAAGCAAAATAAATAAATTA-CCACATATGACTTT
* * *
1685815 AGTATTAAAGACAAAATATTTTCCAGAATAATTTATTTACAATTAGAAAGATTATAATTTGCTTT
259 AGTATTAAAAACAAAATACTTTCCTGAATAATTTATTTACAATTAGAAAGATTATAATTTGCTTT
* *
1685880 TGACTTGTATCATCAAAATCTACCATCTAGCCTTTAAAATCAAGTTTAATCACTCAATACTTATA
324 TGACTTGTATCATCAAAATCTACCATTTAGCC---AAAATCAA-TTTAATCACTCAAAACTTATA
* * *
1685945 TCATAAGTTGTAACTTGAAAAAAATTTATTTATTCCCTTTTAATTTTCTCCTTAGATTCTAAGAC
385 TCACAAGTTGTAACTTGAAATAAATTTATTTATTCCCTTTTATTTTTCTCCTTAGATTCTAAGAC
* * *
1686010 ATAATTTAAAAAAACAAAGCATGAAACACG-T-AGATCAAGACTTGAAAGTAAAATAAATAAATT
450 ATAA-TTAAAAAAA-AAAGCAAGAAACACGTTGAGACCAAGACTTGAAAGCAAAATAAATAAATT
* * *
1686073 AGCCACA-AGTGCCTTTAATATTTAAAGACAAAATACTTTCTTAAATAATTTATTTACAATCGGA
513 AGCCACATA-TGACTTTAATATTAAAAGACAAAACACTTTCTTAAATAATTTATTTACAATCGGA
* ** * * *
1686137 GAGATTGTTGTTTACTTTTGACTTATATCATCAAAATTTACCATCTAGCCCCTAAAATCAAGTAT
577 AAGATTGTCATTTACTTTTGACTTATATCATCAAAATCTACCATCTAACCCCTAAAATCAAATAT
1686202 AATTACTCAAGACTTGATCACAAATTGCATCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTC
642 AATTACTCAAGACTT-ATCACAAATTGCATCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTC
* * * *
1686267 TCCTTAGATTTTAAGACATAATTTAAAAAACAAAGTAGGAAACACGTTAATG-GACGAAGACTTA
706 TCCTTAGATTCTAAGACATAATTTAAAAAACAAAGCAAGAAACACGTTAATGAGACCAAGACTTA
* *
1686331 AAAGCAATATAAATAAATTAGCCACATATGACTTTAGTATTAAAGGCAAAACAT
771 AAAGCAAAATAAATAAATTAGCCACATATGACTTTAGTATTAAAGACAAAACAT
*
1686385 TTTTTTGAATAATTTATTTACAATTAGAAAGATTGTCGTTTACTTTTGACTTATATCATCAAAAT
1 TTTTTTGAATAATTTATTTACAATTAGAAAGATTGTCGTTTACTTTTGACTTGTATCATCAAAAT
*
1686450 CTATTATCTAGCCTCAAAAACCAAGTTTAATTACTCAAGACTTGTATTACAAGTTATAGCTTAGA
66 CTATCATCTAGCCTCAAAAACCAAGTTTAATTACTCAAGACTTGTATTACAAGTTATAGCTTAGA
* * *
1686515 ATAAATTTATTTATTTCTTTTTCTTTTTCTCTTCAAATTCTAAGACATAATTTAAAAAGCAAAAC
131 ATAAATTTATTTATTCCATTTTCTTTTTCTCTTCAGATTCTAAGACATAATTTAAAAAGCAAAAC
* *
1686580 AGGAAACACGTTTATGAGACTAAGACTCGAAAGCAAAATAAATAAATTAACCACATATGACTTTA
196 AGGAAACACGTTTATGAGACCAAAACTCGAAAGCAAAATAAATAAATT-ACCACATATGACTTTA
* * * * * *
1686645 GTATTAAAAACAAATTAGTTTCTTGAATAATTTATTTACAATTAGAAAGACTATCATTTACTTTT
260 GTATTAAAAACAAAATACTTTCCTGAATAATTTATTTACAATTAGAAAGATTATAATTTGCTTTT
* * * * * *
1686710 AACTTGTATCATCAAAATCTACGATTTAGCCCCAAAAAGTAAATTTAATTACTCAAAATTTGTAT
325 GACTTGTATCATCAAAATCTACCATTTAG--CC-AAAA-TCAATTTAATCACTCAAAACTTATAT
* *
1686775 CACAAGTTGTAACTTGGAATAAATTTATTTA--CTCTTTT-TTTTTCTCCTTAG
386 CACAAGTTGTAACTTGAAATAAATTTATTTATTCCCTTTTATTTTTCTCCTTAG
1686826 CTTTCATCTT
Statistics
Matches: 1097, Mismatches: 132, Indels: 60
0.85 0.10 0.05
Matches are distributed among these distances:
807 51 0.05
808 1 0.00
809 74 0.07
810 76 0.07
817 2 0.00
818 50 0.05
819 35 0.03
820 3 0.00
825 1 0.00
826 311 0.28
827 102 0.09
829 364 0.33
830 12 0.01
831 15 0.01
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (824 bp):
TTTTTTGAATAATTTATTTACAATTAGAAAGATTGTCGTTTACTTTTGACTTGTATCATCAAAAT
CTATCATCTAGCCTCAAAAACCAAGTTTAATTACTCAAGACTTGTATTACAAGTTATAGCTTAGA
ATAAATTTATTTATTCCATTTTCTTTTTCTCTTCAGATTCTAAGACATAATTTAAAAAGCAAAAC
AGGAAACACGTTTATGAGACCAAAACTCGAAAGCAAAATAAATAAATTACCACATATGACTTTAG
TATTAAAAACAAAATACTTTCCTGAATAATTTATTTACAATTAGAAAGATTATAATTTGCTTTTG
ACTTGTATCATCAAAATCTACCATTTAGCCAAAATCAATTTAATCACTCAAAACTTATATCACAA
GTTGTAACTTGAAATAAATTTATTTATTCCCTTTTATTTTTCTCCTTAGATTCTAAGACATAATT
AAAAAAAAAAGCAAGAAACACGTTGAGACCAAGACTTGAAAGCAAAATAAATAAATTAGCCACAT
ATGACTTTAATATTAAAAGACAAAACACTTTCTTAAATAATTTATTTACAATCGGAAAGATTGTC
ATTTACTTTTGACTTATATCATCAAAATCTACCATCTAACCCCTAAAATCAAATATAATTACTCA
AGACTTATCACAAATTGCATCTTGGAATAAATTTATTTATTCCCTTTTCTTTTTCTCCTTAGATT
CTAAGACATAATTTAAAAAACAAAGCAAGAAACACGTTAATGAGACCAAGACTTAAAAGCAAAAT
AAATAAATTAGCCACATATGACTTTAGTATTAAAGACAAAACAT
Found at i:1687007 original size:20 final size:21
Alignment explanation
Indices: 1686982--1687028 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1686972 GGCCTAATGG
*
1686982 AAAAAATAATGCAAAACT-AA
1 AAAAAATAAAGCAAAACTGAA
*
1687002 AAAAAATAAAGTAAAACTGAA
1 AAAAAATAAAGCAAAACTGAA
1687023 AAAAAA
1 AAAAAA
1687029 CATTATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (21 bp):
AAAAAATAAAGCAAAACTGAA
Found at i:1687181 original size:9 final size:9
Alignment explanation
Indices: 1687135--1687222 Score: 54
Period size: 10 Copynumber: 8.9 Consensus size: 9
1687125 ATTATGATTT
1687135 TAAAAAAACC
1 TAAAAAAA-C
1687145 TATAAAAAAC
1 TA-AAAAAAC
1687155 -AATAAAAAC
1 TAA-AAAAAC
1687164 AATAAAAAAAC
1 --TAAAAAAAC
*
1687175 TAAAAAAAAT
1 T-AAAAAAAC
1687185 TGAAAAAAAAC
1 T--AAAAAAAC
1687196 TAAAATAAAC
1 TAAAA-AAAC
*
1687206 -AAAAAAAT
1 TAAAAAAAC
1687214 TGAAAAAAA
1 T-AAAAAAA
1687223 AAGCTATACA
Statistics
Matches: 65, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
8 4 0.06
9 16 0.25
10 22 0.34
11 21 0.32
12 2 0.03
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.14
Consensus pattern (9 bp):
TAAAAAAAC
Found at i:1687182 original size:21 final size:20
Alignment explanation
Indices: 1687148--1687212 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
1687138 AAAAACCTAT
*
1687148 AAAAAAC-AATAAAAACAATA
1 AAAAAACTAAAAAAAACAA-A
**
1687168 AAAAAACTAAAAAAAATTGAA
1 AAAAAACTAAAAAAAA-CAAA
*
1687189 AAAAAACTAAAATAAACAAA
1 AAAAAACTAAAAAAAACAAA
1687209 AAAA
1 AAAA
1687213 TTGAAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 13 0.35
21 23 0.62
22 1 0.03
ACGTcount: A:0.80, C:0.08, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAAACTAAAAAAAACAAA
Found at i:1687183 original size:11 final size:10
Alignment explanation
Indices: 1687135--1687212 Score: 70
Period size: 10 Copynumber: 7.8 Consensus size: 10
1687125 ATTATGATTT
*
1687135 TAAAAAAACC
1 TAAAAAAAAC
*
1687145 TATAAAAAAC
1 TAAAAAAAAC
*
1687155 -AATAAAAAC
1 TAAAAAAAAC
*
1687164 AATAAAAAAAC
1 TA-AAAAAAAC
*
1687175 TAAAAAAAAT
1 TAAAAAAAAC
1687185 TGAAAAAAAAC
1 T-AAAAAAAAC
*
1687196 TAAAATAAAC
1 TAAAAAAAAC
1687206 -AAAAAAA
1 TAAAAAAA
1687213 TTGAAAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
9 13 0.24
10 25 0.45
11 17 0.31
ACGTcount: A:0.77, C:0.09, G:0.01, T:0.13
Consensus pattern (10 bp):
TAAAAAAAAC
Found at i:1688214 original size:24 final size:24
Alignment explanation
Indices: 1688159--1688215 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1688149 ATGAGCAATG
**
1688159 ATACAAATATTATATAAGAAAATA
1 ATACAAATACAATATAAGAAAATA
1688183 ATTA-AAATACAATATGAA-AAAATA
1 A-TACAAATACAATAT-AAGAAAATA
1688207 ATACAAATA
1 ATACAAATA
1688216 GTACATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 2 0.07
24 22 0.79
25 4 0.14
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.26
Consensus pattern (24 bp):
ATACAAATACAATATAAGAAAATA
Found at i:1692848 original size:11 final size:11
Alignment explanation
Indices: 1692832--1692856 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1692822 AAATTAAAAG
1692832 AAATAAATTTT
1 AAATAAATTTT
1692843 AAATAAATTTT
1 AAATAAATTTT
1692854 AAA
1 AAA
1692857 AAGTTGATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATAAATTTT
Found at i:1693069 original size:39 final size:39
Alignment explanation
Indices: 1692962--1693070 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 39
1692952 TCGTATTTTA
* * *
1692962 AAAGATATGACTAATGCATAGATTTTTTATTGGAATCTG
1 AAAGATATGACTAATGTATAGATTTTTTATTGAAATTTG
* * * *
1693001 AAAGATATTAGTAACGTATAGATTATTTATTGAAATTTG
1 AAAGATATGACTAATGTATAGATTTTTTATTGAAATTTG
* * *
1693040 AAAGATGTGACTAATATATAAATTTTTTATT
1 AAAGATATGACTAATGTATAGATTTTTTATT
1693071 AGAATTCAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (39 bp):
AAAGATATGACTAATGTATAGATTTTTTATTGAAATTTG
Found at i:1693532 original size:14 final size:14
Alignment explanation
Indices: 1693515--1693544 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1693505 CAAATTGTAA
1693515 CAATTAGACTAATG
1 CAATTAGACTAATG
1693529 CAATTAGACTAATG
1 CAATTAGACTAATG
1693543 CA
1 CA
1693545 TGATTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (14 bp):
CAATTAGACTAATG
Found at i:1696268 original size:22 final size:20
Alignment explanation
Indices: 1696220--1696278 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 20
1696210 ATGCCTTTAT
*
1696220 GTATCGATACATAACA-TTGT
1 GTATCGATACATAA-AGTTGA
1696240 GTATCGATACATAAAGTAATGA
1 GTATCGATACATAAAGT--TGA
1696262 GTATCGATACAATAAAG
1 GTATCGATAC-ATAAAG
1696279 CATGTATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
22 12 0.35
23 6 0.18
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (20 bp):
GTATCGATACATAAAGTTGA
Found at i:1698213 original size:72 final size:71
Alignment explanation
Indices: 1698045--1698812 Score: 534
Period size: 72 Copynumber: 10.7 Consensus size: 71
1698035 TAATTACAAT
* * * * * * *
1698045 ATAAATTTAAAATTCTGTAAATAAGAATAAATTATAGCTTAAAAAATTTGAACTTATATAATCAC
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATACCTT-AAAAATTTAAACTTGTATAATTA-
*
1698110 ACCCAAAA
64 ACCAAAAA
* *
1698118 ATAAATTTAAACTTTTACAAATAAAAATAAA-TATACCTTTAAAAAATTTAAACTTGTATAATTA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATACC-TT-AAAAATTTAAACTTGTATAATTA
*
1698182 ACCAGAAA
64 ACCAAAAA
* * ** *
1698190 ATAAATTTAAAGTTCTATAAATAAAAATAAATCATATATTAAAAATTTAAACTCGTATAATTATA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATTA-A
*
1698255 CTAAAAA
65 CCAAAAA
* * * * * *
1698262 ATAAATTTAAACTTTTATAAATAAAATTAAATTATATCTTAAAAATTTAAACTAGTATACTCATA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATTA-A
*
1698327 CCTATAAA
65 CC-AAAAA
* * * * * * * *
1698335 A-AATTTTTAACTTCTACAAATAAAGATAAATAATATCTTAAAAATTTTAACTTGTAAAATCATA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAAT--TA
*
1698399 CCCAAAAA
64 ACCAAAAA
* * * * **
1698407 ATCAAATTCAAACTACTACAAATAAAGAAT--A--ATACCTTATAAATTTAAACTCATATAATCA
1 AT-AAATTTAAACTTCTATAAATAAA-AATAAATTATACCTTAAAAATTTAAACTTGTATAAT--
*
1698468 TACCCAAAAA
62 TAACCAAAAA
* * * * *
1698478 ATAAATTTAAACTTTTAT-AA-AAAAATAAATTATATCTTCAAAATTTTAAAATTATATAATCCT
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATACCTT-AAAAATTTAAACTTGTATAAT--T
1698541 CAACCCCAAAAA
63 -AA--CCAAAAA
* * * * *
1698553 ATAAATTTTAACTTTTACAAATAAAAATAAATTATA-CTT---AA---AAA-TT-TATCA-TACC
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATTAAC
1698608 CAAAAA
66 CAAAAA
* * * * * ***
1698614 ACAAATATAAACTTCTATAAA-AGAGATAAATAATA-CTCTAAAAATTTAAACACATATAATTAA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATACCT-TAAAAATTTAAACTTGTATAATTAA
1698677 CCCAAAAAA
65 -CC-AAAAA
* * * *
1698686 ATAAATTTAAACTTTTACAAGA-AAAAATAAACTATACCTTCAAAAATTTAAACTCGTATAACTT
1 ATAAATTTAAACTTCTATAA-ATAAAAATAAATTATACCTT-AAAAATTTAAACTTGTATAA--T
1698750 TAAATCCCAAAAA
62 T-AA--CCAAAAA
* * * *
1698763 ATATATGTAAACTTCTATAAATAAAAATAAACTATACCCTAAAAATTTAA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATACCTTAAAAATTTAA
1698813 CTCAAAAATA
Statistics
Matches: 558, Mismatches: 98, Indels: 75
0.76 0.13 0.10
Matches are distributed among these distances:
60 13 0.02
61 24 0.04
63 1 0.00
64 3 0.01
67 10 0.02
68 5 0.01
69 10 0.02
70 14 0.03
71 66 0.12
72 199 0.36
73 73 0.13
74 40 0.07
75 25 0.04
76 18 0.03
77 54 0.10
78 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.32
Consensus pattern (71 bp):
ATAAATTTAAACTTCTATAAATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATTAAC
CAAAAA
Found at i:1698249 original size:40 final size:39
Alignment explanation
Indices: 1698192--1698320 Score: 94
Period size: 40 Copynumber: 3.4 Consensus size: 39
1698182 ACCAGAAAAT
*
1698192 AAATTTAAAGTTC-TATAAATAAAAATAAATCATATATTAA
1 AAATTTAAA-CTCGTATAAATAAAAATAAAT-ATATATTAA
* * *
1698232 AAATTTAAACTCGTAT-AATTATACTAAA-A-A-A-T--
1 AAATTTAAACTCGTATAAATAAAAATAAATATATATTAA
** * *
1698264 AAATTTAAACTTTTATAAATAAAATTAAATTATATCTTAA
1 AAATTTAAACTCGTATAAATAAAAATAAA-TATATATTAA
*
1698304 AAATTTAAACTAGTATA
1 AAATTTAAACTCGTATA
1698321 CTCATACCTA
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
32 14 0.21
33 9 0.13
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 1 0.01
39 11 0.16
40 27 0.40
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.37
Consensus pattern (39 bp):
AAATTTAAACTCGTATAAATAAAAATAAATATATATTAA
Found at i:1698275 original size:144 final size:143
Alignment explanation
Indices: 1698045--1698812 Score: 655
Period size: 144 Copynumber: 5.3 Consensus size: 143
1698035 TAATTACAAT
* * * * * *
1698045 ATAAATTTAAAATTCTGTAAATAAGAATAAATTATAGCTTAAAAAATTTGAACTTATATAATCAC
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATATCTT-AAAAATTTAAACTTATATAATTA-
*
1698110 ACCC-AAAAATAAATTTAAACTTTTACAAATAAAAATAAA-TATACCTTTAAAAAATTTAAACTT
64 ACCCAAAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACC-TT-AAAAATTTAAACTC
*
1698173 GTATAATTAACCAGAAA
127 GTATAATTAACCAAAAA
* * * **
1698190 ATAAATTTAAAGTTCTATAAATAAAAATAAATCATATATTAAAAATTTAAACTCGTATAATTATA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATATCTTAAAAATTTAAACTTATATAATTA-A
* * * * *
1698255 -CTAAAAAATAAATTTAAACTTTTATAAATAAAATTAAATTATATCTTAAAAATTTAAACTAGTA
65 CCCAAAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTA
* * *
1698319 TACTCATACCTATAAA
130 TAATTA-ACC-AAAAA
* * * * * * * * *
1698335 A-AATTTTTAACTTCTACAAATAAAGATAAATAATATCTTAAAAATTTTAACTTGTAAAATCATA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATATCTTAAAAATTTAAACTTATATAATTA-A
* ** * *
1698399 CCCAAAAAATCAAATTCAAACTACTACAAATAAAGAAT--A--ATACCTTATAAATTTAAACTCA
65 CCCAAAAAAT-AAATTTAAACTTTTACAAATAAA-AATAAATTATACCTTAAAAATTTAAACTCG
*
1698460 TATAATCATACCCAAAAA
128 TATAAT--TAACCAAAAA
* * *
1698478 ATAAATTTAAACTTTTAT-AA-AAAAATAAATTATATCTTCAAAATTTTAAAATTATATAATCCT
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATATCTT-AAAAATTTAAACTTATATAAT--T
*
1698541 CAACCCCAAAAAATAAATTTTAACTTTTACAAATAAAAATAAATTATA-CTTAAAAATTT--A-T
63 -AA-CCCAAAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACT
*
1698602 C-----A-TACCCAAAAA
126 CGTATAATTAACCAAAAA
* * * * * **
1698614 ACAAATATAAACTTCTATAAA-AGAGATAAATAATA-CTCTAAAAATTTAAACACATATAATTAA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATATCT-TAAAAATTTAAACTTATATAATTAA
*
1698677 CCCAAAAAAATAAATTTAAACTTTTACAAGA-AAAAATAAACTATACCTTCAAAAATTTAAACTC
65 CCC-AAAAAATAAATTTAAACTTTTACAA-ATAAAAATAAATTATACCTT-AAAAATTTAAACTC
1698741 GTATAACTTTAAATCCCAAAAA
127 GTATAA--TT-AA--CCAAAAA
* * * * *
1698763 ATATATGTAAACTTCTATAAATAAAAATAAACTATACCCTAAAAATTTAA
1 ATAAATTTAAACTTCTATAAATAAAAATAAATTATATCTTAAAAATTTAA
1698813 CTCAAAAATA
Statistics
Matches: 500, Mismatches: 82, Indels: 77
0.76 0.12 0.12
Matches are distributed among these distances:
132 3 0.01
133 39 0.08
134 5 0.01
135 8 0.02
136 44 0.09
137 15 0.03
138 2 0.00
139 1 0.00
142 16 0.03
143 68 0.14
144 129 0.26
145 75 0.15
146 32 0.06
147 13 0.03
148 3 0.01
149 25 0.05
150 21 0.04
151 1 0.00
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.32
Consensus pattern (143 bp):
ATAAATTTAAACTTCTATAAATAAAAATAAATTATATCTTAAAAATTTAAACTTATATAATTAAC
CCAAAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTAT
AATTAACCAAAAA
Found at i:1698627 original size:61 final size:61
Alignment explanation
Indices: 1698545--1698661 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
1698535 AATCCTCAAC
* * * * *
1698545 CCCAAAAAATAAATTTTAACTTTTACAAATAAAAATAAATTATACT-TAAAAATTTATCATA
1 CCCAAAAAACAAATATAAACTTCTACAAA-AAAAATAAATAATACTCTAAAAATTTATCATA
* * *
1698606 CCCAAAAAACAAATATAAACTTCTATAAAAGAGATAAATAATACTCTAAAAATTTA
1 CCCAAAAAACAAATATAAACTTCTACAAAAAAAATAAATAATACTCTAAAAATTTA
1698662 AACACATATA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 13 0.28
61 34 0.72
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.30
Consensus pattern (61 bp):
CCCAAAAAACAAATATAAACTTCTACAAAAAAAATAAATAATACTCTAAAAATTTATCATA
Found at i:1698634 original size:136 final size:135
Alignment explanation
Indices: 1698464--1698735 Score: 349
Period size: 136 Copynumber: 2.0 Consensus size: 135
1698454 AACTCATATA
* * * * *
1698464 ATCATACCCAAAAAATAAATTTAAACTTTTATAAAA-AAATAAATTATA-TCTTCAAAATTTTAA
1 ATCATACCCAAAAAACAAATATAAACTTCTATAAAAGAAATAAATAATACTC-T-AAAAATTTAA
* * * *
1698527 A-ATTATATAATCCTCAACCCCAAAAAATAAATTTTAACTTTTACAA-ATAAAAATAAATTATA-
64 ACA-CATATAAT--T-AACCCAAAAAAATAAATTTAAACTTTTACAAGA-AAAAATAAACTATAC
1698589 CTT-AAAAATTT
124 CTTCAAAAATTT
*
1698600 ATCATACCCAAAAAACAAATATAAACTTCTATAAAAGAGATAAATAATACTCTAAAAATTTAAAC
1 ATCATACCCAAAAAACAAATATAAACTTCTATAAAAGAAATAAATAATACTCTAAAAATTTAAAC
1698665 ACATATAATTAACCCAAAAAAATAAATTTAAACTTTTACAAGAAAAAATAAACTATACCTTCAAA
66 ACATATAATTAACCCAAAAAAATAAATTTAAACTTTTACAAGAAAAAATAAACTATACCTTCAAA
1698730 AATTT
131 AATTT
1698735 A
1 A
1698736 AACTCGTATA
Statistics
Matches: 120, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
133 42 0.35
134 5 0.04
135 9 0.08
136 50 0.42
137 12 0.10
138 2 0.02
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.31
Consensus pattern (135 bp):
ATCATACCCAAAAAACAAATATAAACTTCTATAAAAGAAATAAATAATACTCTAAAAATTTAAAC
ACATATAATTAACCCAAAAAAATAAATTTAAACTTTTACAAGAAAAAATAAACTATACCTTCAAA
AATTT
Found at i:1698820 original size:57 final size:57
Alignment explanation
Indices: 1698759--1698869 Score: 161
Period size: 57 Copynumber: 1.9 Consensus size: 57
1698749 TTAAATCCCA
* * *
1698759 AAAAATATATGTAAACTTCTATAAATAAAAATAAACT-ATACCCTAAAAATTTAACTC
1 AAAAATAAATGTAAACTTATAAAAATAAAAATAAA-TAATACCCTAAAAATTTAACTC
* *
1698816 AAAAATAAATTTAAACTTATAAAAATAAAGATAAATAATACCCTAAAAATTTAA
1 AAAAATAAATGTAAACTTATAAAAATAAAAATAAATAATACCCTAAAAATTTAA
1698870 ACTTGTTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
56 1 0.02
57 47 0.98
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.29
Consensus pattern (57 bp):
AAAAATAAATGTAAACTTATAAAAATAAAAATAAATAATACCCTAAAAATTTAACTC
Found at i:1698829 original size:77 final size:74
Alignment explanation
Indices: 1698605--1698850 Score: 207
Period size: 77 Copynumber: 3.3 Consensus size: 74
1698595 AATTTATCAT
* * * * *
1698605 ACCCAAAAAACAAATATAAACTTCTATAAAAGAGATAAA-TAATACTCTAAAAATTTAA-ACACA
1 ACCCAAAAAATAAATATAAACTTCTATAAAAAAAATAAACT-ATACCCTAAAAATTTAACTCA-A
1698668 TAT-AA-TT-A
64 TATAAATTTAA
* * * *
1698676 ACCCAAAAAAATAAATTTAAACTTTTACAAGAAAAAATAAACTATACCTTCAAAAATTTAAACTC
1 ACCC-AAAAAATAAATATAAACTTCTATAA-AAAAAATAAACTATACCCT-AAAAATTT-AACTC
* *
1698741 -GTATAACTTTAA
62 AATATAAATTTAA
* *
1698753 ATCCCAAAAAATATATGTAAACTTCTATAAATAAAAATAAACTATACCCTAAAAATTTAACTCAA
1 A-CCCAAAAAATAAATATAAACTTCTATAAA-AAAAATAAACTATACCCTAAAAATTTAACTC-A
*
1698818 AAATAAATTTAA
63 ATATAAATTTAA
** *
1698830 ACTTATAAAAATAAAGATAAA
1 ACCCA-AAAAATAAATATAAA
1698851 TAATACCCTA
Statistics
Matches: 137, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
71 4 0.03
72 21 0.15
73 13 0.09
74 12 0.09
75 8 0.06
76 14 0.10
77 62 0.45
78 3 0.02
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (74 bp):
ACCCAAAAAATAAATATAAACTTCTATAAAAAAAATAAACTATACCCTAAAAATTTAACTCAATA
TAAATTTAA
Found at i:1698937 original size:206 final size:207
Alignment explanation
Indices: 1698393--1698954 Score: 583
Period size: 206 Copynumber: 2.7 Consensus size: 207
1698383 AACTTGTAAA
* * *
1698393 ATCATACCCAAAAAATCAAAT-TCAAAC-TACTACAAATAAAG---AATAATACCTTATAAATTT
1 ATCATACCCAAAAAA-CAAATAT-AAACTTA-TA-AAAAAAAGATAAATAATACCCTAAAAATTT
* * *
1698453 AAACTCATATAATCATACCCAAAAAATAAATTTAAACTTTTATAAAAAAATAAATTATATCTTCA
62 AAACTCATATAATCA-ACCAAAAAAATAAATTTAAACTTTTACAAAAAAATAAATTATACCTTCA
* ** * * * *
1698518 AAATTTTAAAATTATATAATCCTCAACCCCAAAAAATAAATTTTAACTTTTACAAATAAAAATAA
126 AAAATTTAAAATCGTATAATCCTAAACCCCAAAAAATAAATGTAAACTTCTACAAATAAAAATAA
* *
1698583 ATTATACTTAAAAATTT
191 ACTATACCTAAAAATTT
* * * *
1698600 ATCATACCCAAAAAACAAATATAAACTTCTATAAAAGAGATAAATAATACTCTAAAAATTTAAAC
1 ATCATACCCAAAAAACAAATATAAACTTATAAAAAAAAGATAAATAATACCCTAAAAATTTAAAC
* * *
1698665 ACATATAATTAACCCAAAAAAATAAATTTAAACTTTTACAAGAAAAAATAAACTATACCTTCAAA
66 TCATATAATCAA-CCAAAAAAATAAATTTAAACTTTTAC-A-AAAAAATAAATTATACCTTCAAA
* * * * *
1698730 AATTTAAACTCGTATAA-CTTTAAATCCCAAAAAATATATGTAAACTTCTATAAATAAAAATAAA
128 AATTTAAAATCGTATAATC-CTAAACCCCAAAAAATAAATGTAAACTTCTACAAATAAAAATAAA
1698794 CTATACCCTAAAAA-TT
192 CTATA-CCTAAAAATTT
* * *
1698810 -T-A-ACTC-AAAAATAAATTTAAACTTATAAAAATAAAGATAAATAATACCCTAAAAATTTAAA
1 ATCATACCCAAAAAACAAATATAAACTTATAAAAA-AAAGATAAATAATACCCTAAAAATTTAAA
** * *
1698871 CTTGTTTAATCAACCTAAAAAATAAATTTAAA-TTTCTACAAATACAAATAAATTATA-CTATCA
65 CTCATATAATCAACCAAAAAAATAAATTTAAACTTT-TACAAA-A-AAATAAATTATACCT-TCA
*
1698934 AAAATTTAAAAACGTATAATC
126 AAAATTTAAAATCGTATAATC
1698955 ATATCTAAAA
Statistics
Matches: 296, Mismatches: 43, Indels: 32
0.80 0.12 0.09
Matches are distributed among these distances:
204 2 0.01
205 12 0.04
206 84 0.28
207 57 0.19
208 54 0.18
209 3 0.01
210 77 0.26
211 7 0.02
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (207 bp):
ATCATACCCAAAAAACAAATATAAACTTATAAAAAAAAGATAAATAATACCCTAAAAATTTAAAC
TCATATAATCAACCAAAAAAATAAATTTAAACTTTTACAAAAAAATAAATTATACCTTCAAAAAT
TTAAAATCGTATAATCCTAAACCCCAAAAAATAAATGTAAACTTCTACAAATAAAAATAAACTAT
ACCTAAAAATTT
Found at i:1699065 original size:72 final size:72
Alignment explanation
Indices: 1698970--1699560 Score: 444
Period size: 73 Copynumber: 8.2 Consensus size: 72
1698960 TAAAAAGCAC
* *
1698970 ATAAAAATAAATTATATCC-TAAAATTTTAAACTTGTATAATTATACCAAAAAAACATATTT-AA
1 ATAAAAATAAATTATA-CCTTAAAAATTTAAACTTGTATAATCATACCAAAAAAA-ATATTTAAA
1699033 CTTTTACAA
64 CTTTTACAA
* * * * * *
1699042 ATCAATATAAATTATACCTTAAAAATTTAAACTCGCAT-A--ATA--AAAAATAA-ATTTAAAAT
1 ATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATCATACCAAAAAAAATATTTAAACT
* *
1699101 TCTGA-AC
66 T-TTACAA
** * * * *
1699108 ATAAAAATAAATTATATATAAAAAATTTAAACTCGTATAATCGTACCCAAAAAACATATTTAAA-
1 ATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATCATA-CCAAAAAAAATATTTAAAC
*
1699172 TTTCTTCAA
65 TTT-TACAA
* *
1699181 ATAAAAATCAATTA-AGCCTTAAAAATTTAAACTAGTATAATCATACTCAAAAAATAA-ATTTAA
1 ATAAAAATAAATTATA-CCTTAAAAATTTAAACTTGTATAATCATAC-CAAAAAA-AATATTTAA
1699244 ACTTTTACAA
63 ACTTTTACAA
* * * * * * *
1699254 ATAAAGATAAATAATATCGTAAAAATTTAAA-TTCATATAATCAAACGAAAAAATAA-ATTTAAA
1 ATAAAAATAAATTATACCTTAAAAATTTAAACTT-GTATAATCATACCAAAAAA-AATATTTAAA
* *
1699317 CTTCTATAA
64 CTTTTACAA
* * * * *
1699326 ATAAAAATAACTTATATCTTCAAAAATTTAAACTTGTATAATCGTACGTAAAAAATATATTTAAA
1 ATAAAAATAAATTATACCTT-AAAAATTTAAACTTGTATAATCATAC-CAAAAAAAATATTTAAA
* *
1699391 TTTTTAAAA
64 CTTTTACAA
* ** *** ** * *
1699400 ATTAAAATAAATTATACCCCAAAAATTTAAACTTACGTAATCA-AATAAAAAGTAA-ACTTAAAC
1 ATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATCATACCAAAAA-AAATATTTAAAC
1699463 TTTTACAA
65 TTTTACAA
* * * * *
1699471 ATAAAAATAAATTATATCTTCAAAATTTAAACTCGTATAATCAT-GCATTACAAACAA-ATTTAA
1 ATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATCATACCA--A-AAAAAATATTTAA
*
1699534 ACTTCTACAA
63 ACTTTTACAA
*
1699544 ATAAAAATAAATAATAC
1 ATAAAAATAAATTATAC
1699561 TTTTAATCAA
Statistics
Matches: 409, Mismatches: 83, Indels: 53
0.75 0.15 0.10
Matches are distributed among these distances:
65 4 0.01
66 38 0.09
67 9 0.02
69 5 0.01
71 58 0.14
72 82 0.20
73 169 0.41
74 44 0.11
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (72 bp):
ATAAAAATAAATTATACCTTAAAAATTTAAACTTGTATAATCATACCAAAAAAAATATTTAAACT
TTTACAA
Found at i:1699240 original size:139 final size:137
Alignment explanation
Indices: 1698816--1699359 Score: 364
Period size: 146 Copynumber: 3.9 Consensus size: 137
1698806 AATTTAACTC
* * * * * * * * * *
1698816 AAAAATAAATTTAAACTTATAAAAATAAAGATAAATAATACCCTAAAAATTTAAACTTGTTTAAT
1 AAAAATAAA-TTAAAATTCTGAACATAAAAATAAATTATATCATAAAAATTTAAACTCGTATAAT
* * * *
1698881 CA-ACCTAAAAAATAAATTTAAATTTCTACAAATACAAATAAATTATA-CTATCAAAAATTTAAA
65 CATACCAAAAAAACATATTTAAATTT-TACAAATAAAAATAAATTATACCT-T-AAAAATTTAAA
* *
1698944 --AACGT-AT-
127 CTAGCATAATA
** * * * * *
1698951 AATCAT--ATCTAAAA---AGCACATAAAAATAAATTATATCCTAAAATTTTAAACTTGTATAAT
1 AAAAATAAAT-TAAAATTCTGAACATAAAAATAAATTATATCATAAAAATTTAAACTCGTATAAT
* * * * *
1699011 TATACCAAAAAAACATATTTAACTTTTACAAATCAATATAAATTATACCTTAAAAATTTAAACTC
65 CATACCAAAAAAACATATTTAAATTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTA
1699076 GCATAATA
130 GCATAATA
1699084 AAAAATAAATTTAAAATTCTGAACATAAAAATAAATTATAT-ATAAAAAATTTAAACTCGTATAA
1 AAAAATAAA-TTAAAATTCTGAACATAAAAATAAATTATATCAT-AAAAATTTAAACTCGTATAA
* * * *
1699148 TCGTACCCAAAAAACATATTTAAATTTCTTCAAATAAAAATCAATTA-AGCCTTAAAAATTTAAA
64 TCATACCAAAAAAACATATTTAAATTT-TACAAATAAAAATAAATTATA-CCTTAAAAATTTAAA
*
1699212 CTAGTATAATCATACTCA
127 CTAG------CATAAT-A
* * * * * * * *
1699230 AAAAATAAATTTAAACTT-TTACAAATAAAGATAAATAATATCGTAAAAATTTAAATTCATATAA
1 AAAAATAAA-TTAAAATTCTGA-ACATAAAAATAAATTATATCATAAAAATTTAAACTCGTATAA
* * * * * *
1699294 TCAAACGAAAAAATA-A-ATTTAAACTTCTATAAATAAAAATAACTTATATCTTCAAAAATTTAA
64 TCATACCAAAAAA-ACATATTTAAA-TTTTACAAATAAAAATAAATTATACCTT-AAAAATTTAA
1699357 ACT
126 ACT
1699360 TGTATAATCG
Statistics
Matches: 322, Mismatches: 58, Indels: 47
0.75 0.14 0.11
Matches are distributed among these distances:
129 11 0.03
130 57 0.18
131 23 0.07
132 3 0.01
133 9 0.03
135 10 0.03
136 1 0.00
137 1 0.00
138 62 0.19
139 33 0.10
145 32 0.10
146 78 0.24
147 2 0.01
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (137 bp):
AAAAATAAATTAAAATTCTGAACATAAAAATAAATTATATCATAAAAATTTAAACTCGTATAATC
ATACCAAAAAAACATATTTAAATTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTAG
CATAATA
Found at i:1699295 original size:146 final size:144
Alignment explanation
Indices: 1698970--1699555 Score: 509
Period size: 146 Copynumber: 4.1 Consensus size: 144
1698960 TAAAAAGCAC
* * * *
1698970 ATAAAAATAAATTATATCCTAAAATTTTAAACTTGTATAAT-TATACCAAAAAAACATATTTAAC
1 ATAAAAATAAATTATATCCTAAAAATTTAAACTTATATAATCTA-A-CAAAAAAACAAATTTAAA
* *
1699034 TTTTACAAATCAATATAAATTATACCTTAAAAATTTAAACTCG------CATA-ATAAAAAATAA
64 TTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACATAAAAAATAA
* * *
1699092 ATTTAAAATTCTGA-AC
129 ATTTAAACTT-TTACAA
* ** * * *
1699108 ATAAAAATAAATTATAT-ATAAAAAATTTAAACTCGTATAATCGTACCCAAAAAACATATTTAAA
1 ATAAAAATAAATTATATCCT-AAAAATTTAAACTTATATAATC-TAACAAAAAAACAAATTTAAA
* * *
1699172 TTTCTTCAAATAAAAATCAATTA-AGCCTTAAAAATTTAAACTAGTATAATCATAC-TCAAAAAA
64 TTT-TACAAATAAAAATAAATTATA-CCTTAAAAATTTAAACTCGTATAATCATACAT-AAAAAA
1699235 TAAATTTAAACTTTTACAA
126 TAAATTTAAACTTTTACAA
* * * * * *
1699254 ATAAAGATAAATAATATCGTAAAAATTTAAA-TTCATATAATCAAACGAAAAAATAAATTTAAAC
1 ATAAAAATAAATTATATCCTAAAAATTTAAACTT-ATATAATCTAACAAAAAAACAAATTTAAA-
* * * * * * *
1699318 TTCTATAAATAAAAATAACTTATATCTTCAAAAATTTAAACTTGTATAATCGTACGTAAAAAATA
64 TTTTACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCGTATAATCATACATAAAAAATA
* * *
1699383 TATTTAAATTTTTAAAA
128 AATTTAAACTTTTACAA
* * * ** ** *
1699400 ATTAAAATAAATTATACCCCAAAAATTTAAACTTACGTAATC-AA-ATAAAAAGTAAACTTAAAC
1 ATAAAAATAAATTATATCCTAAAAATTTAAACTTATATAATCTAACA-AAAAAACAAATTTAAA-
* * * * * *
1699463 TTTTACAAATAAAAATAAATTATATCTTCAAAATTTAAACTCGTATAATCATGCATTACAAACAA
64 TTTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACATAAAAAATAA
*
1699528 ATTTAAACTTCTACAA
129 ATTTAAACTTTTACAA
1699544 ATAAAAATAAAT
1 ATAAAAATAAAT
1699556 AATACTTTTA
Statistics
Matches: 364, Mismatches: 62, Indels: 38
0.78 0.13 0.08
Matches are distributed among these distances:
137 1 0.00
138 56 0.15
139 33 0.09
140 2 0.01
144 52 0.14
145 84 0.23
146 132 0.36
147 4 0.01
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (144 bp):
ATAAAAATAAATTATATCCTAAAAATTTAAACTTATATAATCTAACAAAAAAACAAATTTAAATT
TTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACATAAAAAATAAAT
TTAAACTTTTACAA
Found at i:1699661 original size:25 final size:26
Alignment explanation
Indices: 1699605--1699653 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1699595 TCATATCTTA
* *
1699605 AAAT-AAAATAATTGTGAACTTATAC
1 AAATAAAAATAAATGTGAACTCATAC
1699630 AAATAAAAATAAAT-TGAACTCATA
1 AAATAAAAATAAATGTGAACTCATA
1699654 TAATTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (26 bp):
AAATAAAAATAAATGTGAACTCATAC
Found at i:1701397 original size:21 final size:22
Alignment explanation
Indices: 1701373--1701433 Score: 83
Period size: 20 Copynumber: 2.9 Consensus size: 22
1701363 AGTCAGTTGT
*
1701373 ATTAAA-ATAAAATTTTAAATA
1 ATTAAATATATAATTTTAAATA
*
1701394 ATTAAATATTTAATTTT-AATA
1 ATTAAATATATAATTTTAAATA
1701415 A-TAAATATATAATTTTAAA
1 ATTAAATATATAATTTTAAA
1701434 AGTAAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.40
21 13 0.37
22 8 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTAAATATATAATTTTAAATA
Found at i:1701441 original size:24 final size:22
Alignment explanation
Indices: 1701375--1701446 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 22
1701365 TCAGTTGTAT
* *
1701375 TAAA-ATAAAATTTTAAATAAT
1 TAAATATATAATTTTAAATAAA
*
1701396 TAAATATTTAATTTT-AAT-AA
1 TAAATATATAATTTTAAATAAA
1701416 TAAATATATAATTTTAAAAGTAAA
1 TAAATATATAATTTT-AAA-TAAA
1701440 TAAATAT
1 TAAATAT
1701447 TAAATATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 15 0.36
21 7 0.17
22 10 0.24
23 1 0.02
24 9 0.21
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
TAAATATATAATTTTAAATAAA
Found at i:1702266 original size:2 final size:2
Alignment explanation
Indices: 1702259--1702289 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1702249 GTTCTGTAAT
1702259 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1702290 TTTATTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1703336 original size:34 final size:34
Alignment explanation
Indices: 1703269--1703485 Score: 269
Period size: 34 Copynumber: 6.4 Consensus size: 34
1703259 ATGGAAATGC
* *
1703269 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
1703302 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
1703336 TGTTGACTAAAT-GAAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* *
1703369 TGTTGATTAATTGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
1703403 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
*
1703437 TGTTGACTAAATGGGAGATTTGGTAGGTTGT-CCAT
1 TGTTGATTAAATGGGAGATTTGGTA-GTT-TACCAT
1703472 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1703486 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
33 38 0.24
34 99 0.63
35 20 0.13
36 1 0.01
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
Found at i:1703377 original size:67 final size:66
Alignment explanation
Indices: 1703269--1703487 Score: 285
Period size: 67 Copynumber: 3.2 Consensus size: 66
1703259 ATGGAAATGC
* *
1703269 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TTGCC
1703334 AT
65 AT
* ** * * * *
1703336 TGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAATTGGGAGATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTGCC
1703401 AT
65 AT
* * *
1703403 TATTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGT
1 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTG-
1703468 CCAT
63 CCAT
1703472 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1703488 GTTTTTACCA
Statistics
Matches: 129, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
67 66 0.51
68 48 0.37
69 15 0.12
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (66 bp):
TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTGCCA
T
Found at i:1703420 original size:101 final size:102
Alignment explanation
Indices: 1703269--1703485 Score: 330
Period size: 101 Copynumber: 2.1 Consensus size: 102
1703259 ATGGAAATGC
* * * *
1703269 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1703334 ATTGTTGACTAAAT-GAAGATTTGGTAGCTT-ACCAT
66 ATTGTTGACTAAATGGAAGATTTGGTAGCTTGACCAT
* *
1703369 TGTTGATTAATTGGGAGATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTAC
1 TGTTGATTAAAT-GGAGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTAC
* * *
1703434 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGTCCAT
65 CATTGTTGACTAAATGGAAGATTTGGTAGCTTGACCAT
1703472 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1703486 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
100 11 0.11
101 62 0.60
102 16 0.15
103 15 0.14
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.41
Consensus pattern (102 bp):
TGTTGATTAAATGGAGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACC
ATTGTTGACTAAATGGAAGATTTGGTAGCTTGACCAT
Found at i:1703846 original size:19 final size:19
Alignment explanation
Indices: 1703790--1703852 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1703780 TGGTTGTCGA
**
1703790 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1703809 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1703828 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1703847 GTTACT
1 GGTACT
1703853 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1707987 original size:34 final size:34
Alignment explanation
Indices: 1707918--1708135 Score: 278
Period size: 34 Copynumber: 6.5 Consensus size: 34
1707908 AAGTGGGAGA
* *
1707918 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
1707951 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
1707985 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* *
1708018 ATTGTTGATTAATTGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
1708052 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
1708086 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
1708120 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1708136 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
33 40 0.25
34 119 0.75
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
Found at i:1708006 original size:67 final size:66
Alignment explanation
Indices: 1707918--1708137 Score: 296
Period size: 67 Copynumber: 3.3 Consensus size: 66
1707908 AAGTGGGAGA
* *
1707918 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TTG
1707983 CC
65 CC
* ** * * * *
1707985 ATTGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAATTGGGAGATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTG
1708050 CC
65 CC
* * *
1708052 ATTATTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTT
1708117 GCC
64 GCC
1708120 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1708138 GTTTTTACCA
Statistics
Matches: 131, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
67 72 0.55
68 59 0.45
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (66 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTGC
C
Found at i:1708064 original size:101 final size:101
Alignment explanation
Indices: 1707918--1708135 Score: 339
Period size: 101 Copynumber: 2.2 Consensus size: 101
1707908 AAGTGGGAGA
* * * *
1707918 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTA
1707983 CCATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
* *
1708018 ATTGTTGATTAATTGGGAGATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGATTAAAT-GGAGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTT
* * *
1708083 ACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
1708120 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1708136 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
100 13 0.12
101 64 0.60
102 29 0.27
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTA
CCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
Found at i:1708764 original size:114 final size:114
Alignment explanation
Indices: 1708564--1708792 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
1708554 AAAATGAACT
1708564 TGTTGACATCATCTAAATTTACTATGGAATAAGAAATATTATCATGGAGGGAACAATCAGGTTCC
1 TGTTGACATCATCTAAATTTACTATGGAATAAGAAATATTATCATGGAGGGAACAATCAGGTTCC
1708629 TAAAGAATATTTAGATGATAATGTTTTCATATATATATATATATATATA
66 TAAAGAATATTTAGATGATAATGTTTTCATATATATATATATATATATA
1708678 TGTTGACATCATCTAAATTTACTATGGAATAAGAAATATTATCATGGAGGGAACAATCAGGTTCC
1 TGTTGACATCATCTAAATTTACTATGGAATAAGAAATATTATCATGGAGGGAACAATCAGGTTCC
1708743 TAAAGAATATTTAGATGATAATGTTTTCATATATATATATATATATATA
66 TAAAGAATATTTAGATGATAATGTTTTCATATATATATATATATATATA
1708792 T
1 T
1708793 ATTTTGGTTC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (114 bp):
TGTTGACATCATCTAAATTTACTATGGAATAAGAAATATTATCATGGAGGGAACAATCAGGTTCC
TAAAGAATATTTAGATGATAATGTTTTCATATATATATATATATATATA
Found at i:1709100 original size:20 final size:20
Alignment explanation
Indices: 1709069--1709127 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1709059 AATTGTATTA
* *
1709069 AAATAAAAAATTTAAATATT
1 AAATAAATAATTTAAATAAT
* *
1709089 AAATATATAATTTTAATAAT
1 AAATAAATAATTTAAATAAT
1709109 AAATAAAT-ATTT-AATAAT
1 AAATAAATAATTTAAATAAT
1709127 A
1 A
1709128 TATATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 23 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATAAATAATTTAAATAAT
Found at i:1709132 original size:14 final size:15
Alignment explanation
Indices: 1709105--1709137 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1709095 ATAATTTTAA
1709105 TAATAAATAAATATT
1 TAATAAATAAATATT
*
1709120 TAAT-AATATATATT
1 TAATAAATAAATATT
1709134 TAAT
1 TAAT
1709138 TAAGTAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATAAATAAATATT
Found at i:1710684 original size:31 final size:30
Alignment explanation
Indices: 1710646--1710709 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
1710636 TAAATCTTTT
* *
1710646 AAAATTAAAATTTAGTGACAAAATTCAATCA
1 AAAATTAAAACTTAGCGACAAAATTCAAT-A
*
1710677 AAAATTAAAACTTAGCGGCAAAATTCAATA
1 AAAATTAAAACTTAGCGACAAAATTCAATA
1710707 AAA
1 AAA
1710710 TAATAGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (30 bp):
AAAATTAAAACTTAGCGACAAAATTCAATA
Found at i:1712947 original size:2 final size:2
Alignment explanation
Indices: 1712940--1712964 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1712930 TCTTATTAAT
1712940 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1712965 GTTAATACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1713751 original size:19 final size:19
Alignment explanation
Indices: 1713692--1713758 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
1713682 TTAAGTATTA
* *
1713692 TTATTTATTTAATATAAAAAA
1 TTATTT-TTTAATA-AATAAT
* **
1713713 TTATATTTTAATTATTTAAT
1 TTATTTTTTAA-TAAATAAT
1713733 TTATTTTTTAATAAATAAT
1 TTATTTTTTAATAAATAAT
1713752 TTGATTT
1 TT-ATTT
1713759 AACCGTTCCA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
19 8 0.22
20 21 0.58
21 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (19 bp):
TTATTTTTTAATAAATAAT
Found at i:1721970 original size:3 final size:3
Alignment explanation
Indices: 1721962--1722003 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1721952 CTAACACCCC
*
1721962 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1722004 TTTCAACGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1723433 original size:24 final size:25
Alignment explanation
Indices: 1723383--1723433 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
1723373 TTCTATCTCG
*
1723383 TAATATGAATATAAATAATATATAT
1 TAATATGAATATAAATAATATAAAT
*
1723408 TAATAT-AATCTAAATAA-ATTAAAT
1 TAATATGAATATAAATAATA-TAAAT
1723432 TA
1 TA
1723434 TAATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.04
24 16 0.70
25 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
TAATATGAATATAAATAATATAAAT
Found at i:1725132 original size:12 final size:14
Alignment explanation
Indices: 1725068--1725125 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
1725058 ACTTATCATA
*
1725068 TTATATATTTAGTAT
1 TTATATAATTA-TAT
1725083 TT-TAT-A-TATAT
1 TTATATAATTATAT
*
1725094 ATATATATATTATAT
1 TTATATA-ATTATAT
1725109 TTATATAATTATAT
1 TTATATAATTATAT
1725123 TTA
1 TTA
1725126 AAATTATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
11 4 0.11
12 5 0.14
14 14 0.39
15 13 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TTATATAATTATAT
Found at i:1725990 original size:3 final size:3
Alignment explanation
Indices: 1725982--1726009 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1725972 CTGCTTCTAA
1725982 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1726010 AGGAGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1726480 original size:2 final size:2
Alignment explanation
Indices: 1726467--1726518 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
1726457 AAAGAGAAAT
*
1726467 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1726510 TA TC TA TA T
1 TA TA TA TA T
1726519 GGTCAGTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1730255 original size:16 final size:16
Alignment explanation
Indices: 1730236--1730319 Score: 84
Period size: 16 Copynumber: 5.2 Consensus size: 16
1730226 TGAGTTTAGT
* *
1730236 TTTAATTGAGTTTGGA
1 TTTATTTGAGTTTGAA
*
1730252 TTTATTTGAATTTGAA
1 TTTATTTGAGTTTGAA
1730268 TTTATTTG-GATTTGAA
1 TTTATTTGAG-TTTGAA
1730284 TTTATTTGAGTTT-AA
1 TTTATTTGAGTTTGAA
*
1730299 GTTTATTT-AGATTTGAG
1 -TTTATTTGAG-TTTGAA
1730316 TTTA
1 TTTA
1730320 GATTAAGTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.07
16 52 0.90
17 2 0.03
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (16 bp):
TTTATTTGAGTTTGAA
Found at i:1730292 original size:32 final size:32
Alignment explanation
Indices: 1730246--1730319 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
1730236 TTTAATTGAG
* *
1730246 TTTGGATTTATTTGAATTTGAA-TTTATTTGGA
1 TTTGAATTTATTTGAATTT-AAGTTTATTTAGA
*
1730278 TTTGAATTTATTTGAGTTTAAGTTTATTTAGA
1 TTTGAATTTATTTGAATTTAAGTTTATTTAGA
*
1730310 TTTGAGTTTA
1 TTTGAATTTA
1730320 GATTAAGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 2 0.05
32 35 0.95
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.57
Consensus pattern (32 bp):
TTTGAATTTATTTGAATTTAAGTTTATTTAGA
Found at i:1730409 original size:21 final size:20
Alignment explanation
Indices: 1730344--1730392 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1730334 TGAATTTAAA
* *
1730344 TTTATTTTAAATTATTTTTAT
1 TTTATATTAAA-TATATTTAT
*
1730365 TTTATATTAAATATAATTATT
1 TTTATATTAAATATATTTA-T
1730386 TTTATAT
1 TTTATAT
1730393 AATTTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTATATTAAATATATTTAT
Found at i:1730471 original size:19 final size:18
Alignment explanation
Indices: 1730447--1730516 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 18
1730437 TTTTAAGTAA
1730447 ATTTTTATTATATTATAAT
1 ATTTTTATT-TATTATAAT
*
1730466 ATTTTTAATATATT-TAAT
1 ATTTTT-ATTTATTATAAT
*
1730484 -TATTTATTTATTA-AA-
1 ATTTTTATTTATTATAAT
*
1730499 ATTTATATTTATATATAA
1 ATTTTTATTTAT-TATAA
1730517 AATTAATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
16 17 0.41
17 6 0.15
18 6 0.15
19 10 0.24
20 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATTTATTATAAT
Found at i:1730509 original size:20 final size:19
Alignment explanation
Indices: 1730484--1730538 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
1730474 TATATTTAAT
*
1730484 TATTTATTTATTAAAATTTA
1 TATTTATATA-TAAAATTTA
1730504 TATTTATATATAAAA-TTA
1 TATTTATATATAAAATTTA
*
1730522 -ATTTGTAATATAAAATT
1 TATTTAT-ATATAAAATT
1730539 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 11 0.35
19 6 0.19
20 9 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TATTTATATATAAAATTTA
Found at i:1730551 original size:20 final size:19
Alignment explanation
Indices: 1730495--1730551 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
1730485 ATTTATTTAT
* * *
1730495 TAAAATTTATATTTATATA
1 TAAAATTAATTTTTAAATA
*
1730514 TAAAATTAATTTGT-AATA
1 TAAAATTAATTTTTAAATA
1730532 TAAAATTAATTTTTTAAATA
1 TAAAATTAA-TTTTTAAATA
1730552 ATTTATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 12 0.39
19 15 0.48
20 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TAAAATTAATTTTTAAATA
Found at i:1730733 original size:24 final size:23
Alignment explanation
Indices: 1730697--1730743 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1730687 ATTAATATTC
*
1730697 AAAAATTTTAAAATATATTTAAT
1 AAAAATTTAAAAATATATTTAAT
*
1730720 AAAATATTTAAAAATTTATTTAAT
1 AAAA-ATTTAAAAATATATTTAAT
1730744 CTTAACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAAATTTAAAAATATATTTAAT
Found at i:1730739 original size:12 final size:12
Alignment explanation
Indices: 1730701--1730742 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1730691 ATATTCAAAA
*
1730701 ATTTTAAAATAT
1 ATTTAAAAATAT
1730713 ATTTAATAAA-AT
1 ATTTAA-AAATAT
*
1730725 ATTTAAAAATTT
1 ATTTAAAAATAT
1730737 ATTTAA
1 ATTTAA
1730743 TCTTAACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAAAAATAT
Found at i:1731956 original size:16 final size:16
Alignment explanation
Indices: 1731932--1731986 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1731922 TATAAGTTAT
*
1731932 TTTTAAATTTAAATTG
1 TTTTAAATTTAAATTA
* *
1731948 TTTTGAATTTGAATTA
1 TTTTAAATTTAAATTA
* *
1731964 TTTTAAAATTTAGATAA
1 TTTT-AAATTTAAATTA
1731981 TTTTAA
1 TTTTAA
1731987 TTTTGAGTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:1731992 original size:33 final size:33
Alignment explanation
Indices: 1731928--1731989 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1731918 GACTTATAAG
* **
1731928 TTATTTTTAAATTTAAATTGTTTTGAATTTGAA
1 TTATTTTAAAATTTAAATAATTTTGAATTTGAA
*
1731961 TTATTTTAAAATTTAGATAATTTT-AATTT
1 TTATTTTAAAATTTAAATAATTTTGAATTT
1731990 TGAGTCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 5 0.20
33 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (33 bp):
TTATTTTAAAATTTAAATAATTTTGAATTTGAA
Found at i:1732022 original size:21 final size:21
Alignment explanation
Indices: 1731998--1732041 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1731988 TTTGAGTCAT
* *
1731998 TTGGATTTAAGTTATTTTGGA
1 TTGGATTTAAGTCATTTTAGA
* *
1732019 TTGGGTTTACGTCATTTTAGA
1 TTGGATTTAAGTCATTTTAGA
1732040 TT
1 TT
1732042 TGTATCATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.52
Consensus pattern (21 bp):
TTGGATTTAAGTCATTTTAGA
Found at i:1735856 original size:11 final size:12
Alignment explanation
Indices: 1735828--1735860 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1735818 GTATCCTAAT
1735828 ACTTTTTATTTA
1 ACTTTTTATTTA
1735840 ACTTTTTATTTA
1 ACTTTTTATTTA
*
1735852 ATTTTTTAT
1 ACTTTTTAT
1735861 CGCAAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (12 bp):
ACTTTTTATTTA
Found at i:1736464 original size:29 final size:27
Alignment explanation
Indices: 1736422--1736497 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 27
1736412 TCTCACAACT
* *
1736422 AGTTAACTTCACCACAAATCGACCTTTAA
1 AGTTACCTTCACCACAAACCGA-CTTT-A
1736451 AGTTACCTTCACCACAAACCGACTTTA
1 AGTTACCTTCACCACAAACCGACTTTA
*
1736478 AGATTACCTTTACCACAAAC
1 AG-TTACCTTCACCACAAAC
1736498 TAACCTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 3 0.07
28 20 0.47
29 20 0.47
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (27 bp):
AGTTACCTTCACCACAAACCGACTTTA
Found at i:1736485 original size:28 final size:29
Alignment explanation
Indices: 1736422--1736507 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
1736412 TCTCACAACT
* *
1736422 AGTTAACTTCACCACAAATCGACCTTTAA
1 AGTTACCTTCACCACAAACCGACCTTTAA
1736451 AGTTACCTTCACCACAAACCGA-CTTT-A
1 AGTTACCTTCACCACAAACCGACCTTTAA
* **
1736478 AGATTACCTTTACCACAAACTAACCTTTAA
1 AG-TTACCTTCACCACAAACCGACCTTTAA
1736508 CCATGGCCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
27 3 0.06
28 21 0.43
29 24 0.49
30 1 0.02
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.28
Consensus pattern (29 bp):
AGTTACCTTCACCACAAACCGACCTTTAA
Found at i:1736682 original size:20 final size:20
Alignment explanation
Indices: 1736659--1736699 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1736649 CAGACCTTAT
1736659 TCCACCCATGATTACCTGTA
1 TCCACCCATGATTACCTGTA
1736679 TCCACCCATGATTACCTGTA
1 TCCACCCATGATTACCTGTA
1736699 T
1 T
1736700 ATTTTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.34, G:0.10, T:0.32
Consensus pattern (20 bp):
TCCACCCATGATTACCTGTA
Found at i:1740259 original size:13 final size:13
Alignment explanation
Indices: 1740241--1740267 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1740231 ACATGTTGCT
1740241 TTGTATCGATACA
1 TTGTATCGATACA
1740254 TTGTATCGATACA
1 TTGTATCGATACA
1740267 T
1 T
1740268 GTTTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1740264 original size:33 final size:32
Alignment explanation
Indices: 1740222--1740286 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
1740212 CAGACCTAGA
1740222 TGTATCGATACATGTTGCT-TTGTATCGATACAT
1 TGTATCGATACATGTT--TATTGTATCGATACAT
1740255 TGTATCGATACATGTTTATTGTATCGATACAT
1 TGTATCGATACATGTTTATTGTATCGATACAT
1740287 GGACAAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 1 0.03
32 14 0.45
33 16 0.52
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (32 bp):
TGTATCGATACATGTTTATTGTATCGATACAT
Found at i:1746539 original size:13 final size:13
Alignment explanation
Indices: 1746521--1746562 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1746511 ACAACATTCC
1746521 TTGTATCGATACA
1 TTGTATCGATACA
*
1746534 TTGTATTGATACA
1 TTGTATCGATACA
*
1746547 TTGTATCAATACA
1 TTGTATCGATACA
1746560 TTG
1 TTG
1746563 GGTACTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1752978 original size:33 final size:34
Alignment explanation
Indices: 1752911--1752980 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
1752901 CCGTTACAAG
* *
1752911 CAATGTATCGATAGAATTTCATCATGTATTGATA
1 CAATGTATCGATAGAATTTCACCATGTATCGATA
*
1752945 CAATGTATCGATA-CATTATC-CCATGTATCGATA
1 CAATGTATCGATAGAATT-TCACCATGTATCGATA
1752978 CAA
1 CAA
1752981 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (34 bp):
CAATGTATCGATAGAATTTCACCATGTATCGATA
Found at i:1753034 original size:20 final size:20
Alignment explanation
Indices: 1753009--1753063 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1752999 CTACCAATCT
*
1753009 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAC
*
1753029 CATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAC
*
1753048 CAAGTATCGATACAAT
1 CATGTATCGATACAAT
1753064 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATTGAC
Found at i:1753069 original size:13 final size:13
Alignment explanation
Indices: 1753051--1753075 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1753041 CAATGAGCAA
1753051 GTATCGATACAAT
1 GTATCGATACAAT
1753064 GTATCGATACAA
1 GTATCGATACAA
1753076 AACATAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:1753858 original size:21 final size:21
Alignment explanation
Indices: 1753834--1753879 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1753824 GATAACACAA
*
1753834 TCATAAAACAAATATTGCATT
1 TCATAAAACAAACATTGCATT
1753855 TCATAAAACAAACATTGCATT
1 TCATAAAACAAACATTGCATT
1753876 TCAT
1 TCAT
1753880 GAATTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (21 bp):
TCATAAAACAAACATTGCATT
Found at i:1755591 original size:13 final size:13
Alignment explanation
Indices: 1755573--1755614 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1755563 AAATAGTACC
1755573 CAATGTATCGATA
1 CAATGTATCGATA
*
1755586 CAATGTATCAATA
1 CAATGTATCGATA
1755599 CAATGTATCGATA
1 CAATGTATCGATA
1755612 CAA
1 CAA
1755615 GGAATGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1761849 original size:20 final size:20
Alignment explanation
Indices: 1761824--1761878 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1761814 CTGCCAATCT
*
1761824 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAC
*
1761844 CATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAC
*
1761863 CAAGTATCGATACAAT
1 CATGTATCGATACAAT
1761879 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATTGAC
Found at i:1761884 original size:13 final size:13
Alignment explanation
Indices: 1761866--1761890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1761856 CAATGAGCAA
1761866 GTATCGATACAAT
1 GTATCGATACAAT
1761879 GTATCGATACAA
1 GTATCGATACAA
1761891 AATATAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:1799804 original size:21 final size:21
Alignment explanation
Indices: 1799765--1799804 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1799755 GACATGGTCC
*
1799765 TGTATCAATACATTCACTTCT
1 TGTATCAATACATTAACTTCT
1799786 TGTATCAATACGA-TAACTT
1 TGTATCAATAC-ATTAACTT
1799805 TGCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (21 bp):
TGTATCAATACATTAACTTCT
Found at i:1799948 original size:58 final size:57
Alignment explanation
Indices: 1799830--1800305 Score: 300
Period size: 58 Copynumber: 8.2 Consensus size: 57
1799820 ATTTCACGTT
* * * *
1799830 ATTTAGGAT-ATTTTTCATGACATAGGGACTTTAATATAATTTCATGTATTTTCATA-TC
1 ATTTAGG-TCATTTTTCATGACTTAGGGACTTTTATGTAATTTCATGTATGTT-A-AGTC
* * * * *
1799888 ATTTAGGGCACTTTTCATGACTTAGGAATTTTTATGTAATTTCATGTATTTTGAAGTC
1 ATTTAGGTCATTTTTCATGACTTAGGGACTTTTATGTAATTTCATGTATGTT-AAGTC
* * * ** * * * **
1799946 ATTTAAGTTATTTTTCATGATTTAGGGACTTCGATGCAAATTTTATATATGTTGGGATC
1 ATTTAGGTCATTTTTCATGACTTAGGGACTTTTATG-TAATTTCATGTATGTTAAG-TC
* * * * *
1800005 ATTTAGGTTATTTTTCATGACTTAGGGACTATTATGTAATTTCTTGTAAGTTAAGATT
1 ATTTAGGTCATTTTTCATGACTTAGGGACTTTTATGTAATTTCATGTATGTTAAG-TC
* * *
1800063 ATTTAGGTCATTTTTCATGATCGT-GGGACTTTTATGCAATTTCATGTATATTAGAGTC
1 ATTTAGGTCATTTTTCATGA-CTTAGGGACTTTTATGTAATTTCATGTATGTTA-AGTC
* * * *** * * * *
1800121 ATTTAGGTTATTTTTCGTTA-TCTAAAAACTTTTATGCAATTTTATATATGTTAGGGTC
1 ATTTAGGTCATTTTTCATGACT-TAGGGACTTTTATGTAATTTCATGTATGTTA-AGTC
* * * * * * * *
1800179 ATTTAAGTCATTTTTTACGA-TCTAGAGACTTTTATGCAATTTTATATATGTTAGGATC
1 ATTTAGGTCATTTTTCATGACT-TAGGGACTTTTATGTAATTTCATGTATGTTAAG-TC
* * * * * *
1800237 ATTTAGGTCATTTTTCATGA-TCAAAGGACTTTCATGCAAATTT-ACGTATTTTAATGTC
1 ATTTAGGTCATTTTTCATGACT-TAGGGACTTTTATG-TAATTTCATGTATGTTAA-GTC
1800295 ATTTAGGTCAT
1 ATTTAGGTCAT
1800306 GCAATTTCAT
Statistics
Matches: 332, Mismatches: 75, Indels: 22
0.77 0.17 0.05
Matches are distributed among these distances:
57 4 0.01
58 273 0.82
59 55 0.17
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (57 bp):
ATTTAGGTCATTTTTCATGACTTAGGGACTTTTATGTAATTTCATGTATGTTAAGTC
Found at i:1800040 original size:117 final size:114
Alignment explanation
Indices: 1799885--1800256 Score: 370
Period size: 116 Copynumber: 3.2 Consensus size: 114
1799875 GTATTTTCAT
* * * *
1799885 ATCATTTAGGGCACTTTTCATGACTTAGGAATTTTTATGTAATTTCATGTATTTTGAAGTCATTT
1 ATCATTTAGGTCATTTTTCATGACTTAGGAACTTTTATGTAATTTCATGTATGTT-AAGTCATTT
* * **
1799950 AAGTTATTTTTCATGATTTAGGGACTTCGATGCAAATTTTATATATGTTGGG
65 AAGTCATTTTTCATGATCTAGGGACTTTTATGC-AATTTTATATATGTT-GG
* * * * * *
1800002 ATCATTTAGGTTATTTTTCATGACTTAGGGACTATTATGTAATTTCTTGTAAGTTAAGATTATTT
1 ATCATTTAGGTCATTTTTCATGACTTAGGAACTTTTATGTAATTTCATGTATGTTAAG-TCATTT
* * * * *
1800067 AGGTCATTTTTCATGATCGT-GGGACTTTTATGCAATTTCATGTATATTAG
65 AAGTCATTTTTCATGATC-TAGGGACTTTTATGCAATTTTATATATGTTGG
* * * ** * * * *
1800117 AGTCATTTAGGTTATTTTTCGTTA-TCTAAAAACTTTTATGCAATTTTATATATGTTAGGGTCAT
1 A-TCATTTAGGTCATTTTTCATGACT-TAGGAACTTTTATGTAATTTCATGTATGTTA-AGTCAT
* * *
1800181 TTAAGTCATTTTTTACGATCTAGAGACTTTTATGCAATTTTATATATGTTAGG
63 TTAAGTCATTTTTCATGATCTAGGGACTTTTATGCAATTTTATATATGTT-GG
1800234 ATCATTTAGGTCATTTTTCATGA
1 ATCATTTAGGTCATTTTTCATGA
1800257 TCAAAGGACT
Statistics
Matches: 205, Mismatches: 43, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
115 4 0.02
116 120 0.59
117 80 0.39
118 1 0.00
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (114 bp):
ATCATTTAGGTCATTTTTCATGACTTAGGAACTTTTATGTAATTTCATGTATGTTAAGTCATTTA
AGTCATTTTTCATGATCTAGGGACTTTTATGCAATTTTATATATGTTGG
Found at i:1800123 original size:175 final size:174
Alignment explanation
Indices: 1799830--1800275 Score: 447
Period size: 175 Copynumber: 2.6 Consensus size: 174
1799820 ATTTCACGTT
* * * * * * *
1799830 ATTTAGGATATTTTTCATGACATAGGGACTTTAATATAATTTCATGTATTTTCATATCATTTAGG
1 ATTTAGGTTATTTTTCATGACTTAGGGACTTT-ATGTAATTTCTTGTATGTTAAGATCATTTAGG
* * * * * *
1799895 GCACTTTTCATGA-CTTAGGAATTTTTATGTAATTTCATGTATTTTGAAGTCATTTAAGTTATTT
65 TCATTTTTCATGATCGTAGGAACTTTTATGCAATTTCATGTATTTAGAAGTCATTTAAGTTATTT
* ***
1799959 TTCATGATTTAGGGACTTCGATGCAAATTTTATATATGTT-GGGATC
130 TTCATGATCTAAAAACTTCGATGC-AATTTTATATATGTTAGGG-TC
* *
1800005 ATTTAGGTTATTTTTCATGACTTAGGGACTATTATGTAATTTCTTGTAAGTTAAGATTATTTAGG
1 ATTTAGGTTATTTTTCATGACTTAGGGACT-TTATGTAATTTCTTGTATGTTAAGATCATTTAGG
* *
1800070 TCATTTTTCATGATCGT-GGGACTTTTATGCAATTTCATGTATATTAG-AGTCATTTAGGTTATT
65 TCATTTTTCATGATCGTAGGAACTTTTATGCAATTTCATGTAT-TTAGAAGTCATTTAAGTTATT
* * **
1800133 TTTCGTTATCTAAAAACTTTTATGCAATTTTATATATGTTAGGGTC
129 TTTCATGATCTAAAAACTTCGATGCAATTTTATATATGTTAGGGTC
* * * * * * * *
1800179 ATTTAAGTCATTTTTTACGA-TCTAGAGACTTTTATGCAATTT-TATATATGTTAGGATCATTTA
1 ATTTAGGTTATTTTTCATGACT-TAGGGAC-TTTATGTAATTTCT-TGTATGTTAAGATCATTTA
** *
1800242 GGTCATTTTTCATGATCAAAGG-ACTTTCATGCAA
63 GGTCATTTTTCATGATCGTAGGAACTTTTATGCAA
1800276 ATTTACGTAT
Statistics
Matches: 225, Mismatches: 38, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
173 2 0.01
174 92 0.41
175 124 0.55
176 7 0.03
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (174 bp):
ATTTAGGTTATTTTTCATGACTTAGGGACTTTATGTAATTTCTTGTATGTTAAGATCATTTAGGT
CATTTTTCATGATCGTAGGAACTTTTATGCAATTTCATGTATTTAGAAGTCATTTAAGTTATTTT
TCATGATCTAAAAACTTCGATGCAATTTTATATATGTTAGGGTC
Found at i:1800183 original size:29 final size:29
Alignment explanation
Indices: 1800151--1800241 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
1800141 TCTAAAAACT
1800151 TTTATGCAATTTTATATATGTTAGGGTCA
1 TTTATGCAATTTTATATATGTTAGGGTCA
* * * * *
1800180 TTTAAGTC-ATTTT-T-TACGATCTAGAGACT
1 TTTATG-CAATTTTATATATG-T-TAGGGTCA
*
1800209 TTTATGCAATTTTATATATGTTAGGATCA
1 TTTATGCAATTTTATATATGTTAGGGTCA
1800238 TTTA
1 TTTA
1800242 GGTCATTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
27 3 0.07
28 3 0.07
29 33 0.73
30 3 0.07
31 3 0.07
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (29 bp):
TTTATGCAATTTTATATATGTTAGGGTCA
Found at i:1800257 original size:174 final size:174
Alignment explanation
Indices: 1799885--1800302 Score: 418
Period size: 174 Copynumber: 2.4 Consensus size: 174
1799875 GTATTTTCAT
* * * * * * *
1799885 ATCATTTAGGGCACTTTTCATGA-CTTAGGAATTTTTATGTAATTTCATGTATTTTGAAGTCATT
1 ATCATTTAGGTCATTTTTCATGATCAT-GGGACTTTTATGCAATTTCATGTATTTAG-AGTCATT
* * *** * *
1799949 TAAGTTATTTTTCATGATTTAGGGACTTCGATGCAAATTTTATATATGTTGGGATCATTTAGGTT
64 TAGGTTATTTTTCATGATCTAAAAACTTCGATGCAAATTTTATATATGTTGGGATCATTTAAGTC
* * * *
1800014 ATTTTTCATGACTTAGGGACTATTATGTAATTTCTTGTAAGTTAAG
129 ATTTTTCACGACTTAGAGACTATTATGCAATTTCTTATAAGTTAAG
* *
1800060 ATTATTTAGGTCATTTTTCATGATCGTGGGACTTTTATGCAATTTCATGTATATTAGAGTCATTT
1 ATCATTTAGGTCATTTTTCATGATCATGGGACTTTTATGCAATTTCATGTAT-TTAGAGTCATTT
* * **
1800125 AGGTTATTTTTCGTTATCTAAAAACTTTTATGC-AATTTTATATATGTTAGGG-TCATTTAAGTC
65 AGGTTATTTTTCATGATCTAAAAACTTCGATGCAAATTTTATATATGTT-GGGATCATTTAAGTC
* * * *
1800188 ATTTTTTACGA-TCTAGAGACTTTTATGCAATTT-TATATATGTTAGG
129 ATTTTTCACGACT-TAGAGACTATTATGCAATTTCT-TATAAGTTAAG
** * *
1800234 ATCATTTAGGTCATTTTTCATGATCAAAGGACTTTCATGCAAATTT-ACGTATTTTA-ATGTCAT
1 ATCATTTAGGTCATTTTTCATGATCATGGGACTTTTATGC-AATTTCATGTA-TTTAGA-GTCAT
1800297 TTAGGT
63 TTAGGT
1800303 CATGCAATTT
Statistics
Matches: 202, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
173 3 0.01
174 111 0.55
175 83 0.41
176 5 0.02
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.46
Consensus pattern (174 bp):
ATCATTTAGGTCATTTTTCATGATCATGGGACTTTTATGCAATTTCATGTATTTAGAGTCATTTA
GGTTATTTTTCATGATCTAAAAACTTCGATGCAAATTTTATATATGTTGGGATCATTTAAGTCAT
TTTTCACGACTTAGAGACTATTATGCAATTTCTTATAAGTTAAG
Found at i:1800306 original size:34 final size:34
Alignment explanation
Indices: 1800268--1800336 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
1800258 CAAAGGACTT
*
1800268 TCATGCAAATTT-ACGTATTTTAATGTCATTTAGG
1 TCATGC-AATTTCACGTATTTTAATGTCATCTAGG
*
1800302 TCATGCAATTTCATGTATTTTAATGTCATCTAGG
1 TCATGCAATTTCACGTATTTTAATGTCATCTAGG
1800336 T
1 T
1800337 TATTTTTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 5 0.16
34 27 0.84
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (34 bp):
TCATGCAATTTCACGTATTTTAATGTCATCTAGG
Found at i:1800380 original size:59 final size:58
Alignment explanation
Indices: 1800308--1800419 Score: 152
Period size: 59 Copynumber: 1.9 Consensus size: 58
1800298 TAGGTCATGC
* * *
1800308 AATTTCATGTATTTTAATGTCATCTAGGTTATTTTTCTATGATCTAAAGATTTTGGTGT
1 AATTTCATATATTTTAATGTCATCTAGGTCA-TTTTCTATGATCTAAAAATTTTGGTGT
* ** *
1800367 AATTTCATATATTTTGATGTTGTTTAGGTCATTTTCTATGATCTAAAAATTTT
1 AATTTCATATATTTTAATGTCATCTAGGTCATTTTCTATGATCTAAAAATTTT
1800420 TATACAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 21 0.46
59 25 0.54
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (58 bp):
AATTTCATATATTTTAATGTCATCTAGGTCATTTTCTATGATCTAAAAATTTTGGTGT
Found at i:1800429 original size:58 final size:59
Alignment explanation
Indices: 1800307--1800429 Score: 140
Period size: 58 Copynumber: 2.1 Consensus size: 59
1800297 TTAGGTCATG
* * * * *
1800307 CAATTTCATGTATTTTAATGTCATCTAGGTTATTTTTCTATGATCTAAAGATTTTGGTG
1 CAATTTCATATATTTTAATGTCATCTAGGTCATTTTTCTATGATCTAAAAATTTTGATA
* * ** * *
1800366 TAATTTCATATATTTTGATGTTGTTTAGGTCA-TTTTCTATGATCTAAAAATTTTTATA
1 CAATTTCATATATTTTAATGTCATCTAGGTCATTTTTCTATGATCTAAAAATTTTGATA
1800424 CAATTT
1 CAATTT
1800430 TATTAATTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
58 27 0.52
59 25 0.48
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (59 bp):
CAATTTCATATATTTTAATGTCATCTAGGTCATTTTTCTATGATCTAAAAATTTTGATA
Found at i:1804340 original size:24 final size:27
Alignment explanation
Indices: 1804303--1804351 Score: 68
Period size: 24 Copynumber: 1.9 Consensus size: 27
1804293 TTGATTTAAA
*
1804303 TTACTATTTATTTAAT-A-AAAAATTT
1 TTACTATTAATTTAATCATAAAAATTT
1804328 TTACT-TTAATTTAATCATAAAAAT
1 TTACTATTAATTTAATCATAAAAAT
1804352 ATATAGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 6 0.29
26 6 0.29
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (27 bp):
TTACTATTAATTTAATCATAAAAATTT
Found at i:1804737 original size:21 final size:22
Alignment explanation
Indices: 1804713--1804757 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1804703 TTTTAAAAAA
*
1804713 TTAT-ATTAATATTTATAT-ATT
1 TTATAATTAA-ATTTAAATAATT
1804734 TTATAATTAAATTTAAATAATT
1 TTATAATTAAATTTAAATAATT
1804756 TT
1 TT
1804758 TTTTAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATAATTAAATTTAAATAATT
Found at i:1805111 original size:22 final size:21
Alignment explanation
Indices: 1805086--1805141 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
1805076 TAATTAAAAA
* *
1805086 AATTAATAACTTAAATTGATTT
1 AATTAA-AACTTAAAATAATTT
*
1805108 AATTAAAATTTAAAATAATTT
1 AATTAAAACTTAAAATAATTT
1805129 AAATTTAAAACTT
1 -AA-TTAAAACTT
1805142 GAACAATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 12 0.43
22 8 0.29
23 8 0.29
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (21 bp):
AATTAAAACTTAAAATAATTT
Found at i:1805132 original size:16 final size:16
Alignment explanation
Indices: 1805107--1805138 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1805097 TAAATTGATT
1805107 TAATTAAAATTTAAAA
1 TAATTAAAATTTAAAA
*
1805123 TAATTTAAATTTAAAA
1 TAATTAAAATTTAAAA
1805139 CTTGAACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATTAAAATTTAAAA
Found at i:1805219 original size:16 final size:16
Alignment explanation
Indices: 1805200--1805242 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1805190 TTAAAAAATT
**
1805200 AATAATTTAAATTTGA
1 AATAATTTAAATTCCA
*
1805216 AATAATTTACA-TCCA
1 AATAATTTAAATTCCA
1805231 AATAATTTAAAT
1 AATAATTTAAAT
1805243 AATCAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (16 bp):
AATAATTTAAATTCCA
Found at i:1805477 original size:22 final size:22
Alignment explanation
Indices: 1805449--1805491 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1805439 ATATTTAAAA
1805449 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
1805471 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
1805492 AAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:1813153 original size:14 final size:14
Alignment explanation
Indices: 1813134--1813161 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1813124 ATCAAACAAT
1813134 CATGTAGCATTCCA
1 CATGTAGCATTCCA
1813148 CATGTAGCATTCCA
1 CATGTAGCATTCCA
1813162 ACCATGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (14 bp):
CATGTAGCATTCCA
Found at i:1814693 original size:40 final size:40
Alignment explanation
Indices: 1814649--1814841 Score: 359
Period size: 40 Copynumber: 4.8 Consensus size: 40
1814639 CTGACCGCTG
*
1814649 AAGCTGAGCCCAATTGAAGGGAGCGTTGGCGATACTGCTA
1 AAGCTGAGCCCAATTGAAGGGGGCGTTGGCGATACTGCTA
1814689 AAGCTGAGCCCAATTGAAGGGGGCGTTGGCGATACTGCTA
1 AAGCTGAGCCCAATTGAAGGGGGCGTTGGCGATACTGCTA
1814729 AAGCTGAGCCCAATTGAAGGGGGCGTTGGCGATACTGCTA
1 AAGCTGAGCCCAATTGAAGGGGGCGTTGGCGATACTGCTA
*
1814769 AAGCTGAGCCCAATTGAAGGGGGCGTTGGCGATACAGCTA
1 AAGCTGAGCCCAATTGAAGGGGGCGTTGGCGATACTGCTA
*
1814809 TAGCTGAGCCCAATTGAAGGGGGCGTTGGCGAT
1 AAGCTGAGCCCAATTGAAGGGGGCGTTGGCGAT
1814842 GGCAGCAGTC
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 150 1.00
ACGTcount: A:0.25, C:0.20, G:0.35, T:0.20
Consensus pattern (40 bp):
AAGCTGAGCCCAATTGAAGGGGGCGTTGGCGATACTGCTA
Found at i:1815135 original size:20 final size:19
Alignment explanation
Indices: 1815072--1815127 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
1815062 ATAAGTGAAA
1815072 TAAAA-TTTT-AT-AAATT
1 TAAAATTTTTAATAAAATT
1815088 TAAAATTTTTAATAAAATT
1 TAAAATTTTTAATAAAATT
*
1815107 TAAAATTTTTTATAATAATT
1 TAAAATTTTTAATAA-AATT
1815127 T
1 T
1815128 TATATTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 2 0.06
19 19 0.54
20 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAAATTTTTAATAAAATT
Found at i:1815429 original size:2 final size:2
Alignment explanation
Indices: 1815422--1815446 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1815412 TCCCTCTATC
1815422 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1815447 ATTTTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1816131 original size:12 final size:13
Alignment explanation
Indices: 1816100--1816133 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1816090 ATAAAAATAT
1816100 TAAATTTAAAAAA
1 TAAATTTAAAAAA
*
1816113 TAAATTTAAATAA
1 TAAATTTAAAAAA
1816126 -AAATTTAA
1 TAAATTTAA
1816134 GCTCATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAATTTAAAAAA
Found at i:1816241 original size:25 final size:24
Alignment explanation
Indices: 1816193--1816255 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
1816183 ACTTAGTTCG
1816193 ATTTTA-ATTATATAATATAATTA
1 ATTTTATATTATATAATATAATTA
*
1816216 ATTTTATATCTATATACAT-TATTTA
1 ATTTTATAT-TATATA-ATATAATTA
1816241 ATTTT-TATTATATAA
1 ATTTTATATTATATAA
1816256 AAAATAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 1 0.03
23 12 0.33
24 5 0.14
25 16 0.44
26 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTATATTATATAATATAATTA
Found at i:1816470 original size:16 final size:16
Alignment explanation
Indices: 1816449--1816481 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1816439 AAAATAATAT
1816449 TTTAAATTAAAT-TAAA
1 TTTAAA-TAAATATAAA
1816465 TTTAAATAAATATAAA
1 TTTAAATAAATATAAA
1816481 T
1 T
1816482 ATTATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAATAAATATAAA
Found at i:1817884 original size:16 final size:19
Alignment explanation
Indices: 1817849--1817935 Score: 60
Period size: 18 Copynumber: 4.8 Consensus size: 19
1817839 GGGTTGAAAG
1817849 TTTATTTTATTATTAAA-A
1 TTTATTTTATTATTAAATA
1817867 TATTATTTTA-TATT-AATA
1 T-TTATTTTATTATTAAATA
* *
1817885 TTTA-TTTATTTTTATA-A
1 TTTATTTTATTATTAAATA
* ** *
1817902 TTAATTTTAAAAATAAATA
1 TTTATTTTATTATTAAATA
1817921 -TTATTTTTATTATTA
1 TTTA-TTTTATTATTA
1817936 TATAATAATT
Statistics
Matches: 50, Mismatches: 12, Indels: 13
0.67 0.16 0.17
Matches are distributed among these distances:
16 4 0.08
17 12 0.24
18 17 0.34
19 17 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATTTTATTATTAAATA
Found at i:1818934 original size:13 final size:14
Alignment explanation
Indices: 1818903--1818935 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1818893 AAAAAAGAAT
1818903 TAAAAATGACATGA
1 TAAAAATGACATGA
1818917 TAAAAATGACATGA
1 TAAAAATGACATGA
1818931 -AAAAA
1 TAAAAA
1818936 AAAATAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
TAAAAATGACATGA
Found at i:1819224 original size:18 final size:18
Alignment explanation
Indices: 1819185--1819224 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1819175 ATTCTTTATA
*
1819185 TTTCTCTTTCTCTTTCCT
1 TTTCTCTTTCTCTCTCCT
1819203 TTTCTCTTT-TCTCTCCT
1 TTTCTCTTTCTCTCTCCT
1819220 CTTTC
1 -TTTC
1819225 ATATTGCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCTCTTTCTCTCTCCT
Found at i:1820758 original size:2 final size:2
Alignment explanation
Indices: 1820751--1820798 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
1820741 ATAACCATCC
* * *
1820751 TA TA TA TA TA TA TA TA TC TT TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1820793 TA TA TA
1 TA TA TA
1820799 AATTTGCATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1822085 original size:23 final size:23
Alignment explanation
Indices: 1822040--1822086 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1822030 AATTTGCTTG
* *
1822040 ATAAATAAACATTTTAAGCTTTT
1 ATAAATAAACATTTCAAGATTTT
1822063 ATAAATAAA-ATTATCAAGATTTT
1 ATAAATAAACATT-TCAAGATTTT
1822086 A
1 A
1822087 AAACAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (23 bp):
ATAAATAAACATTTCAAGATTTT
Found at i:1822618 original size:25 final size:28
Alignment explanation
Indices: 1822589--1822647 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
1822579 GATATGTTTA
1822589 TGATA-TA-TACT-TTAATCTTTTATTG
1 TGATAGTACTACTGTTAATCTTTTATTG
* *
1822614 TGATAAGTACTATTGTTAATTTTTTATTG
1 TGAT-AGTACTACTGTTAATCTTTTATTG
1822643 TGATA
1 TGATA
1822648 AGTATTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 4 0.14
26 1 0.04
27 2 0.07
28 4 0.14
29 17 0.61
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (28 bp):
TGATAGTACTACTGTTAATCTTTTATTG
Found at i:1822642 original size:29 final size:29
Alignment explanation
Indices: 1822600--1822656 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1822590 GATATATACT
1822600 TTAATCTTTTATTGTGATAAGTACTATTG
1 TTAATCTTTTATTGTGATAAGTACTATTG
* *
1822629 TTAATTTTTTATTGTGATAAGTATTATT
1 TTAATCTTTTATTGTGATAAGTACTATT
1822657 ATTCTGGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.04, G:0.12, T:0.56
Consensus pattern (29 bp):
TTAATCTTTTATTGTGATAAGTACTATTG
Found at i:1822906 original size:22 final size:22
Alignment explanation
Indices: 1822880--1822959 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
1822870 GTTTTAATAA
*
1822880 AGAAAGGGTTGGTTCCTTAGTG
1 AGAAAGGGTTAGTTCCTTAGTG
* * *
1822902 AGAAAAGGTTAGTTCTTTTGT-
1 AGAAAGGGTTAGTTCCTTAGTG
*
1822923 A-AAAGGGTTATTTCCTTAGTG
1 AGAAAGGGTTAGTTCCTTAGTG
*
1822944 ATAAAGGGTTAGTTCC
1 AGAAAGGGTTAGTTCC
1822960 ATAATAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 15 0.32
21 2 0.04
22 30 0.64
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.36
Consensus pattern (22 bp):
AGAAAGGGTTAGTTCCTTAGTG
Found at i:1822968 original size:42 final size:42
Alignment explanation
Indices: 1822882--1822968 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 42
1822872 TTTAATAAAG
* ** **
1822882 AAAGGGTTGGTTCCTTAGTGAGAAAAGGTTAGTTCTTTTGTA
1 AAAGGGTTAGTTCCTTAGTGAGAAAAGGTTAGTTCCATAATA
* * *
1822924 AAAGGGTTATTTCCTTAGTGATAAAGGGTTAGTTCCATAATA
1 AAAGGGTTAGTTCCTTAGTGAGAAAAGGTTAGTTCCATAATA
1822966 AAA
1 AAA
1822969 AAGTTATCTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (42 bp):
AAAGGGTTAGTTCCTTAGTGAGAAAAGGTTAGTTCCATAATA
Found at i:1822971 original size:22 final size:22
Alignment explanation
Indices: 1822923--1822971 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1822913 GTTCTTTTGT
* * * *
1822923 AAAAGGGTTATTTCCTTAGTGA
1 AAAAGGGTTAGTTCCATAATAA
*
1822945 TAAAGGGTTAGTTCCATAATAA
1 AAAAGGGTTAGTTCCATAATAA
1822967 AAAAG
1 AAAAG
1822972 TTATCTCCCT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (22 bp):
AAAAGGGTTAGTTCCATAATAA
Found at i:1823015 original size:20 final size:20
Alignment explanation
Indices: 1822979--1823019 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1822969 AAGTTATCTC
*
1822979 CCTTTGTGAAGGGTTTGGTT
1 CCTTTGTGAAGGATTTGGTT
1822999 CCTTTAGTGAA-GATTTGGTT
1 CCTTT-GTGAAGGATTTGGTT
1823019 C
1 C
1823020 TTATATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (20 bp):
CCTTTGTGAAGGATTTGGTT
Found at i:1823180 original size:20 final size:21
Alignment explanation
Indices: 1823157--1823199 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1823147 TATATAGCTA
* *
1823157 ATATCAATTAGTTAT-ATATT
1 ATATCAAATAGCTATGATATT
*
1823177 ATATTAAATAGCTATGATATT
1 ATATCAAATAGCTATGATATT
1823198 AT
1 AT
1823200 TATAATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (21 bp):
ATATCAAATAGCTATGATATT
Found at i:1825060 original size:16 final size:16
Alignment explanation
Indices: 1825019--1825084 Score: 71
Period size: 16 Copynumber: 3.9 Consensus size: 16
1825009 ACTCTATATT
*
1825019 TATCTCAATAAATAATAT
1 TATCT-AATAAAT-ATAA
1825037 TCATCTAATAAATATAA
1 T-ATCTAATAAATATAA
*
1825054 TATCTAATAATTATAA
1 TATCTAATAAATATAA
1825070 -ATCTAGATAAATATA
1 TATCTA-ATAAATATA
1825085 TTAGAAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
15 5 0.12
16 22 0.51
17 4 0.09
18 8 0.19
19 4 0.09
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (16 bp):
TATCTAATAAATATAA
Found at i:1825893 original size:20 final size:21
Alignment explanation
Indices: 1825851--1825903 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1825841 TTCTACAATT
* *
1825851 TGTATTGATACAACAAGTTAA
1 TGTATCGATACAACAAGTGAA
*
1825872 TGTATCGATA-AATAAGTGAA
1 TGTATCGATACAACAAGTGAA
1825892 TGTATCGATACA
1 TGTATCGATACA
1825904 TGCCTGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAACAAGTGAA
Found at i:1825989 original size:21 final size:21
Alignment explanation
Indices: 1825963--1826017 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1825953 CTGAAAAAAT
* *
1825963 TGTATCGATATATGCTTATAA
1 TGTATCGATACATGCTTACAA
* *
1825984 TGTATCAATACATGCTTGCAA
1 TGTATCGATACATGCTTACAA
1826005 TGTATCGATACAT
1 TGTATCGATACAT
1826018 TCTTTAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATGCTTACAA
Found at i:1828675 original size:19 final size:20
Alignment explanation
Indices: 1828653--1828690 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1828643 TATCGAAAAC
1828653 AAGC-ACATGTATCGATACA
1 AAGCAACATGTATCGATACA
* *
1828672 AAGCAATATGTATTGATAC
1 AAGCAACATGTATCGATAC
1828691 TTCTGAGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
AAGCAACATGTATCGATACA
Found at i:1830440 original size:13 final size:13
Alignment explanation
Indices: 1830424--1830458 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1830414 CGATGCAGTA
* *
1830424 TATCGATATAGTG
1 TATCGATACAATG
1830437 TATCGATACAATG
1 TATCGATACAATG
1830450 TATCGATAC
1 TATCGATAC
1830459 TAAGATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1832469 original size:29 final size:30
Alignment explanation
Indices: 1832436--1832495 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1832426 GCCAAACTTG
**
1832436 TATCGATACACCAAGTA-TGTATCGATACA
1 TATCGATACACCAAAAATTGTATCGATACA
1832465 TATCGATACACCAAAAATTGTATCGATACA
1 TATCGATACACCAAAAATTGTATCGATACA
1832495 T
1 T
1832496 TGGCTTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (30 bp):
TATCGATACACCAAAAATTGTATCGATACA
Found at i:1834725 original size:21 final size:22
Alignment explanation
Indices: 1834692--1834741 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1834682 TTGTAAGTTG
* **
1834692 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAAAAA
*
1834714 AAATAATG-AGTTAGCTAAAAA
1 AAATAAAGAAGTTAGCTAAAAA
1834735 AAATAAA
1 AAATAAA
1834742 AACTTGCATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAAAAA
Found at i:1836559 original size:15 final size:15
Alignment explanation
Indices: 1836539--1836569 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1836529 TAAAAATGTC
*
1836539 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1836554 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1836569 C
1 C
1836570 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1838666 original size:13 final size:13
Alignment explanation
Indices: 1838648--1838673 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1838638 ACATTTTTCT
1838648 TTGTATCGATACA
1 TTGTATCGATACA
1838661 TTGTATCGATACA
1 TTGTATCGATACA
1838674 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1838837 original size:20 final size:20
Alignment explanation
Indices: 1838794--1838839 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1838784 AAATCTTTTG
1838794 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1838815 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1838835 CAAAA
1 CAAAA
1838840 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1840833 original size:13 final size:13
Alignment explanation
Indices: 1840815--1840840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1840805 TACACCAAGT
1840815 ATGTATCGATACA
1 ATGTATCGATACA
1840828 ATGTATCGATACA
1 ATGTATCGATACA
1840841 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1840838 original size:32 final size:33
Alignment explanation
Indices: 1840797--1840860 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1840787 TAGCCAAACT
**
1840797 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
1840829 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1840861 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Done.