Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016288.1 Corchorus olitorius cultivar O-4 contig16321, whole genome shotgun sequence
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: 256043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4210 original size:32 final size:32
Alignment explanation
Indices: 4146--4210 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
4136 TCTTTCAAGG
* *
4146 AAAAATGCAAACCGTTGATCATGTCTTCTCTA
1 AAAAATGCAAACCGTTGATCAGGCCTTCTCTA
* *
4178 AAAAATGCAAACTGTTGATCAGGCCTTTTCTA
1 AAAAATGCAAACCGTTGATCAGGCCTTCTCTA
4210 A
1 A
4211 TATTTGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (32 bp):
AAAAATGCAAACCGTTGATCAGGCCTTCTCTA
Found at i:7127 original size:216 final size:215
Alignment explanation
Indices: 6732--7190 Score: 701
Period size: 216 Copynumber: 2.1 Consensus size: 215
6722 GTGGTGGCCG
*
6732 AGATGAACTGGAAAATGGGAGAGAGAGAATAGAGACTACAACTGTCTCTATGCCCTGTAATTTCA
1 AGATGAACTGGAAAATGGGAGAGAAAGAATAGAGACTACAACTGTCTCTATGCCCTGTAATTTCA
* *
6797 TTCATATATATCCATGAACTAGCACATGTGTAAAACATGCAAAGATTTTACACATGCAACACAAC
66 TTCATATATATCCATGAACTAGCACATGTGCAAAACATGCAAAGATTTTAAACATGCAACACAAC
* *
6862 AAGTGTACAATATTACAAATTCCTATCAAAGCGTTTCAAAGGAATCATCATCAT-TGCATTGTTT
131 AAGTGTACAATATTACAAATTCCTATCAAAGCCTTTCAAAGGAATCATCAT--TGTACATTGTTT
* *
6926 GAACTTAGCATAAACATCAAGA
194 GAACTCAACATAAACATCAAGA
* * * * *
6948 AGATAAACAGGAAAATGGAAGAGAAAGAATAGAGACTACAATTGTCTCTATGCCCTGTAGTTTCA
1 AGATGAACTGGAAAATGGGAGAGAAAGAATAGAGACTACAACTGTCTCTATGCCCTGTAATTTCA
* *
7013 TTCATATATATCCATGAACTAGGACATGTGCAAAACATGCAAAGATTTTAAACATGCAACATAAC
66 TTCATATATATCCATGAACTAGCACATGTGCAAAACATGCAAAGATTTTAAACATGCAACACAAC
*
7078 AAGTGTAC-A-A-TACAAATTCCTATCAAAGCCTTTCAAAGGAAATATCATCATTGTATATTGTT
131 AAGTGTACAATATTACAAATTCCTATCAAAGCCTTTCAAAGG--A-ATCATCATTGTACATTGTT
*
7140 TGAACTCAACATAAACGTCAAGA
193 TGAACTCAACATAAACATCAAGA
7163 AGATGAACTGGAAAATGGGAGAGAAAGA
1 AGATGAACTGGAAAATGGGAGAGAAAGA
7191 GCAAAGACAA
Statistics
Matches: 220, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
213 28 0.13
214 2 0.01
215 54 0.25
216 136 0.62
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (215 bp):
AGATGAACTGGAAAATGGGAGAGAAAGAATAGAGACTACAACTGTCTCTATGCCCTGTAATTTCA
TTCATATATATCCATGAACTAGCACATGTGCAAAACATGCAAAGATTTTAAACATGCAACACAAC
AAGTGTACAATATTACAAATTCCTATCAAAGCCTTTCAAAGGAATCATCATTGTACATTGTTTGA
ACTCAACATAAACATCAAGA
Found at i:7840 original size:28 final size:28
Alignment explanation
Indices: 7787--7841 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
7777 TTTCCAAACT
* ***
7787 AAATGAATACAAATATTATTGCCAAAAA
1 AAATGAATACAAATATAATAAACAAAAA
7815 AAATGAATACAAATATAATAAACAAAA
1 AAATGAATACAAATATAATAAACAAAA
7842 CATTAGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.64, C:0.09, G:0.05, T:0.22
Consensus pattern (28 bp):
AAATGAATACAAATATAATAAACAAAAA
Found at i:18414 original size:28 final size:30
Alignment explanation
Indices: 18383--18438 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
18373 ATAAGTATTC
* * *
18383 TTTTTAGTCATTTATCTTTTTT-TTAAAAT
1 TTTTTAATCATTCAACTTTTTTATTAAAAT
18412 TTTTTAATCATTCAACTTTTTTATTAA
1 TTTTTAATCATTCAACTTTTTTATTAA
18439 TTATGGGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTTTAATCATTCAACTTTTTTATTAAAAT
Found at i:18568 original size:15 final size:16
Alignment explanation
Indices: 18543--18572 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18533 AATAATTATT
18543 TTTAGATTATAATATA
1 TTTAGATTATAATATA
18559 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
18573 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:19665 original size:324 final size:322
Alignment explanation
Indices: 19090--20278 Score: 1149
Period size: 324 Copynumber: 3.6 Consensus size: 322
19080 AACGTTGACT
* * * * *
19090 TATATATTTTTATAAGTTTTTTAGCCAAAAATTGAGGAGACATCTTTCGTTTCAATTTTTGCAAA
1 TATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGTTCAATTTTTGCAAA
* * * * * * * * *
19155 AATTTAGCCGAAATAGTGTACTTACTAACCATAACAGTTTTTGGCTAAAAATGCGTTCCAGAGAC
66 ATTTTAGCCAAAATCGTGTA--TA-TAACCATCACAATTTTTGGCTAAAAACGCGTT-CTGGGGC
* * * * * * * *
19220 CCGCCTCAATTTTGCATGATTTTTGACTCCGAGGCTACTTGAAACATCTATAATCATCTAATCAA
127 CCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAA
** * * *
19285 ATCTCAACCACATAGGATTTAAGGATTTATTTTACGAGCATCTTAATCTTGTTTCGATTTAATTA
192 ATCTCAA-CACATTTGATTTAAGGATTTTTTTTACGAGCATCTGAATCTAGTTTCGATTTAATTA
* * * * *
19350 TAAATTAATTCGGAAAAAAT-AGGATATTAGAAA-CGTCAAAATCCCTTCAATCTTTTTGGCGTT
256 AAAATTAATTCAGAAAAAATAAGGATATTA-AAAGCGT-AAAAGCCCTACAATCTTTTTGGTGTT
19413 GAAA
319 GAAA
** * *
19417 TATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGCCCATTTTTTACAA
1 TATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTC-GGTTCAATTTTTGCAA
* ** *
19482 AATTTTAGCCGAAATCGTGTA-ATAATTATCACAATTTTTGGCTAAAAAAGCGTTCTGGGGCTCC
65 AATTTTAGCCAAAATCGTGTATATAACCATCACAATTTTTGGCTAAAAACGCGTTCTGGGGC-CC
* * * * *
19546 GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAGATATCCATATTCATTTAATCAAAC
129 GGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAAT
* *
19611 CTCAACTACATTTGATTTAAGAATTTTTTTTACGAGCTTCTGAATCTAGTTTCGATTTAATTAAA
194 CTCAAC-ACATTTGATTTAAGGATTTTTTTTACGAGCATCTGAATCTAGTTTCGATTTAATTAAA
* * * *
19676 AATTAATTCAAAAAAAATGAAAAAACGATATTAAAAGCGTAAGAAGACCTCCAATCTTTTTGGTG
258 AATTAATTCAGAAAAAAT-----AAGGATATTAAAAGCGTAA-AAGCCCTACAATCTTTTTGGTG
19741 TT-AAA
317 TTGAAA
* * *
19746 TTATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAAAT-TGTTCGGTTCATTTTTTTT
1 -TATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCT-TTCGGTTCA---ATTTT
* * **
19810 TTCAAAATTTTAACCAAAATCGTGTACTATAACCATCATGATCTTTTGGCTAAAAACGCGTT-TC
60 TGCAAAATTTTAGCCAAAATCGTGTA-TATAACCATCACAAT-TTTTGGCTAAAAACGCGTTCT-
* ** *
19874 GGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCATCGAGACTCCTTGAAAAATCTATATTCATCT
122 GGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCT
* * * * * *
19939 ATTAAAATCTTAGC-CATATTGCATTTAAGGATTTGTTTTCACGAGCATCTGAATCTTA-TTTTG
186 AATCAAATCTCAACACAT-TTG-ATTTAAGGATTT-TTTTTACGAGCATCTGAATC-TAGTTTCG
* * * *
20002 ATTTAATTAGAAATTAATTCTGAAAAATATGAAAAAGGATATTAAAAGTGTGAAAAGCTCTACAA
247 ATTTAATTAAAAATTAATTCAGAAAAA-AT----AAGGATATTAAAAGCGT-AAAAGCCCTACAA
* *
20067 TCTTTTTGGTGTAGAAT
306 TCTTTTTGGTGTTGAAA
* * ** * * *
20084 TATATATTTTTTATGAGTATTGTGGTTAAAATTTGA-AAACATATCTTGT-GGGTCAATTTTTGC
1 TATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAA-ATATCTT-TCGGTTCAATTTTTGC
* * *
20147 AAAATTTTAGCCTAAAATCGTGTA-ATAATCATCACAATTTTTGGCTAAAAACGCATTCCGGGGC
63 AAAATTTTAGCC-AAAATCGTGTATATAACCATCACAATTTTTGGCTAAAAACGCGTTCTGGGGC
** * *
20211 CCGATTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTTATCTAACCAA
127 CCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAA
20276 ATC
192 ATC
20279 ACAGCTATTG
Statistics
Matches: 713, Mismatches: 114, Indels: 66
0.80 0.13 0.07
Matches are distributed among these distances:
323 5 0.01
324 152 0.21
325 1 0.00
327 44 0.06
328 30 0.04
329 8 0.01
330 43 0.06
331 96 0.13
332 22 0.03
333 39 0.05
334 20 0.03
335 25 0.04
336 95 0.13
337 122 0.17
338 11 0.02
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (322 bp):
TATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGTTCAATTTTTGCAAA
ATTTTAGCCAAAATCGTGTATATAACCATCACAATTTTTGGCTAAAAACGCGTTCTGGGGCCCGG
CTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
CAACACATTTGATTTAAGGATTTTTTTTACGAGCATCTGAATCTAGTTTCGATTTAATTAAAAAT
TAATTCAGAAAAAATAAGGATATTAAAAGCGTAAAAGCCCTACAATCTTTTTGGTGTTGAAA
Found at i:20474 original size:667 final size:658
Alignment explanation
Indices: 19177--20558 Score: 1357
Period size: 660 Copynumber: 2.1 Consensus size: 658
19167 ATAGTGTACT
* * * * * *
19177 TACTAACCATAAC-AGTTTTTGGCTAAAAATGCGTTCCAGAGACCC-GCCTCAATTTTGCATGAT
1 TACTAACCATCACGA-TTTTTGGCTAAAAACGCGTTTCGGGGCCCCAG-CTCAATTTTGCATGAT
* * * *
19240 TTTTGACTCCGAGGCTACTTGAAACATCTATAATCATCTAATCAAATCTCAACCACATAGGATTT
64 TTTTGACTCCGAGACTACTTGAAAAATCTATAATCATCTAATAAAATCTCAACCACATAGCATTT
* * *
19305 AAGGATTTATTTTACGAGCATCTTAATCTTGTTTCGATTTAATTATAAATTAATTCGGAAAAAAT
129 AAGGATTTATTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAT
* * *
19370 AGGATATTAGAAACGTCAAAATCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTATGAGTA
194 AGGATATTAGAAACGTCAAAAGCCCTACAATCTTTTTGGCGTAGAAATATATATTTTTATGAGTA
* * * *
19435 TTTTAGCCAAAAATTGAGGAAATATCTTTCGGGCCCATTTTTTACAAAATTTTAGCCGAAATCGT
259 TTGTAGCCAAAAATTGAGAAAATATCTTTCGGGCCCAATTTTTACAAAATTTTAGCCAAAATCGT
* * * *
19500 GTAATAATTATCACAATTTTTGGCTAAAAAAGCGTTCTGGGGCTCCGGCTCAGTTTTGCATGATT
324 GTAATAATCATCACAATTTTTGGCTAAAAAAGCATTCCGGGGCTCCGACTCAGTTTTGCATGATT
* * **
19565 TTTGGCGCCAAGACTCCTTGAGATATCCATATTCATTTAATCAAACCTCAACTACATTTGATTTA
389 TTTGGCGCCAAGACTCCTTGAAATATCCATATTCATTTAATCAAACCTAAACTACAGCTGATTT-
* * *
19630 AGAATTTTTTTTACGAGCTTCTGAATCTAGTTTCGATTTAATTAAAAATTAATTCAAAAAAAATG
453 AGAA---TTTTTACAAGCATCTAAATCTAGTTTCGATTTAATTAAAAATTAATTCAAAAAAAATG
* * *
19695 AAAAAACGATATTAAAAGCGTAAGAAGACCTCCAATCTTTTTGGTGTTAAATTATATATATTTTA
515 AAAAAACGATATTAAAACCGTAAGAAGACCTCCAATCTTTTTGGCGTTAAATTATAAATATTTTA
** * * * *
19760 TGAGTATTTTATCCAAAAATTGAGGAAAAATTGTTCGGTTCA-TTTT-T-TTTT-T-CAAAATTT
580 TGAAAATTGTAGCCAAAAATTGAGGAAAAATTGTTCGATTAATTTTTGTATTTTCTGCAAAA-TT
19820 TAA-CCAAAATCGTG
644 TAAGCCAAAATCGTG
* *
19834 TACTATAACCATCATGATCTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGA
1 TAC--TAACCATCACGAT-TTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCTCAATTTTGCATGA
* * * * * * * *
19899 TTTTTGGCAT-CGAGACTCCTTGAAAAATCTATATTCATCTATTAAAATCTTAGCCATATTGCAT
63 TTTTTGAC-TCCGAGACTACTTGAAAAATCTATAATCATCTAATAAAATCTCAACCACATAGCAT
* * *
19963 TTAAGGATTTGTTTTCACGAGCATCTGAATCTTATTTTGATTTAATTAGAAATTAATTCTGAAAA
127 TTAAGGATTTATTTT-ACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAA
* * * * *
20028 ATATGAAAAAGGATATTA-AAAGTGTGAAAAGCTCTACAATCTTTTTGGTGTAGAATTATATATT
191 A-AT-----AGGATATTAGAAA-CGTCAAAAGCCCTACAATCTTTTTGGCGTAGAAATATATA-T
* ** * * *
20092 TTTTATGAGTATTGTGGTTAAAATTTGA-AAACATATCTTGT-GGG-TCAATTTTTGCAAAATTT
248 TTTTATGAGTATTGTAGCCAAAAATTGAGAAA-ATATCTT-TCGGGCCCAATTTTTACAAAATTT
* *
20154 TAGCCTAAAATCGTGTAATAATCATCACAATTTTTGGCTAAAAACGCATTCCGGGGC-CCGATTC
311 TAGCC-AAAATCGTGTAATAATCATCACAATTTTTGGCTAAAAAAGCATTCCGGGGCTCCGACTC
* *
20218 AGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATAT-C-TA-T-ATTT-ATCTAACC-AAA
375 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATTTAATCAAACCTAAA
* * *
20277 -TCACAGCT-A-TT-G-A-TTTTACAAGCATCTAAATC-ATGTTTTGATTTAATTAGAAATTAGT
440 CT-ACAGCTGATTTAGAATTTTTACAAGCATCTAAATCTA-GTTTCGATTTAATTAAAAATTAAT
** * * * *
20335 TCGGAAAAAATAGGAAAAACGATATTAAAACCGTGAA-AAG-CTCTTCGATCTTTTTGGCGTTGA
503 TCAAAAAAAAT-GAAAAAACGATATTAAAACCGT-AAGAAGAC-CTCCAATCTTTTTGGCGTTAA
* * * * *
20398 ATTATAAATTTTTTTATGAAAATTGTGGCTAAACATTGATGAAAAATAT-TTCGCCAAAAATTGA
565 ATTATAAA-TATTTTATGAAAATTGTAGCCAAAAATTGAGGAAAAAT-TGTTCG------ATT--
***
20462 GGAGAAATTTTTTGGGTCATTTTCTGCAAAATTTAAGCTGGAATCGTG
620 -----AA-TTTTT--GT-ATTTTCTGCAAAATTTAAGCCAAAATCGTG
*
20510 TACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCT
1 TACTAACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCT
20559 TTTCGGGTCA
Statistics
Matches: 590, Mismatches: 87, Indels: 80
0.78 0.11 0.11
Matches are distributed among these distances:
651 1 0.00
652 47 0.08
653 47 0.08
654 35 0.06
655 1 0.00
656 1 0.00
657 4 0.01
659 11 0.02
660 107 0.18
661 53 0.09
662 9 0.02
663 4 0.01
664 1 0.00
665 2 0.00
666 4 0.01
667 107 0.18
668 80 0.14
669 5 0.01
672 1 0.00
673 33 0.06
674 15 0.03
675 6 0.01
676 16 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (658 bp):
TACTAACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCTCAATTTTGCATGATTT
TTGACTCCGAGACTACTTGAAAAATCTATAATCATCTAATAAAATCTCAACCACATAGCATTTAA
GGATTTATTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAATAG
GATATTAGAAACGTCAAAAGCCCTACAATCTTTTTGGCGTAGAAATATATATTTTTATGAGTATT
GTAGCCAAAAATTGAGAAAATATCTTTCGGGCCCAATTTTTACAAAATTTTAGCCAAAATCGTGT
AATAATCATCACAATTTTTGGCTAAAAAAGCATTCCGGGGCTCCGACTCAGTTTTGCATGATTTT
TGGCGCCAAGACTCCTTGAAATATCCATATTCATTTAATCAAACCTAAACTACAGCTGATTTAGA
ATTTTTACAAGCATCTAAATCTAGTTTCGATTTAATTAAAAATTAATTCAAAAAAAATGAAAAAA
CGATATTAAAACCGTAAGAAGACCTCCAATCTTTTTGGCGTTAAATTATAAATATTTTATGAAAA
TTGTAGCCAAAAATTGAGGAAAAATTGTTCGATTAATTTTTGTATTTTCTGCAAAATTTAAGCCA
AAATCGTG
Found at i:21343 original size:333 final size:330
Alignment explanation
Indices: 20558--22067 Score: 1786
Period size: 333 Copynumber: 4.6 Consensus size: 330
20548 GGGCCCCAGC
* *
20558 TTTTCGGGTCATTTTTTGCAAATTTTTAGCCGAAATCGTG---AA--ATCACGGTTTTTTGCGAA
1 TTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGGTTTTTTGCTAA
* * **
20618 AAACGCGTTTCGGAGCTCTGGCTCAGTTTTGCATGATTTTTGGCGTTGAGACTCCTTGAAATATC
66 AAACGCGTTTCGG-GCTCCGGCTCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATC
* * * * *
20683 TATATTCATCTAATCAAATCTCAG-CACA-TTGCATTTAAGCATTTGTTTGTACGAGCATTTGAA
130 TATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCATCTGAA
20746 TCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAA
195 TCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAA
* * * *
20811 AGTCCTCCAATCGTTTTAGAC-TTAAATTATATATA-TTTATGACTATTTTAGCCAAAAATT-AA
260 AGTCCTCCAA-CCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAA
*
20873 GGAGAAAT
324 -GAAAAAT
* ** * * * * * *
20881 TTTTCGGGCCATTTTCCGCAAGATTTAAGCTGGAATCGTGTACTAATCATCACGGTTTTTGGCTA
1 TTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTA-TAACCATCACGGTTTTTTGCTA
* * *
20946 AAAACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTTGTGCCGAGACTCCTTGAAATAT
65 AAAACGCGTTTC-GGGCTCCGGCTCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATAT
* * *
21011 CTATACTCATCTAATCAAATCTCAGGCACATTTGAATTTAATGATTTGTTTTTATGAGCATCCTG
129 CTATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCAT-CTG
* * *
21076 AATCTTGTTTTGATTTAATTAGAAATTAATTC-GTAAAAATATGAAAAGCGATATTAAAAAC-TC
193 AATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGT-
* *
21139 GAAAAGTCCTTCAACCTTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAATT
256 GAAAAGTCCTCCAACCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATT
21204 GAAGAAAAAT
321 GAAGAAAAAT
* *
21214 TTTTCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACAGTTTTTTGCTA
1 TTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTA-TAACCATCACGGTTTTTTGCTA
* * * *
21279 AAATCGCGTTTCAGGGCTCCGACTCAGTTTTGCATGATTTTTGGTGTCAAGACTCCTTGAAATAT
65 AAAACGCGTTTC-GGGCTCCGGCTCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATAT
* * * * * *
21344 CTATATTCATCTAATCAAATCTCAGTCACA-TTGCATTTAAGGATTTGTTTATACAAGCATTTGA
129 CTATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCATCTGA
*
21408 ATCTTATTTCGATTTAATTAGAAATTAATTTC-GAAAAATATGAAAAACGATATTAAAAGCGTGA
194 ATCTTGTTTCGATTTAATTAGAAATTAA-TTCAGAAAAATATGAAAAACGATATTAAAAGCGTGA
* ** *
21472 AAAATCCTCCAATATTTTTGGCGTTAAATTATATATATATATATATTATGAGTATTTTAGCTAAA
258 AAAGTCCTCCAACCTTTTTGGCGTT-AA--AT-TATATATAT-T-TTATGAGTATTTTAGCCAAA
*
21537 AATTGAGGAAAAAT
317 AATTGAAGAAAAAT
* * * * *
21551 TTGTCGGGTCATTTTCTGCAAAATTTAAGCTGGAATCGTGTACTAACCATCACGGTTTTTTGGCT
1 TTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTA-TAACCATCACGGTTTTTT-GCT
* * * ** *
21616 AAAAACGTGTTTCGGGGC-CCAGCTTAGTTTTGCATGATTTTTGGCACCGAGATTCCTTGAAATA
64 AAAAACGCGTTTC-GGGCTCCGGCTCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATA
** *
21680 TCTATACTCATCTAATCAAATCTCAGCCGTATTTGAATTTAATGATTTGTTTTTACGAGCATCTG
128 TCTATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCATCTG
* * * *
21745 AATCTTGTTTTGATTTAATTAGAATTTGATTCAGAAAAATATGGAAAACGATATTAAAAGCGTGA
193 AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGA
* * * * * *
21810 AAAGTTCTCCAATCTTTTTGGAGTTAAA-TATATATATTTTATGAGTATTGTGGCTAAAAATTGA
258 AAAGTCCTCCAACCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGA
*
21874 GGAAAAAT
323 AGAAAAAT
** *
21882 ACTTCGGGTC-TATTTTTGCAAAATTTTAGCCGAAATCGTG--T-ACCATCACGATTTTTTGCCT
1 TTTTCGGGTCAT-TTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGGTTTTTTG-CT
* ** * * * *
21943 AAAAACGCGTTTC-GGCATCCCGGGTCAGTTTTGCATGATTTTTTTATGGCAAAACTCCTTCAAA
64 AAAAACGCGTTTCGGGC-T-CCGGCTCAGTTTTGCATGA-TTTTTGGTGCCGAGACTCCTTGAAA
* * * * * *
22007 TATCTATAGTCATCTAACCTAATCTTAGCCACATTAG-ATTTAAGGATTTGTTTTTATGAGC
126 TATCTATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGC
22068 TGTAGAGCAA
Statistics
Matches: 1013, Mismatches: 142, Indels: 59
0.83 0.12 0.05
Matches are distributed among these distances:
323 32 0.03
325 3 0.00
326 1 0.00
327 31 0.03
328 39 0.04
329 140 0.14
330 7 0.01
331 174 0.17
332 118 0.12
333 176 0.17
334 4 0.00
335 10 0.01
336 1 0.00
337 154 0.15
338 123 0.12
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37
Consensus pattern (330 bp):
TTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGGTTTTTTGCTAA
AAACGCGTTTCGGGCTCCGGCTCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATCT
ATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCATCTGAAT
CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
GTCCTCCAACCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAAGA
AAAAT
Found at i:21720 original size:670 final size:655
Alignment explanation
Indices: 20558--22059 Score: 2094
Period size: 670 Copynumber: 2.3 Consensus size: 655
20548 GGGCCCCAGC
* *
20558 TTTTCGGGTCATTTTTTGCAAATTTTTAGCCGAAATCGTG-AA--ATCACGGTTTTTTGCGAAAA
1 TTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCAC-GTTTTTTGCTAAAA
* * **
20620 ACGCGTTTCGGAGCTCTGGCTCAGTTTTGCATGATTTTTGGCGTTGAGACTCCTTGAAATATCTA
65 ACGCGTTTCGG-GCTCCGGCTCAGTTTTGCATGATTTTTGGTGTCAAGACTCCTTGAAATATCTA
* * *
20685 TATTCATCTAATCAAATCTCAGCACATTGCATTTAAGCATTTGTTTGTACGAGCATTTGAATCTT
129 TATTCATCTAATCAAATCTCAGCACATTGCATTTAAGGATTTGTTTATACAAGCATTTGAATCTT
* *
20750 GTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTC
194 ATTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAATC
* *
20815 CTCCAATCGTTTTAGACTTAAATTATATATATTTATGACTATTTTAGCCAAAAATTAAGGAGAAA
259 CTCCAATCATTTTAGACTTAAATTATATATATTTATGACTATTTTAGCCAAAAATTAAGGAAAAA
* * *
20880 TTTTTCGGGCCATTTTCCGCAAGATTTAAGCTGGAATCGTGTACTAATCATCACGGTTTTTGGCT
324 TTTGTCGGGCCATTTTCCGCAAAATTTAAGCTGGAATCGTGTACTAACCATCACGGTTTTTGGCT
* * **
20945 AAAAACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTTGTGCCGAGACTCCTTGAAATA
389 AAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATA
* *
21010 TCTATACTCATCTAATCAAATCTCAGGCACATTTGAATTTAATGATTTGTTTTTATGAGCATCCT
454 TCTATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCAT-CT
21075 GAATCTTGTTTTGATTTAATTAGAAATTAATTC-GTAAAAATAT-GAAAAGCGATATTAAAAAC-
518 GAATCTTGTTTTGATTTAATTAGAAATTAATTCAG-AAAAATATGGAAAA-CGATATTAAAAACG
* * *
21137 TCGAAAAGTCCTTCAACCTTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAA
581 T-GAAAAGTCCTCCAACCTTTTTGGAGTTAAA-TATATATATTTCATGAGTATTGTAGCCAAAAA
21202 TTGAAGAAAAAT
644 TTGAAGAAAAAT
*
21214 TTTTCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACAGTTTTTTGCTA
1 TTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTG---TAACCATCAC-GTTTTTTGCTA
* *
21279 AAATCGCGTTTCAGGGCTCCGACTCAGTTTTGCATGATTTTTGGTGTCAAGACTCCTTGAAATAT
62 AAAACGCGTTTC-GGGCTCCGGCTCAGTTTTGCATGATTTTTGGTGTCAAGACTCCTTGAAATAT
21344 CTATATTCATCTAATCAAATCTCAGTCACATTGCATTTAAGGATTTGTTTATACAAGCATTTGAA
126 CTATATTCATCTAATCAAATCTCAG-CACATTGCATTTAAGGATTTGTTTATACAAGCATTTGAA
21409 TCTTATTTCGATTTAATTAGAAATTAATTTC-GAAAAATATGAAAAACGATATTAAAAGCGTGAA
190 TCTTATTTCGATTTAATTAGAAATTAA-TTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
* * * *
21473 AAATCCTCCAAT-ATTTTTGGCGTTAAATTATATATATATATATATTATGAGTATTTTAGCTAAA
254 AAATCCTCCAATCATTTTAGAC-TT--A--A-AT-TATATATAT-TTATGACTATTTTAGCCAAA
* * *
21537 AATTGAGGAAAAATTTGTCGGGTCATTTTCTGCAAAATTTAAGCTGGAATCGTGTACTAACCATC
311 AATTAAGGAAAAATTTGTCGGGCCATTTTCCGCAAAATTTAAGCTGGAATCGTGTACTAACCATC
*
21602 ACGGTTTTTTGGCTAAAAACGTGTTTCGGGG-CCCAGCTTAGTTTTGCATGATTTTTGGCACCGA
376 ACGG-TTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGA
* **
21666 GATTCCTTGAAATATCTATACTCATCTAATCAAATCTCAGCCGTATTTGAATTTAATGATTTGTT
440 GACTCCTTGAAATATCTATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTT
* *
21731 TTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAATTTGATTCAGAAAAATATGGAAAACGA
505 TTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGGAAAACGA
* * * *
21796 TATTAAAAGCGTGAAAAGTTCTCCAATCTTTTTGGAGTTAAATATATATATTTTATGAGTATTGT
570 TATTAAAAACGTGAAAAGTCCTCCAACCTTTTTGGAGTTAAATATATATATTTCATGAGTATTGT
* * *
21861 GGCTAAAAATTGAGGAAAAAT
635 AGCCAAAAATTGAAGAAAAAT
**
21882 ACTTCGGGTC-TATTTTTGCAAAATTTTAGCCGAAATCGTGT-ACCATCACGATTTTTTGCCTAA
1 TTTTCGGGTCAT-TTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCACG-TTTTTTG-CTAA
* ** * * *
21945 AAACGCGTTTC-GGCATCCCGGGTCAGTTTTGCATGATTTTTTTATGGCAAAACTCCTTCAAATA
63 AAACGCGTTTCGGGC-T-CCGGCTCAGTTTTGCATGA-TTTTTGGTGTCAAGACTCCTTGAAATA
* * * *
22009 TCTATAGTCATCTAACCTAATCTTAGCCACATTAG-ATTTAAGGATTTGTTT
125 TCTATATTCATCTAATCAAATCTCAG-CACATT-GCATTTAAGGATTTGTTT
22060 TTATGAGCTG
Statistics
Matches: 753, Mismatches: 65, Indels: 46
0.87 0.08 0.05
Matches are distributed among these distances:
656 38 0.05
660 2 0.00
662 102 0.14
663 114 0.15
664 19 0.03
665 33 0.04
666 66 0.09
667 3 0.00
668 76 0.10
669 88 0.12
670 187 0.25
671 25 0.03
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37
Consensus pattern (655 bp):
TTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCACGTTTTTTGCTAAAAA
CGCGTTTCGGGCTCCGGCTCAGTTTTGCATGATTTTTGGTGTCAAGACTCCTTGAAATATCTATA
TTCATCTAATCAAATCTCAGCACATTGCATTTAAGGATTTGTTTATACAAGCATTTGAATCTTAT
TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAATCCT
CCAATCATTTTAGACTTAAATTATATATATTTATGACTATTTTAGCCAAAAATTAAGGAAAAATT
TGTCGGGCCATTTTCCGCAAAATTTAAGCTGGAATCGTGTACTAACCATCACGGTTTTTGGCTAA
AAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATATC
TATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAA
TCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGGAAAACGATATTAAAAACGTGAAA
AGTCCTCCAACCTTTTTGGAGTTAAATATATATATTTCATGAGTATTGTAGCCAAAAATTGAAGA
AAAAT
Found at i:22510 original size:37 final size:37
Alignment explanation
Indices: 22467--22538 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
22457 ATTATTGAAA
*
22467 GAAGATCCACGTATGTGGAGGATTATTTTCAAAGATT
1 GAAGATCCACGTATGTGGAGGATTATTATCAAAGATT
22504 GAAGATCCACGTATGTGGAGGATTATTATCAAAGA
1 GAAGATCCACGTATGTGGAGGATTATTATCAAAGA
22539 AGATTGAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (37 bp):
GAAGATCCACGTATGTGGAGGATTATTATCAAAGATT
Found at i:22861 original size:62 final size:57
Alignment explanation
Indices: 22757--22879 Score: 165
Period size: 62 Copynumber: 2.1 Consensus size: 57
22747 AAGACCCTCG
* * * *
22757 AATCAAATCAAACTCCCAAGTCATCAATTCAAGATAAGTCATTCGACCCTTGAATCA
1 AATCAAATCAAACTCCAAAATCATCAATTCAAGATAAGTCATTCGACCCTTAAAGCA
22814 AATCAAATCAAACTCTCAAATTATCATCAAATTCAAGATCAAGTCATTCGACCCTTAAAGCA
1 AATCAAATCAAACTC-CAAA--ATCATC-AATTCAAGAT-AAGTCATTCGACCCTTAAAGCA
22876 AATC
1 AATC
22880 TTGAAGCATA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
57 15 0.26
58 3 0.05
60 5 0.09
61 10 0.18
62 24 0.42
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (57 bp):
AATCAAATCAAACTCCAAAATCATCAATTCAAGATAAGTCATTCGACCCTTAAAGCA
Found at i:22878 original size:57 final size:56
Alignment explanation
Indices: 22714--22879 Score: 160
Period size: 57 Copynumber: 2.9 Consensus size: 56
22704 AACCCTTGAA
* * * **
22714 TCAAATTATCATCGATTCGAGATCAAGTCATTAAAGACCCTCGAATCAAATCAAACTC
1 TCAAATTATCATCAATTCAAGATCAAGTCATT--CGACCCTTAAATCAAATCAAACTC
* *
22772 -CCAA--GTCATCAATTCAAGAT-AAGTCATTCGACCCTTGAATCAAATCAAATCAAACTC
1 TCAAATTATCATCAATTCAAGATCAAGTCATTCGACCC-T---T-AAATCAAATCAAACTC
*
22829 TCAAATTATCATCAAATTCAAGATCAAGTCATTCGACCCTTAAAGCAAATC
1 TCAAATTATCATC-AATTCAAGATCAAGTCATTCGACCCTTAAATCAAATC
22880 TTGAAGCATA
Statistics
Matches: 88, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
52 5 0.06
53 1 0.01
54 8 0.09
55 13 0.15
57 27 0.31
58 4 0.05
60 5 0.06
61 11 0.12
62 14 0.16
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (56 bp):
TCAAATTATCATCAATTCAAGATCAAGTCATTCGACCCTTAAATCAAATCAAACTC
Found at i:23673 original size:332 final size:330
Alignment explanation
Indices: 23051--23857 Score: 972
Period size: 332 Copynumber: 2.4 Consensus size: 330
23041 CGAGTATTTG
* * *
23051 AATCATGTTTCGATTTAATCAGAAATTAATTT-GAAAAAAAAAAGAAAAAACGATATTAGAAGCG
1 AATCTTGTTTCGATTTAATCAGAAATTAATTTAG-AAAAAAATAGAAAAAACGATATTAGAAACG
* * * * *
23115 TGAGAAGCCCTACAATCTTTTTGGCATTGAATTATATAATTTTTTATGAGTATTATGGCTAAAAA
65 TGAAAAG-ACTACAATCTTTTTGGCGTTGAATTATAT-A-TTTTTATGAGTATTTTCGCTAAAAA
* * *
23180 TTGA-GATAAATATTTAGGGTCAATTTTTGCAAAACTTTAGCCAAAATCGTGTACCATCACGGTT
127 TTGAGGAAAAATCTTTAGGGTCAATATTTGCAAAACTTTAGCCAAAATCGTGTACCATCACGGTT
**
23244 TTTTGGCTAAAAACGCGTTTTGGGGCCCCATGTCAGTTTTGCATGATTTTTTACACCAAGACTCC
192 TTTTGGCTAAAAACGCGTTGCGGGGCCCCATGTCAGTTTTGCATGATTTTTTACACCAAGACTCC
* * *
23309 TTAAAATATATCTTTATTCATGTAACCAAATCTCAGCCACATTGTATTTAAGAATTTGTTTTTAC
257 TTAAAATATATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTCTAC
23374 GA-GCATCTA
322 -ATGCATCTA
23383 AATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAATAAAATAGAAAAAACGATATTAGAAACG
1 AATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAA-AAAATAGAAAAAACGATATTAGAAACG
* * * * * *
23448 TGAAAAAGGCTTTCAAT-TGTTTTGGTGTTGATTTATATATTTTTCTGAGTATTTTCGCTAGAAA
65 TG-AAAAGAC-TACAATCT-TTTTGGCGTTGAATTATATATTTTTATGAGTATTTTCGCTAAAAA
* * * *
23512 TTGAGGAAAAATCTTTTGGGTCAATATTTGCAAAATTTTAGCCGAAATCGTGTACGTTATCACGG
127 TTGAGGAAAAATCTTTAGGGTCAATATTTGCAAAACTTTAGCCAAAATCGTGTAC--CATCACGG
* * * *
23577 -TTTTTGGCTAAAAACGGGTTGCGGGGCCACGGAT-TTA-TTTTGCATGATTTTTTGCACCAAGA
190 TTTTTTGGCTAAAAACGCGTTGCGGGGCC-C-CATGTCAGTTTTGCATGATTTTTTACACCAAGA
* * *
23639 CTCCTT-GAA-ATATCTTTATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
253 CTCCTTAAAATATATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTT
*
23702 CTACATGCATCTG
318 CTACATGCATCTA
* * * * **
23715 AATCTTATTTTGATTTAATTAGAAATTAATTCAG-AAAAAATATG-GGAAACGATATTA-AAAGC
1 AATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAAAAAATA-GAAAAAACGATATTAGAAA-C
* * * *
23777 GTGAAAAGTACTCCAGTCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTTGCCAAAAA
64 GTGAAAAG-ACTACAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTCGCTAAAAA
*
23842 TTGAGAAAAAATCTTT
127 TTGAGGAAAAATCTTT
23858 CCGGTCATTT
Statistics
Matches: 410, Mismatches: 49, Indels: 34
0.83 0.10 0.07
Matches are distributed among these distances:
329 31 0.08
330 58 0.14
331 4 0.01
332 148 0.36
333 77 0.19
334 80 0.20
335 10 0.02
336 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (330 bp):
AATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAAAAAATAGAAAAAACGATATTAGAAACGT
GAAAAGACTACAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTCGCTAAAAATTGA
GGAAAAATCTTTAGGGTCAATATTTGCAAAACTTTAGCCAAAATCGTGTACCATCACGGTTTTTT
GGCTAAAAACGCGTTGCGGGGCCCCATGTCAGTTTTGCATGATTTTTTACACCAAGACTCCTTAA
AATATATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTCTACATGC
ATCTA
Found at i:29335 original size:331 final size:331
Alignment explanation
Indices: 28689--32410 Score: 3306
Period size: 332 Copynumber: 11.3 Consensus size: 331
28679 CATTTTTTTG
* * * * * * * *
28689 AATTAATTTTTAATTAAATCGAAACAAAATTTAAATGTTCGTAAAAACAAATTCGTATATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* ** * * * * *
28754 ATACCTGATATTTGATTAGAT-AATAAAGATATTTCAAGGTGTCTCGGCGCCAAAAATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAA
* * * *
28818 AACTGAGACGGGACCCCGGAACGCGTTTTTAGTCAAGAACCGTGATGGTTAGTACACAATTTCGA
131 AACTGAG-CGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGA
* ** * *
28883 CTAAAATTTTACAAAAATTGACCCGAAAGATAATTCCTCAATTTTTTTGCTAAAATACTCAT-AA
195 CTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAA-TTTTTAGCTAAAATACTCATAAA
*** ** * * * *
28947 AAATATATAATTTGGCATCAAAAAGATTGAAGGGTTTTTTACGCTTCTAATATTGTTTTTCCTAT
259 AAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTAT
*
29012 TTTTTCCG
324 TTTTTCCA
* * * * *
29020 AATTAATTTTTAATTAAATCGAAATAAGATTCAGATACTCATAAAAACAAATCATTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * *
29085 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGTTTTGGCACAAAAAAACATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAA
* * * * * * * *
29150 AACTGAGCAGGGCCTCGGAACGGGTTTTTAGCCGAAATCCGTGATGGTTAGTATACCATTTCGGC
131 AACTGAGCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGAC
* * * * *
29215 TAGAATTTTGTAAAAA-TGACCCGAAAGATTTTTTCTCAAATTCTAGCGAAAATACTCATAAAAA
196 TAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTTTTAGCTAAAATACTCATAAAAA
* * * * *
29279 ATATATAATTCAACGCCAAAAAAATTGAAAGTCTTTTTCACG-TTTCTAACATTGTTTTTCCTAT
261 ATATATAATTCAACGCCAAAAAGATTGAAGGGC-TTTTCACGCTTT-TAATATCGTTTTTCCTAT
29343 TCTATTTCCA
324 T-T-TTTCCA
* * * * * *
29353 AATTAATTGT-TGATTAAATCGAAATAAGATTTAGATACTCTTAAAAACAAATCCTTAAATACAA
1 AATTAATT-TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * * * *
29417 TGTGACTGAGATTTGGTTAGATGCATACAGATATATTTTAAGGAGTCTTGGCACCGAAAATCATG
65 TGTGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTCTTGGCACCAAAAATCATG
* * ** * *
29482 CAAAACTGACCCGGGGACTTGGAACGCGTTTTGTAGCCAAAAAAGCGTGA----TAGTACACAAT
128 CAAAACTGA-GCGGGGCCCCGGAACGCGTTTT-TAGCC-AAAAACCGTGATGGTTAGTACACGAT
* * * * *
29543 TTCGGCTAAAATTTTGCAAAAATGTTA--C-AAA-TTATTTTTCT-AATTTTTAGCCACAATACT
190 TTCGACTAAAATTTTGCAAAAAT-TGACCCGAAAGAT-TTTTTCTCAATTTTTAGCTAAAATACT
* * * **
29603 CAGAAAAAATATATATAATTCAATGCCAAAAAGATTGAAGGGCTTCTCACGCTTCCAATATCGTT
253 CA-TAAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTT
*
29668 TTTCCTATTTTTTTCA
316 TTTCCTATTTTTTCCA
* * *
29684 AATTAATTTCTAATTAAATTGAAACATA-ATTCAAATGCTCGTAAAAAAAAAATCCTTAAATCCA
1 AATTAATTTCTAATTAAATCGAAACA-AGATTCAGATGCTCGT-AAAAACAAATCCTTAAATCCA
* * * * *** * *
29748 ATGTAGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTAAAACTAAAAACCATGC
64 ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGC
* * * *
29813 AAAACTGACCCGGGGCCCCGGAACGCGATTTTAGCCAAAAAACCATGAT-G---GTACACAATTT
129 AAAACTGA-GCGGGGCCCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTT
* * * * * * *
29874 CGACTAAAATTTTACAAAAGTTAACCC----GA-TTTTCCTCAATTTTTAGCCACAATACTCACA
192 CGACTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTTTTAGCTAAAATACTCATA
* * * * *
29934 AAATATATATAATTCAACTG-AAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCT
257 AAAAATATATAATTCAAC-GCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCC
*
29998 TA-TTTTTCAA
321 TATTTTTTCCA
* * * * *
30008 AATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCATAAAAATAAATCCTTATATGCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * *
30073 GTGGTTGAGATTTTGATTAGATGAATATAGATATTTCAAGGAGTCTAGACGCCAAAAATCATACA
66 GTGGCTGAGA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCA
* * * * ** *
30138 AAACTGAGTCGGGGCTCCGAAACGCATTATTAGGAAAAAAAAACTGTGATGG-TAGTACACGATT
130 AAACTGAG-CGGGGCCCCGGAACGCGTTTTTA-G--CCAAAAACCGTGATGGTTAGTACACGATT
* * * * * * ** *
30202 TTGACTAAAATTTTGCAAAAAATGA-CCTAAAAATTTTTTTCTTAATTTTTGGAAAAAATACTAA
191 TCGACTAAAATTTTGCAAAAATTGACCCGAAAGA-TTTTTTCTCAATTTTTAGCTAAAATACTCA
* * * * * * * * * * *
30266 TGAAATATATATAATTTAATGCCAAAAATATTGGAGGACTTTTAACGCTTTTCATATTGTTTTTT
255 TAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTC
*
30331 C-ATATTTTTCTA
320 CTAT-TTTTTCCA
* * * * * *
30343 GATTAATGTCTAATTAAATCGAAACAAGATTCGGATGTTCGCAAAAACAAATCCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * *
30408 GTGCCTGAGATTTGATTAGATGAATAT-GAATATCTCAAGGAGTCTTGG-AGCAAAAAATCATGC
66 GTGGCTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGAGTCTTGGCA-CCAAAAATCATGC
* ** * * * ** * *
30471 AAAACTGA-CTTGGGGCTCTAGAATGCATTTTTAGCCAAAAATCGTGATCATTATTATACGATTT
129 AAAACTGAGC--GGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT
* * * * * *
30535 CAACTAAAATTTTGGAAAAATTGAACCAAAAGATATTTCCTCAATTTTT-GACTAAAATACTCAT
192 CGACTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTTTTAG-CTAAAATACTCAT
* * * * * * *
30599 AAAAAATATATAATTCAACACCAAAAATATTGAAGGGTTTTTGTACAC-TTCAA-AT--TTTTTT
256 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTT-CACGCTTTTAATATCGTTTTTC
* *
30660 TTAACTTTTTTCCG
320 CT-A-TTTTTTCCA
* * *
30674 AATTAATTTGTAATTAAATCGAAACAAGATTTATATGCTCGTAAAAACAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* *
30739 GTGGCTGAGATTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGGCATCAAAAATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAA
* * *
30804 AACTGACTCGGGGCCCCGGAACGCGTTTTTAGCAAAAAAAAACC--G-T-GTTGGTACACGATTT
131 AACTGA-GCGGGGCCCCGGAACGCGTTTTTAGC---CAAAAACCGTGATGGTTAGTACACGATTT
* * * * *
30865 TGGCTAATATTTTGCAAAAATTGACCCGAAA-ATATTTTTCCTCAATTTTTAGCCACAATACTCA
192 CGACTAAAATTTTGCAAAAATTGACCCGAAAGAT-TTTTT-CTCAATTTTTAGCTAAAATACTCA
* *
30929 TAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTC
255 TAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTC
*
30994 CTATTTTTTCCG
320 CTATTTTTTCCA
* * * *
31006 AATTAATTTCTAATTAAATTGAAACATGATTCAAATGCTTGT-------AA-----AAA--CAA-
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
** *
31056 -TGGCTGAGATTTGGCTAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAA
* * **** * * * * *
31120 AACTGAATCGGGACCAAAAAAACGTGTTTTTATCCAAAAACTGTGATGATTATTACACGATTTCG
131 AACTG-AGCGGGGCC-CCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
** * * * * *
31185 GTTAAAATTTTGCAAAAATTGACCCGAAAGATATTTTCTCAAATTTTAACCACAATACTCATAAA
194 ACTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTTTTAGCTAAAATACTCATAAA
* * * *
31250 AAATATATAATTCAATGTCAAAAAGATTGAAGGGCTTTTCACGATTTTAATATCGTTTTTCATAA
259 AAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCT-A
***
31315 TTTTTTTTG
323 TTTTTTCCA
* * * *
31324 AATTAATATCTAAATAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * * * ** *
31389 GCGGCTAACATTTTATTAGATGAATATTGATATTTCAAGGAGTCTCGGCGTCAAATATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAA
* * * * * * *
31454 AACTGAATCGGGGCCCCGAAACGTGTTTTTATCCAAAAA-CATAATGGTTAGTACACGATTTTGA
131 AACTG-AGCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGA
* * * * *
31518 CTAAAATTTTGCAAAAGA-TGACACGAAAAATTTTTTCCTCAATTTTTGGATAAAATACTCATTA
195 CTAAAATTTTGCAAAA-ATTGACCCGAAAGATTTTTT-CTCAATTTTTAGCTAAAATACTCATAA
* * * * * * * *
31582 AATATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCATGCTTTTAATTTCTTTTTTCTTA
258 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTA
*
31647 TTTTTTTCTA
323 -TTTTTTCCA
* * **
31657 AATTAATTTTTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA-AAATTTTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * * * ** *
31721 GTGGCTAAGATTTGATTATATGAATATGGATATCTCAAGAAGGCTTGGGGCAAAAAAT-ATTGCA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCA-TGCA
* * * * * * *
31785 AAATTGAGCCGGGTCCCCAGAACGC-TTTGTTAGCCAAAAGCTGTGATGGTTATTACACGATTCC
130 AAACTGAG-CGGGGCCCCGGAACGCGTTT-TTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
* * * * *
31849 GACTAAAATTTTGTAAAAATTGACTCGAAAGATATTTCCTCAATTTTTAGCTAAAATAGTCATAA
193 GACTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTTTTAGCTAAAATACTCATAA
* * * * *
31914 AAAATATATAATTTAGCACCAAAAAGATTGAAGTGCTTTTCACGCTTTTAATATCGTTTTTCATT
258 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTC-CT
* *
31979 TTTTTTTCTA
322 ATTTTTTCCA
* * *
31989 ATTTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATAATGC
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT--A-AATCC
* * * * * * * * *
32054 AATGCGGCTAACATTTTATTAGATGAATATAGATATTTCTAGGAGTCCTAGCGCCAAAAATTATG
63 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATG
* * * * * *
32119 CTAAATTGAGCCAGGGCCCCAGAATGCGTTTTCAGCCAAAAACCGTGATGGTTAGTTAGTACACG
128 CAAAACTGAG-CGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G---GTTAGTACACG
* * * * * * * * *
32184 ACTTCGGCTAAAATTATGCAAAAATTGACACGAAAGATTTCTGCTCGATATTTGGCTAAAATACT
188 ATTTCGACTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTTTTAGCTAAAATACT
* * * *
32249 TAT-AAAAATATATAATTCAACGCCAAAAAGATTGGATGGCTTTTCACGCTTTTAATATCGTATT
253 CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTT
* **
32313 TCTTATTTTTTGTA
318 TCCTATTTTTTCCA
* * * **
32327 AATTAATTTCTAATTAAATCGAAATAAGATTGAGATACTCGTAAAAACAAATTTTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
** *
32392 GTTACTGAGATTTGGTTAG
66 GTGGCTGAGATTTGATTAG
32411 TTGATGCAAT
Statistics
Matches: 2770, Mismatches: 507, Indels: 224
0.79 0.14 0.06
Matches are distributed among these distances:
314 6 0.00
316 72 0.03
317 97 0.04
318 91 0.03
319 2 0.00
320 3 0.00
323 28 0.01
324 114 0.04
325 57 0.02
326 21 0.01
327 22 0.01
328 4 0.00
329 97 0.04
330 149 0.05
331 418 0.15
332 523 0.19
333 343 0.12
334 286 0.10
335 127 0.05
336 112 0.04
337 10 0.00
338 68 0.02
339 56 0.02
340 64 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (331 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAA
AACTGAGCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGAC
TAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCTCAATTTTTAGCTAAAATACTCATAAAAA
ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTT
TTTCCA
Found at i:32776 original size:15 final size:16
Alignment explanation
Indices: 32758--32787 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
32748 ATAAATAATA
32758 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
32773 ATATTATAATCTAAA
1 ATATTATAATCTAAA
32788 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:34144 original size:29 final size:29
Alignment explanation
Indices: 34112--34187 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
34102 ATTGGCGTCA
*
34112 AGGATATTTTGCCCCATAAA-TTTCAAATC
1 AGGATATTTTGCCCC-TAAACTTCCAAATC
* * *
34141 AGGACATTTTATCCCCTAAACTTCCAAATT
1 AGGATATTTT-GCCCCTAAACTTCCAAATC
34171 AGGATATTTTGTCCCCT
1 AGGATATTTTG-CCCCT
34188 GATTTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 13 0.34
30 25 0.66
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.36
Consensus pattern (29 bp):
AGGATATTTTGCCCCTAAACTTCCAAATC
Found at i:37412 original size:13 final size:13
Alignment explanation
Indices: 37396--37422 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37386 GCAAAAAAAT
37396 CATGCAAAACTGA
1 CATGCAAAACTGA
37409 CATGCAAAACTGA
1 CATGCAAAACTGA
37422 C
1 C
37423 CTGGGGCCCC
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:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (13 bp):
CATGCAAAACTGA
Found at i:38098 original size:322 final size:320
Alignment explanation
Indices: 37478--38103 Score: 824
Period size: 322 Copynumber: 1.9 Consensus size: 320
37468 GATTTCGGCT
* * * *
37478 AAAATTTTGTAAAAATTGACCCGAAATATTTTTCCTCAATTTTAAGCCACAATACTCATAGAATA
1 AAAATTTTGCAAAAAATGACCCGAAAAATTTTTCCTCAATTTTAAGCCAAAATACTCATAGAATA
** * * *
37543 TATATAATCAAATGCCAAAAAGATTGGAGGACTCTTCACACGTTTAATATCGTTTTTCATATTTT
66 TATATAATCAAACACCAAAAAGATTGGAGAACTCTTCACAAGTTTAATATCATTTTTCATATTTT
* * *
37608 TCTGAATTAATTTCGAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATT
131 CCTAAATTAATTTCGAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATC
* * * * * * *
37673 TAATGTGGCTAAAATTTGATTTGATGAATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCAT
196 TAATATAGCTAAAATTTGATTAGATGAATAAAGAAATCTCAAAGACTCTCGGCGCCAAAAATCAT
* *
37738 GCAAAACTAAGCCGGGGTCCCGAAACGCGTTTTTAACCAAAAACTGTGATGCTTAATATC
261 CCAAAACTAAGCCGGGGCCCCGAAACGCGTTTTTAACCAAAAACTGTGATGCTTAATATC
* *
37798 AAAACTTTTGCAAAAAATGACCTGAAAAATTTTTCCGTCAATTTTTAG-CATAAATACTCATA-A
1 AAAA-TTTTGCAAAAAATGACCCGAAAAATTTTTCC-TCAATTTTAAGCCA-AAATACTCATAGA
** * *
37861 GATATATATAATTTAACACCAAAAAGATTGGAGAACTTTTCACAATTTTAATATCATTTTTCATA
63 -ATATATATAATCAAACACCAAAAAGATTGGAGAACTCTTCACAAGTTTAATATCATTTTTCATA
* * **
37926 TTTTCCTAAATTAATTTCTAATTAAATGAAAACAAGATTTAGATGCTCGTAAAAACAAATTTTTA
127 TTTTCCTAAATTAATTTCGAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTA
* * ** *
37991 AATCTAATATAGCTGAGATTTGATTAGATGAATATGGAAATCTCAAAGACTCTTGGCGCCAAAAA
192 AATCTAATATAGCTAAAATTTGATTAGATGAATAAAGAAATCTCAAAGACTCTCGGCGCCAAAAA
* ** * **
38056 TCATCCAAAACTTAGTTGGGGCCCCGGATTGCGTTTTTAACCAAAAAC
257 TCATCCAAAACTAAGCCGGGGCCCCGAAACGCGTTTTTAACCAAAAAC
38104 CATGATGATT
Statistics
Matches: 260, Mismatches: 42, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
320 4 0.02
321 30 0.12
322 226 0.87
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (320 bp):
AAAATTTTGCAAAAAATGACCCGAAAAATTTTTCCTCAATTTTAAGCCAAAATACTCATAGAATA
TATATAATCAAACACCAAAAAGATTGGAGAACTCTTCACAAGTTTAATATCATTTTTCATATTTT
CCTAAATTAATTTCGAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATC
TAATATAGCTAAAATTTGATTAGATGAATAAAGAAATCTCAAAGACTCTCGGCGCCAAAAATCAT
CCAAAACTAAGCCGGGGCCCCGAAACGCGTTTTTAACCAAAAACTGTGATGCTTAATATC
Found at i:42806 original size:15 final size:16
Alignment explanation
Indices: 42788--42821 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42778 ATTTGATTGA
*
42788 GAAAAA-TTATTTTAT
1 GAAAAATTTATTTCAT
42803 GAAAAATTTATTTCAT
1 GAAAAATTTATTTCAT
42819 GAA
1 GAA
42822 TGAAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (16 bp):
GAAAAATTTATTTCAT
Found at i:50663 original size:21 final size:21
Alignment explanation
Indices: 50624--50665 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
50614 CCATGTACTC
*
50624 ATCATTTCTATATCTATCTCT
1 ATCATTTCTATATCGATCTCT
50645 ATCATTTCTGA-ATCGATCTCT
1 ATCATTTCT-ATATCGATCTCT
50666 TTTTTGGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (21 bp):
ATCATTTCTATATCGATCTCT
Found at i:59975 original size:40 final size:41
Alignment explanation
Indices: 59917--59997 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
59907 TTTATAACTA
*
59917 GGGGCTAAACCTGAATTTAATTT-CTACCTTAATTATTAGG
1 GGGGCTAAACATGAATTTAATTTACTACCTTAATTATTAGG
* * * *
59957 GGGGCTAAATATGGATTTAATTTATTTCCTTAATTATTAGG
1 GGGGCTAAACATGAATTTAATTTACTACCTTAATTATTAGG
59998 AGGGTCAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 20 0.57
41 15 0.43
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (41 bp):
GGGGCTAAACATGAATTTAATTTACTACCTTAATTATTAGG
Found at i:61308 original size:107 final size:105
Alignment explanation
Indices: 61136--61397 Score: 411
Period size: 107 Copynumber: 2.5 Consensus size: 105
61126 AGTTTAGCCT
*
61136 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
*
61201 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA--TATTGTTATAGGGTTCTAGAAATAAAATACAAAAC
*
61243 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* *
61308 AATAATATTGTTATAGGGTTCTAGAAATAAAATATATAAC
66 AATAATATTGTTATAGGGTTCTAGAAATAAAATACAAAAC
* ** *
61348 TAA-TTCACTAAGTTTAG-TCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
61398 TAGAAAAATT
Statistics
Matches: 146, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
103 29 0.20
104 14 0.10
105 35 0.24
107 68 0.47
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGGTTCTAGAAATAAAATACAAAAC
Found at i:61598 original size:2 final size:2
Alignment explanation
Indices: 61591--61621 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
61581 TATTATGCTG
61591 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61622 TAACTCGTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74841 original size:19 final size:19
Alignment explanation
Indices: 74821--74857 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
74811 AATTAATTAT
74821 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
74839 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
74858 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:74868 original size:19 final size:19
Alignment explanation
Indices: 74827--74868 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
74817 TTATTTTAAT
* * *
74827 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
74846 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
74865 ATTA
1 ATTA
74869 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:76464 original size:37 final size:37
Alignment explanation
Indices: 76414--76488 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
76404 CGTTAATAAT
76414 CTTCTTTATTTGAGACACTGACATAAATTGGGAAGGC
1 CTTCTTTATTTGAGACACTGACATAAATTGGGAAGGC
76451 CTTCTTTATTTGAGACACTGACATAAATTGGGAAGGC
1 CTTCTTTATTTGAGACACTGACATAAATTGGGAAGGC
76488 C
1 C
76489 ATAAATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (37 bp):
CTTCTTTATTTGAGACACTGACATAAATTGGGAAGGC
Found at i:77601 original size:19 final size:20
Alignment explanation
Indices: 77572--77677 Score: 85
Period size: 19 Copynumber: 5.3 Consensus size: 20
77562 TGCATGTAAA
77572 CCAATTAACACCTGGCTTAG
1 CCAATTAACACCTGGCTTAG
** *
77592 CTTA-TAACACTTGG-TTGAG
1 CCAATTAACACCTGGCTT-AG
*
77611 CCCAATTAACACCTAGCTTAG
1 -CCAATTAACACCTGGCTTAG
** * *
77632 CTTA-TAACACTTGGCTGAG
1 CCAATTAACACCTGGCTTAG
77651 CCCAATTAACACCTGGCTTAG
1 -CCAATTAACACCTGGCTTAG
77672 -CAATTA
1 CCAATTA
77678 TAAGAGCTGG
Statistics
Matches: 64, Mismatches: 16, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
18 2 0.03
19 29 0.45
20 8 0.12
21 23 0.36
22 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
CCAATTAACACCTGGCTTAG
Found at i:77622 original size:21 final size:21
Alignment explanation
Indices: 77596--77662 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
77586 GCTTAGCTTA
77596 TAACACTTGGTTGAGCCCAAT
1 TAACACTTGGTTGAGCCCAAT
* * **
77617 TAACACCTAGCTT-AG-CTTA-
1 TAACA-CTTGGTTGAGCCCAAT
*
77636 TAACACTTGGCTGAGCCCAAT
1 TAACACTTGGTTGAGCCCAAT
77657 TAACAC
1 TAACAC
77663 CTGGCTTAGC
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
18 4 0.12
19 7 0.21
20 4 0.12
21 13 0.39
22 5 0.15
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (21 bp):
TAACACTTGGTTGAGCCCAAT
Found at i:77630 original size:40 final size:40
Alignment explanation
Indices: 77572--77672 Score: 184
Period size: 40 Copynumber: 2.5 Consensus size: 40
77562 TGCATGTAAA
*
77572 CCAATTAACACCTGGCTTAGCTTATAACACTTGGTTGAGC
1 CCAATTAACACCTGGCTTAGCTTATAACACTTGGCTGAGC
*
77612 CCAATTAACACCTAGCTTAGCTTATAACACTTGGCTGAGC
1 CCAATTAACACCTGGCTTAGCTTATAACACTTGGCTGAGC
77652 CCAATTAACACCTGGCTTAGC
1 CCAATTAACACCTGGCTTAGC
77673 AATTATAAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (40 bp):
CCAATTAACACCTGGCTTAGCTTATAACACTTGGCTGAGC
Found at i:85283 original size:18 final size:18
Alignment explanation
Indices: 85260--85294 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
85250 ACAAAAATTG
85260 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
85278 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
85295 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:85443 original size:16 final size:16
Alignment explanation
Indices: 85422--85453 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
85412 TTTATAATCT
85422 TTATTAATAATATATA
1 TTATTAATAATATATA
*
85438 TTATTATTAATATATA
1 TTATTAATAATATATA
85454 AATAATTATA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:85446 original size:19 final size:19
Alignment explanation
Indices: 85422--85469 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
85412 TTTATAATCT
* *
85422 TTATTAATAATATATATTA
1 TTATTAATAATATAAATAA
85441 TTATTAAT-ATATAAATAA
1 TTATTAATAATATAAATAA
85459 TTATATAATAA
1 TTAT-TAATAA
85470 ATGAACGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATAAATAA
Found at i:85534 original size:35 final size:35
Alignment explanation
Indices: 85495--85569 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
85485 TTATATAAAC
*
85495 GAACACTTAAATGAACAATAAACGAGGCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
85530 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
85565 GAACA
1 GAACA
85570 TAAACAAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:86785 original size:111 final size:111
Alignment explanation
Indices: 86600--87351 Score: 760
Period size: 111 Copynumber: 6.8 Consensus size: 111
86590 ATGAGTAACA
* * * * **
86600 GTTGTTACAAGCGCCTTACGTGTACATTCCATGTTGAATGATTTTGTCACGTGAATGTAAAATCC
1 GTTGTTACAAGCGCCTTACGTGTACATT-CATGTTTAATGATGTTGTCACGTGGACGTGGAATCC
* * *
86665 ATACACTTTTGTTTCACCCCA-AAAAGCGTATCCACGCGTAAGTAATG
65 ATACACTTTTGTTTTA-CCCAGAAAAGCATATACACGCGTAAGTAATG
* ** * * *
86712 GTTGTTACAA-TGCCTTACGTGTATGTTCCATGTTTAATGATGTTGTCACATGGACATGGAATTC
1 GTTGTTACAAGCGCCTTACGTGTACATT-CATGTTTAATGATGTTGTCACGTGGACGTGGAATCC
** * * *
86776 ATATGCTTTTGTTTTATTCCA-AAAAGTATATCCACGCGTAAGTAATG
65 ATACACTTTTGTTTTA-CCCAGAAAAGCATATACACGCGTAAGTAATG
* * * *
86823 GTTGTTACAAGCGCCTTACGTTTACATT-ATGCATT-ATGATGTTGTCACGTGAACGTTGAATCC
1 GTTGTTACAAGCGCCTTACGTGTACATTCATG-TTTAATGATGTTGTCACGTGGACGTGGAATCC
86886 ATACACTTTTGTTTTACCCAGAAAAGCATAATACACGCGTAAGTAATG
65 ATACACTTTTGTTTTACCCAGAAAAGCAT-ATACACGCGTAAGTAATG
* ** * * * *
86934 GTTGTTACAAGTGCCTTATTTTTACATT-TTGCATT-ATGATGTTGTCACGTGTACGTGGAATCC
1 GTTGTTACAAGCGCCTTACGTGTACATTCATG-TTTAATGATGTTGTCACGTGGACGTGGAATCC
86997 ATACACTTTTGTTTTACCCAGAAAAGCATATACACGCGTAAGTAATG
65 ATACACTTTTGTTTTACCCAGAAAAGCATATACACGCGTAAGTAATG
*
87044 GTTGTTACAAGCGCCTTACGCT-TACATTC-TGCATT-ATGATGTTGTCACGTGGACGTGGAATC
1 GTTGTTACAAGCGCCTTACG-TGTACATTCATG-TTTAATGATGTTGTCACGTGGACGTGGAATC
* * * *
87106 CATATACTTTTGTTTTACCCATAAAAGCATATACATGCGTAAGTGATG
64 CATACACTTTTGTTTTACCCAGAAAAGCATATACACGCGTAAGTAATG
* * * * * *
87154 GTTGTTACAA--GCCTTACGTGTACATTCACGTTTAATAATGTTGTCACATGAACGTTGAAT-TA
1 GTTGTTACAAGCGCCTTACGTGTACATTCATGTTTAATGATGTTGTCACGTGGACGTGGAATCCA
* * * * * *
87216 TACACTTCTGTTTTATCCA-ATAAAACGTATACACGTGTATGTAATG
66 TACACTTTTGTTTTACCCAGA-AAAGCATATACACGCGTAAGTAATG
* * * * * ** * *
87262 ATTATTACAAGCACCTTACGTGTGCAATCCACATTTAATGATGTTGTCACGTGGATGTGAAATCC
1 GTTGTTACAAGCGCCTTACGTGTAC-ATTCATGTTTAATGATGTTGTCACGTGGACGTGGAATCC
* * *
87327 GTACGCTTTTG-TTTAACCAGAAAAG
65 ATACACTTTTGTTTTACCCAGAAAAG
87352 AAATAATATG
Statistics
Matches: 543, Mismatches: 82, Indels: 31
0.83 0.12 0.05
Matches are distributed among these distances:
107 2 0.00
108 61 0.11
109 26 0.05
110 185 0.34
111 237 0.44
112 32 0.06
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (111 bp):
GTTGTTACAAGCGCCTTACGTGTACATTCATGTTTAATGATGTTGTCACGTGGACGTGGAATCCA
TACACTTTTGTTTTACCCAGAAAAGCATATACACGCGTAAGTAATG
Found at i:87008 original size:221 final size:220
Alignment explanation
Indices: 86600--87282 Score: 746
Period size: 221 Copynumber: 3.1 Consensus size: 220
86590 ATGAGTAACA
* * * *
86600 GTTGTTACAAGCGCCTTACGTGTACATTCCATG--TTGAATGATTTTGTCACGTGAATGTAAAAT
1 GTTGTTACAAGCGCCTTACGTTTACATT--ATGCATT--ATGATGTTGTCACGTGAACGTAGAAT
* * *
86663 CCATACACTTTTGTTTCACCCCAAAAAGCGTATCCACGCGTAAGTAATGGTTGTTACAA-TGCCT
62 CCATACACTTTTGTTTTA-CCCAAAAAGCATATACACGCGTAAGTAATGGTTGTTACAAGTGCCT
* * **
86727 TACGTGTATGTTCCATGTTTAATGATGTTGTCACATGGACATGGAATTCATATGCTTTTGTTTTA
126 TAC-TGTATGTTACATGTTTAATGATGTTGTCACATGGACATGGAATCCATACACTTTTGTTTTA
* * *
86792 TTCCA-AAAAGTATATCCACGCGTAAGTAATG
190 -CCCAGAAAAGCATATACACGCGTAAGTAATG
*
86823 GTTGTTACAAGCGCCTTACGTTTACATTATGCATTATGATGTTGTCACGTGAACGTTGAATCCAT
1 GTTGTTACAAGCGCCTTACGTTTACATTATGCATTATGATGTTGTCACGTGAACGTAGAATCCAT
86888 ACACTTTTGTTTTACCCAGAAAAGCATAATACACGCGTAAGTAATGGTTGTTACAAGTGCCTTA-
66 ACACTTTTGTTTTACCCA-AAAAGCAT-ATACACGCGTAAGTAATGGTTGTTACAAGTGCCTTAC
* * *
86952 T-T-T-TTACAT-TTTGCATTATGATGTTGTCACGTGTACGTGGAATCCATACACTTTTGTTTTA
129 TGTATGTTACATGTTT--A--ATGATGTTGTCACATGGACATGGAATCCATACACTTTTGTTTTA
87013 CCCAGAAAAGCATATACACGCGTAAGTAATG
190 CCCAGAAAAGCATATACACGCGTAAGTAATG
* * * *
87044 GTTGTTACAAGCGCCTTACGCTTACATTCTGCATTATGATGTTGTCACGTGGACGTGGAATCCAT
1 GTTGTTACAAGCGCCTTACGTTTACATTATGCATTATGATGTTGTCACGTGAACGTAGAATCCAT
* * *
87109 ATACTTTTGTTTTACCCATAAAAGCATATACATGCGTAAGTGATGGTTGTTACAA--GCCTTACG
66 ACACTTTTGTTTTACCCA-AAAAGCATATACACGCGTAAGTAATGGTTGTTACAAGTGCCTTAC-
** * * * * * * * *
87172 TGTACATT-CACGTTTAATAATGTTGTCACATGAACGTTGAAT-TATACACTTCTGTTTTATCCA
129 TGTATGTTACATGTTTAATGATGTTGTCACATGGACATGGAATCCATACACTTTTGTTTTACCCA
* * * *
87235 -ATAAAACGTATACACGTGTATGTAATG
194 GA-AAAGCATATACACGCGTAAGTAATG
* * *
87262 ATTATTACAAGCACCTTACGT
1 GTTGTTACAAGCGCCTTACGT
87283 GTGCAATCCA
Statistics
Matches: 400, Mismatches: 43, Indels: 39
0.83 0.09 0.08
Matches are distributed among these distances:
217 4 0.01
218 67 0.17
219 24 0.06
220 35 0.09
221 200 0.50
222 29 0.07
223 41 0.10
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (220 bp):
GTTGTTACAAGCGCCTTACGTTTACATTATGCATTATGATGTTGTCACGTGAACGTAGAATCCAT
ACACTTTTGTTTTACCCAAAAAGCATATACACGCGTAAGTAATGGTTGTTACAAGTGCCTTACTG
TATGTTACATGTTTAATGATGTTGTCACATGGACATGGAATCCATACACTTTTGTTTTACCCAGA
AAAGCATATACACGCGTAAGTAATG
Found at i:87904 original size:20 final size:20
Alignment explanation
Indices: 87879--87916 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
87869 ATAAATGAAT
*
87879 TTTTCAAAAATTATTATTTA
1 TTTTCAAAAATTAGTATTTA
*
87899 TTTTCAAATATTAGTATT
1 TTTTCAAAAATTAGTATT
87917 GAATTCGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTCAAAAATTAGTATTTA
Found at i:88901 original size:19 final size:19
Alignment explanation
Indices: 88854--88911 Score: 100
Period size: 19 Copynumber: 3.1 Consensus size: 19
88844 CCTAACTTTG
88854 AACATTTAACCAAAGATAT
1 AACATTTAACCAAAGATAT
*
88873 AA-AATTAACCAAAGATAT
1 AACATTTAACCAAAGATAT
88891 AACATTTAACCAAAGATAT
1 AACATTTAACCAAAGATAT
88910 AA
1 AA
88912 AATTAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 17 0.47
19 19 0.53
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (19 bp):
AACATTTAACCAAAGATAT
Found at i:88926 original size:19 final size:18
Alignment explanation
Indices: 88859--88917 Score: 100
Period size: 18 Copynumber: 3.2 Consensus size: 18
88849 CTTTGAACAT
88859 TTAACCAAAGATATAAAA
1 TTAACCAAAGATATAAAA
*
88877 TTAACCAAAGATATAACAT
1 TTAACCAAAGATATAA-AA
88896 TTAACCAAAGATATAAAA
1 TTAACCAAAGATATAAAA
88914 TTAA
1 TTAA
88918 TAAATAGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 21 0.55
19 17 0.45
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (18 bp):
TTAACCAAAGATATAAAA
Found at i:101570 original size:23 final size:23
Alignment explanation
Indices: 101543--101592 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
101533 AGGTAAAATT
*
101543 TTCT-CTATCTCCAATTTTGTTTC
1 TTCTCCTATCTCAAATTTT-TTTC
* *
101566 TTCTCCTCTCTCAAATTTTTTTT
1 TTCTCCTATCTCAAATTTTTTTC
101589 TTCT
1 TTCT
101593 GGAATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.12, C:0.26, G:0.02, T:0.60
Consensus pattern (23 bp):
TTCTCCTATCTCAAATTTTTTTC
Found at i:102595 original size:107 final size:108
Alignment explanation
Indices: 102471--102695 Score: 344
Period size: 107 Copynumber: 2.1 Consensus size: 108
102461 CTAAAAAGTA
* * *
102471 AAAACCCTATAACAATAAGTTATTAATTATGGAATTTATCCTTAAAATAAAAATAAAATTTTAAT
1 AAAACCCTATAACAATAAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAATTTTAAT
* *
102536 TTGGGGCTAAACTTAATGAAATTAG-TTTTGTATTTTATTTCT
66 TTGGGGCTAAACTTAATGAAATGAGTTTTTATATTTTATTTCT
* * *
102578 AAAACCTTATAATAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTTAAT
1 AAAACCCTATAACAATAAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAATTTTAAT
* *
102643 TTGGGGCTAAACTTAGTGAACTGAGTTTTTATATTTTATTTCT
66 TTGGGGCTAAACTTAATGAAATGAGTTTTTATATTTTATTTCT
*
102686 AAAACTCTAT
1 AAAACCCTAT
102696 TATAGAAAAC
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
107 81 0.77
108 24 0.23
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (108 bp):
AAAACCCTATAACAATAAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAATTTTAAT
TTGGGGCTAAACTTAATGAAATGAGTTTTTATATTTTATTTCT
Found at i:102774 original size:21 final size:21
Alignment explanation
Indices: 102750--102789 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
102740 TCAAATTAAT
* *
102750 AAAAAGAATGAAAAAAGAGGG
1 AAAAAAAAAGAAAAAAGAGGG
*
102771 AAAAAAAAAGACAAAAGAG
1 AAAAAAAAAGAAAAAAGAG
102790 AGGCGGGAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAGAAAAAAGAGGG
Found at i:105680 original size:5 final size:5
Alignment explanation
Indices: 105672--105716 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
105662 ACTTCCCTCC
* *
105672 CCTTT CCTTT CCTTT CCTTT CCTTT CCCTT CCTTC CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
105717 AATTACTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (5 bp):
CCTTT
Found at i:105823 original size:17 final size:17
Alignment explanation
Indices: 105801--105833 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
105791 AATTTTCACT
105801 ACCCGTTAAGAACCCGA
1 ACCCGTTAAGAACCCGA
105818 ACCCGTTAAGAACCCG
1 ACCCGTTAAGAACCCG
105834 TATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.36, G:0.18, T:0.12
Consensus pattern (17 bp):
ACCCGTTAAGAACCCGA
Found at i:106084 original size:2 final size:2
Alignment explanation
Indices: 106079--106132 Score: 85
Period size: 2 Copynumber: 27.5 Consensus size: 2
106069 TTTTTTTATC
106079 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
106119 AT CAT AT AT AT AT A
1 AT -AT AT AT AT AT A
106133 ATCGGGTTCG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:109386 original size:7 final size:6
Alignment explanation
Indices: 109374--109415 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
109364 TCCTCCCACC
*
109374 AAAATG AAAAATG AAAAAGG AAAAA- AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAA-G AAAAA-G AAAAAG AAAAAG AAAAAG AAAAA
109416 CAACCCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 5 0.16
6 15 0.47
7 12 0.38
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:109483 original size:45 final size:45
Alignment explanation
Indices: 109420--109513 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
109410 GAAAAACAAC
*
109420 CCATTTTTTTTTCTCTATAACCATTTGAATTTCAACATTTTCCA-
1 CCATTTTTTTTTCTCTATAACCATTTGAATTTCAACAATTTCCAT
109464 CCATTATTTTTTTCTCTATAACCATTTGAATTTCAACAATTTCCAT
1 CCATT-TTTTTTTCTCTATAACCATTTGAATTTCAACAATTTCCAT
109510 CCAT
1 CCAT
109514 CGAGATTTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 5 0.11
45 38 0.81
46 4 0.09
ACGTcount: A:0.27, C:0.23, G:0.02, T:0.48
Consensus pattern (45 bp):
CCATTTTTTTTTCTCTATAACCATTTGAATTTCAACAATTTCCAT
Found at i:109550 original size:43 final size:43
Alignment explanation
Indices: 109492--109621 Score: 235
Period size: 43 Copynumber: 3.0 Consensus size: 43
109482 TAACCATTTG
*
109492 AATTTCAACAATTTCCATCCATCGAGATTTCTCATAACCAACA
1 AATTTCAACATTTTCCATCCATCGAGATTTCTCATAACCAACA
109535 AATTTCAACATTTTCCATCCATCGAGATTTCTCATAACCAACA
1 AATTTCAACATTTTCCATCCATCGAGATTTCTCATAACCAACA
109578 AATTTCAACATTTTCCATCCATCGAGATTTCTCATCAA-CAACA
1 AATTTCAACATTTTCCATCCATCGAGATTTCTCAT-AACCAACA
109621 A
1 A
109622 CAACAACAAC
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
43 83 0.98
44 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.32
Consensus pattern (43 bp):
AATTTCAACATTTTCCATCCATCGAGATTTCTCATAACCAACA
Found at i:119981 original size:12 final size:11
Alignment explanation
Indices: 119966--120000 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
119956 AAAACCCACA
119966 ACAAACTTACC
1 ACAAACTTACC
119977 GACAAACTTACC
1 -ACAAACTTACC
119989 ATCAAACTTACC
1 A-CAAACTTACC
120001 CTTGGCAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 1 0.05
12 21 0.95
ACGTcount: A:0.43, C:0.34, G:0.03, T:0.20
Consensus pattern (11 bp):
ACAAACTTACC
Found at i:120274 original size:31 final size:31
Alignment explanation
Indices: 120171--120339 Score: 133
Period size: 31 Copynumber: 5.5 Consensus size: 31
120161 ACGGTATCCG
* * * *
120171 ACGTGGCATGCCACGTGTACCAAAAAGCGAA
1 ACGTAGCACGCCACGTGTACCAAAAAGTGAC
* * ** *
120202 ATGTGGCACGCCACGTGTATTAAAAAGCGAC
1 ACGTAGCACGCCACGTGTACCAAAAAGTGAC
* *
120233 ATGT-GACACGCCACGTGTACAAAAAAGTGAC
1 ACGTAG-CACGCCACGTGTACCAAAAAGTGAC
* * * *
120264 ACGTATCACGCTATGTGTACCCAAAAGTGAC
1 ACGTAGCACGCCACGTGTACCAAAAAGTGAC
* * **
120295 ACGTAGCATGCCATGTGTTTCAAAAAGTGAC
1 ACGTAGCACGCCACGTGTACCAAAAAGTGAC
* *
120326 ACGTGGCATGCCAC
1 ACGTAGCACGCCAC
120340 ATGCACAAAA
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
30 1 0.01
31 113 0.99
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (31 bp):
ACGTAGCACGCCACGTGTACCAAAAAGTGAC
Found at i:121494 original size:19 final size:20
Alignment explanation
Indices: 121470--121512 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
121460 ATACAAATCC
121470 TTTCGTTTTC-TTGTTTTTG
1 TTTCGTTTTCTTTGTTTTTG
121489 TTTCGTTTTCGTTTTGTTTTTG
1 TTTCGTTTTC--TTTGTTTTTG
121511 TT
1 TT
121513 GTGTTGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
22 11 0.52
ACGTcount: A:0.00, C:0.09, G:0.16, T:0.74
Consensus pattern (20 bp):
TTTCGTTTTCTTTGTTTTTG
Found at i:123756 original size:12 final size:13
Alignment explanation
Indices: 123739--123768 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
123729 AAGAGGTAAA
123739 AACTAC-AAAAAG
1 AACTACAAAAAAG
123751 AACTACAAAAAAG
1 AACTACAAAAAAG
123764 AACTA
1 AACTA
123769 TATTTACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.10
Consensus pattern (13 bp):
AACTACAAAAAAG
Found at i:125867 original size:14 final size:14
Alignment explanation
Indices: 125848--125876 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
125838 CTATCTGATT
125848 ACTAAAAGTCTAAA
1 ACTAAAAGTCTAAA
125862 ACTAAAAGTCTAAA
1 ACTAAAAGTCTAAA
125876 A
1 A
125877 TAAGACTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
ACTAAAAGTCTAAA
Found at i:132177 original size:4 final size:4
Alignment explanation
Indices: 132170--132218 Score: 57
Period size: 4 Copynumber: 12.5 Consensus size: 4
132160 AGTATATATA
* *
132170 TAAG TAAG TAAG TTAT TAAG T-A- TAAG TAAG TAAG TAAAG TAAG TAAG
1 TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG T-AAG TAAG TAAG
132217 TA
1 TA
132219 TAAGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 2 0.05
4 31 0.82
5 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (4 bp):
TAAG
Found at i:132217 original size:27 final size:26
Alignment explanation
Indices: 132170--132225 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
132160 AGTATATATA
* *
132170 TAAGTAAGTAAGTTATTAAGTATAAG
1 TAAGTAAGTAAGTAAGTAAGTATAAG
132196 TAAGTAAGTAAAGTAAGTAAGTATAAG
1 TAAGTAAGT-AAGTAAGTAAGTATAAG
132223 TAA
1 TAA
132226 TAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (26 bp):
TAAGTAAGTAAGTAAGTAAGTATAAG
Found at i:132233 original size:6 final size:6
Alignment explanation
Indices: 132224--132259 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
132214 AAGTATAAGT
132224 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
132260 GGTATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:137069 original size:2 final size:2
Alignment explanation
Indices: 137062--137125 Score: 66
Period size: 2 Copynumber: 33.0 Consensus size: 2
137052 ATTTGATTAT
137062 TA TA TA TA T- TA TA TA T- TA TGA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
137102 TA T- TA GTA CTA TA TA TA T- TA TA TA
1 TA TA TA -TA -TA TA TA TA TA TA TA TA
137126 GTACCAAAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
1 5 0.09
2 43 0.80
3 6 0.11
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:137100 original size:27 final size:27
Alignment explanation
Indices: 137055--137125 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 27
137045 GATCACAATT
137055 TGAT-TAT-TATATATATTATATATTA
1 TGATATATATATATATATTATATATTA
137080 TGATATATATATATATATTATATATTA
1 TGATATATATATATATATTATATATTA
137107 -GTACTATATATATTATATA
1 TG-A-TATATATA-TATATA
137126 GTACCAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
25 4 0.10
26 4 0.10
27 19 0.46
28 8 0.20
29 6 0.15
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (27 bp):
TGATATATATATATATATTATATATTA
Found at i:137114 original size:22 final size:19
Alignment explanation
Indices: 137057--137125 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 19
137047 TCACAATTTG
137057 ATTAT-TATATATATTATAT
1 ATTATATATATATA-TATAT
137076 ATTATGATATATATATATAT
1 ATTAT-ATATATATATATAT
137096 ATTATATATTAGTACTATATAT
1 ATTATATA-TA-TA-TATATAT
137118 ATTATATA
1 ATTATATA
137126 GTACCAAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.18
20 12 0.27
21 10 0.22
22 15 0.33
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (19 bp):
ATTATATATATATATATAT
Found at i:143211 original size:157 final size:155
Alignment explanation
Indices: 142934--143390 Score: 538
Period size: 157 Copynumber: 3.0 Consensus size: 155
142924 ACGTTAAGCG
* * * * *
142934 CGTGACCAGCAAACGCAAAGAGGATAAACGACAAAGTTTTTGTCTATTCCAAGTGGAAAT---TG
1 CGTGACCAGCAAATGCAAAGAGGATAAACGACAAAGATTTTGTCTATTACAAGAGGAAATCGATA
* * *
142996 ACAATTATTGCATCTTTTATCAGAACAAATCATTTTAACGGCTTCTAACTATGCCACCATGCATT
66 ACAA-TATTGCATCTTTTAT-AGAACAATTCATTTTAACGGTTTCTAACTATACCACCATGCATT
143061 CAAAACAGAGAATCTAAAACAAACGCA
129 CAAAACAGAGAATCTAAAACAAACGCA
*
143088 CGTGACCAGCAAATGCAAAGAGGATAAACGACAAAGATTTTGTCTATTACATGAGGAAATCGATA
1 CGTGACCAGCAAATGCAAAGAGGATAAACGACAAAGATTTTGTCTATTACAAGAGGAAATCGATA
** * * *
143153 ACAATCATTGCATCTTTTATAAGAACGGTTCATTTTAACGGTTTCTAAGTATATCACCATGCATC
66 ACAAT-ATTGCATCTTTTAT-AGAACAATTCATTTTAACGGTTTCTAACTATACCACCATGCATT
* * *
143218 CCAAACAGAGAATCTAAAACAAACACG
129 CAAAACAGAGAATCTAAAACAAACGCA
* * * * * **
143245 CGTCACCAGCGAATACAAAGAGGATTAATGACAAAGA-TTTGTCTATTTTAAGAGGAAATCGATA
1 CGTGACCAGCAAATGCAAAGAGGATAAACGACAAAGATTTTGTCTATTACAAGAGGAAATCGATA
* * * * *
143309 AAAATATTGC--C---TAT-TAACTATTCATTTTAATGGTTCCTAACTATACCACCATGCATTCA
66 ACAATATTGCATCTTTTATAGAACAATTCATTTTAACGGTTTCTAACTATACCACCATGCATTCA
*
143368 AAACAAAGAATCTAAAACAAACG
131 AAACAGAGAATCTAAAACAAACG
143391 ACAAAATCCG
Statistics
Matches: 261, Mismatches: 38, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
148 57 0.22
150 3 0.01
153 1 0.00
154 55 0.21
155 5 0.02
156 29 0.11
157 111 0.43
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (155 bp):
CGTGACCAGCAAATGCAAAGAGGATAAACGACAAAGATTTTGTCTATTACAAGAGGAAATCGATA
ACAATATTGCATCTTTTATAGAACAATTCATTTTAACGGTTTCTAACTATACCACCATGCATTCA
AAACAGAGAATCTAAAACAAACGCA
Found at i:154404 original size:13 final size:13
Alignment explanation
Indices: 154386--154410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
154376 CATACGCAAC
154386 TGTCCATGTTGAG
1 TGTCCATGTTGAG
154399 TGTCCATGTTGA
1 TGTCCATGTTGA
154411 TAGACTCACC
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:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (13 bp):
TGTCCATGTTGAG
Found at i:158472 original size:42 final size:42
Alignment explanation
Indices: 158415--158503 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
158405 AGATGATTTT
158415 ATATTGTTATCTGAGACGCTAAATCATCTAATTAAATGATGA
1 ATATTGTTATCTGAGACGCTAAATCATCTAATTAAATGATGA
*
158457 ATATTGTTATTTGAGACGCTAAATCATCTAATTAAATGATGA
1 ATATTGTTATCTGAGACGCTAAATCATCTAATTAAATGATGA
158499 ATATT
1 ATATT
158504 CTTGATGCTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (42 bp):
ATATTGTTATCTGAGACGCTAAATCATCTAATTAAATGATGA
Found at i:164827 original size:18 final size:18
Alignment explanation
Indices: 164806--164842 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
164796 TTCTCGTTAT
164806 TTAGTAATAGCCTTTTAG
1 TTAGTAATAGCCTTTTAG
164824 TTAGTAATAGCCTTTTAG
1 TTAGTAATAGCCTTTTAG
164842 T
1 T
164843 ATCATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (18 bp):
TTAGTAATAGCCTTTTAG
Found at i:164881 original size:24 final size:24
Alignment explanation
Indices: 164849--164898 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
164839 TAGTATCATA
164849 TATATTGAGTGGTCTAGCTATAAG
1 TATATTGAGTGGTCTAGCTATAAG
164873 TATATTGAGTGGTCTAGCTATAAG
1 TATATTGAGTGGTCTAGCTATAAG
164897 TA
1 TA
164899 CATAAGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.38
Consensus pattern (24 bp):
TATATTGAGTGGTCTAGCTATAAG
Found at i:169030 original size:29 final size:29
Alignment explanation
Indices: 168965--169036 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
168955 AAAGTTCATA
*
168965 GGCAAATTGTCCTGGATTTGGAGATTCAGG
1 GGCAAATTGTCC-GGATTTGAAGATTCAGG
168995 GGACAAATTGT-CGCGATTTGAAG-TTCAGG
1 GG-CAAATTGTCCG-GATTTGAAGATTCAGG
*
169024 GAGCAAAATGTCC
1 G-GCAAATTGTCC
169037 TTGTTATAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
29 15 0.42
30 13 0.36
31 8 0.22
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (29 bp):
GGCAAATTGTCCGGATTTGAAGATTCAGG
Found at i:176674 original size:2 final size:2
Alignment explanation
Indices: 176629--176657 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
176619 AGTTTTAATC
176629 AT AT 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 AT AT A
176658 GTTTGGTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:177449 original size:16 final size:14
Alignment explanation
Indices: 177428--177479 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 14
177418 CAATTCAAAG
177428 TTTATAAGTATTATTT
1 TTTATAA-TATT-TTT
*
177444 TTTATATTTATTTTT
1 TTTATA-ATATTTTT
177459 CTTTAT-ATATTTTT
1 -TTTATAATATTTTT
177473 TTTATAA
1 TTTATAA
177480 ACAGTGGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 5 0.16
14 8 0.26
15 3 0.10
16 15 0.48
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTATAATATTTTT
Found at i:177476 original size:13 final size:13
Alignment explanation
Indices: 177439--177478 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
177429 TTATAAGTAT
* *
177439 TATTTTTTATATT
1 TATTTTTTTTATA
177452 TATTTTTCTTTATA
1 TATTTTT-TTTATA
177466 TATTTTTTTTATA
1 TATTTTTTTTATA
177479 AACAGTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (13 bp):
TATTTTTTTTATA
Found at i:177547 original size:2 final size:2
Alignment explanation
Indices: 177540--177575 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
177530 ACAGCGGGAG
177540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
177576 CTAAATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:178179 original size:20 final size:21
Alignment explanation
Indices: 178143--178184 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
178133 ACAAGCTACG
178143 ATTTTATCAACAAAAAA-TGA
1 ATTTTATCAACAAAAAACTGA
*
178163 ATTTTA-CAACTATAAAACTGA
1 ATTTTATCAAC-AAAAAACTGA
178184 A
1 A
178185 CCACCATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 11 0.58
21 4 0.21
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (21 bp):
ATTTTATCAACAAAAAACTGA
Found at i:195300 original size:2 final size:2
Alignment explanation
Indices: 195293--195325 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
195283 CTTGGGACTT
195293 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
195326 AATCTAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:195597 original size:39 final size:40
Alignment explanation
Indices: 195541--195621 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
195531 TTTAATTCCT
195541 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
195581 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
195620 AT
1 AT
195622 TCTTAGGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:196057 original size:201 final size:202
Alignment explanation
Indices: 195721--196107 Score: 695
Period size: 201 Copynumber: 1.9 Consensus size: 202
195711 CAGATATTTA
195721 ATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAA
1 ATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAA
* **
195786 TGTTCAACTAAGTTTTTTTTGGTATAGTTCTATATATAATAGTAATGTGTTCTATCTTATTCACT
66 TGTTCAACTAAG-TTTTTTTGGTATAATTCTATATATAATAAAAATGTGTTCTATCTTATTCACT
195851 ACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGA
130 ACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGA
195916 TCTTTAAT
195 TCTTTAAT
*
195924 ATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAATTCAACCACTAA
1 ATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAA
* *
195989 TGTTCAACTAA-TTTTTTTGGTATAATTTTATATATAATAAAAATGTGTTGTATCTTATTCACTA
66 TGTTCAACTAAGTTTTTTTGGTATAATTCTATATATAATAAAAATGTGTTCTATCTTATTCACTA
*
196053 CAACTTTGTTAGTAATGTTAGACTTAAAAAATTAATAACATTCACCATTGATAAA
131 CAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAA
196108 GTTATTAAGC
Statistics
Matches: 177, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
201 102 0.58
203 75 0.42
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (202 bp):
ATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAA
TGTTCAACTAAGTTTTTTTGGTATAATTCTATATATAATAAAAATGTGTTCTATCTTATTCACTA
CAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGAT
CTTTAAT
Found at i:196620 original size:72 final size:72
Alignment explanation
Indices: 196503--196642 Score: 262
Period size: 72 Copynumber: 1.9 Consensus size: 72
196493 ACTAGGAACC
*
196503 AATTTTGTAGACCTAATTTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTAAAACCTT
1 AATTTTGTACACCTAATTTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTAAAACCTT
196568 ATAACTA
66 ATAACTA
*
196575 AATTTTGTACACCTAATTTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTATAACCTT
1 AATTTTGTACACCTAATTTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTAAAACCTT
196640 ATA
66 ATA
196643 TGGAAATTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (72 bp):
AATTTTGTACACCTAATTTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTAAAACCTT
ATAACTA
Found at i:196743 original size:36 final size:36
Alignment explanation
Indices: 196696--196765 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
196686 GAGATTTTGG
*
196696 AGAAATATGATAATCAAAATAACAAAAAG-TGTAATA
1 AGAAATATGATAACCAAAATAA-AAAAAGATGTAATA
196732 AGAAATATGATAACCAAAATAAAAAAAGATGTAA
1 AGAAATATGATAACCAAAATAAAAAAAGATGTAA
196766 GGTTATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 6 0.19
36 26 0.81
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.20
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATAAAAAAAGATGTAATA
Found at i:202763 original size:21 final size:22
Alignment explanation
Indices: 202737--202781 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
202727 TATATCTGAA
202737 TTGCTAAACACCGC-CCCCTTT
1 TTGCTAAACACCGCTCCCCTTT
***
202758 TTGCTAGTTACCGCTCCCCTTT
1 TTGCTAAACACCGCTCCCCTTT
202780 TT
1 TT
202782 ACACTTTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.13, C:0.38, G:0.11, T:0.38
Consensus pattern (22 bp):
TTGCTAAACACCGCTCCCCTTT
Found at i:209643 original size:23 final size:23
Alignment explanation
Indices: 209617--209660 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
209607 TTTTCTTGTT
* *
209617 TTTTTATTTTTGTTTCGTTTTCG
1 TTTTCATTTTCGTTTCGTTTTCG
*
209640 TTTTCATTTTCGTTTTGTTTT
1 TTTTCATTTTCGTTTCGTTTT
209661 TGTTGTATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.05, C:0.09, G:0.11, T:0.75
Consensus pattern (23 bp):
TTTTCATTTTCGTTTCGTTTTCG
Found at i:210954 original size:16 final size:17
Alignment explanation
Indices: 210926--210958 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
210916 AGTTCCGTCC
210926 TTGTTTCCTTTTTTTTT
1 TTGTTTCCTTTTTTTTT
210943 TTGTTT-CTTTTTTTTT
1 TTGTTTCCTTTTTTTTT
210959 ATCCCATCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (17 bp):
TTGTTTCCTTTTTTTTT
Found at i:211215 original size:30 final size:30
Alignment explanation
Indices: 211179--211235 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
211169 GGAATGAATC
211179 CTTGTCTGATGTCTCAATTTTATTTTATTT
1 CTTGTCTGATGTCTCAATTTTATTTTATTT
*
211209 CTTGTCTGATGTCTCGATTTTATTTTA
1 CTTGTCTGATGTCTCAATTTTATTTTA
211236 ATCTTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (30 bp):
CTTGTCTGATGTCTCAATTTTATTTTATTT
Found at i:214484 original size:28 final size:28
Alignment explanation
Indices: 214440--214519 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
214430 TGTACAATAT
214440 ATAACATTTG-AAATTCTAACATGTCAA
1 ATAACATTTGAAAATTCTAACATGTCAA
* * * *
214467 TTTATATTTTAAAATTCTAACATGTCAA
1 ATAACATTTGAAAATTCTAACATGTCAA
*
214495 ATAACATTTGACAATTCTAACATGT
1 ATAACATTTGAAAATTCTAACATGT
214520 ACAAGATGGC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 6 0.14
28 37 0.86
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (28 bp):
ATAACATTTGAAAATTCTAACATGTCAA
Found at i:215581 original size:18 final size:18
Alignment explanation
Indices: 215558--215592 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
215548 CTCCAGCATA
215558 TCATCACCACCGACAAAG
1 TCATCACCACCGACAAAG
*
215576 TCATCACCTCCGACAAA
1 TCATCACCACCGACAAA
215593 ATCAGATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.40, G:0.09, T:0.14
Consensus pattern (18 bp):
TCATCACCACCGACAAAG
Found at i:217678 original size:10 final size:10
Alignment explanation
Indices: 217665--217689 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
217655 CGTTCTTGAA
217665 GATTTCAGAG
1 GATTTCAGAG
217675 GATTTCAGAG
1 GATTTCAGAG
217685 GATTT
1 GATTT
217690 AAAATGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (10 bp):
GATTTCAGAG
Found at i:226498 original size:4 final size:4
Alignment explanation
Indices: 226489--226516 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
226479 TACCCAGAAG
226489 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
226517 GCTACCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:253982 original size:331 final size:332
Alignment explanation
Indices: 253262--254887 Score: 1426
Period size: 331 Copynumber: 4.9 Consensus size: 332
253252 TCTAAGTAAC
** *
253262 ATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGTTTC-ATTTTAATTAGAAATTAAT
1 ATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATTAAT
* * * * *
253326 TTAGAAAAAATAAGAAATACGATATTAAAAGTGTGAAAAGCCCTCCAA---------T-TTGAAT
65 TCAGAAAAAA-ATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAAT
** *
253381 TATATA-TTTTTAAAAGTATTTTAGCCAAAAATTGAGCAGAA-ATCTTTCGTGTCAATTTTTGCA
129 TATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AATATCTTTCGTGTCAATTTTTGCA
* * * * * * *
253444 CAATTTTAGCCGAAATCGTGTACTAACTAACCATCACGGTTTTTGGC-TGAAAATGCATTTCGGG
193 AAATTTTAGCCAAAATCGTG---TAA-TAACCATCACAGTTTTAGGCTTAAAAACGCGTTTCGGG
* * * * * * ** *
253508 GCCCTGGCTCAATTTAGCATAATTTTTGGTGCTGAGACTCCTTGAAATATATATATATTCATCTA
254 GCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG-AA-ATATCTATATTCATCTA
* *
253573 ATAAAATGTTAGCCGC
317 ATAAAATGTCAGCCGA
* * * *
253589 ATTGCATTTAAGGATTTATTTTTACGAACATCTAAATCTTGTTTCGATTTAATTAGAAATTAAAT
1 ATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
** *
253654 CAGAAAAAAATGAAAAACGATATTAAAAGCGTGAAAAGCATTTCAATCTTTTTGTTGTTGAATTA
66 CAGAAAAAAATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTA
* ** * * *
253719 TATATTTTTTATGACTATTTTAGTTAAAAATTGAGGAAATATCTTTCGAGTCACTTTTTACAAAA
131 TATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGTGTCAATTTTTGCAAAA
* * * * *
253784 TTTTAGTCAAAATCGTGTAATAACCATCACAACTTTT-GGCTTACAAA-GCGTTGCAGGGCCCCG
196 TTTTAGCCAAAATCGTGTAATAACCATCAC-AGTTTTAGGCTTAAAAACGCGTTTCGGGGCCCCG
* * * * * **
253847 ACTCAGTTTTGCATGATTTTTGGCCCCAAGCCTCCTTGAGATATCCATATTCATCTAATCAAACC
260 ACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATAAAATG
253912 TCAGCC-A
325 TCAGCCGA
** * * *
253919 AGTTGGATTTAAAAATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTGAATTAAAAATTAAT
1 A-TTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT
* * * * ** * * *
253984 TTAGAAAAAAATAAGAAAAAAGAAATTAAAAGCGTTAAAATTCCTCCAATCTTTTTGGCGTTAAA
65 TCAGAAAAAAAT--GAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAA
* * * * * * *
254049 TTATATATATATAATGAGTATTTTATCCAAAAATTGAGGAAATTTTTTTTGTGTC-ATCTTTTGC
128 TTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGTGTCAAT-TTTTGC
* ** * *
254113 AAAATTTTAGCCAAAATCGTGTACTAACCATCATGGTTTTCGG-ATAAAAACGCGTTTC-GGGCC
192 AAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTAGGCTTAAAAACGCGTTTCGGGGCC
* * *
254176 CCGACTTAGTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAA
257 CCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATAAA
* *
254241 ATGTTAGCCGC
322 ATGTCAGCCGA
* * * *
254252 ATTGCATTTAAGGATTTATTTTTACGAGAATCTGAATCTTGTTTCGATTTATTTAGATATTAATT
1 ATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
* * * *
254317 CAGAAAAAATATGAAAAACGATATTAAAATCGAGAAAAGCCCTTCAATCTTTTTGGCGTTGAATC
66 CAGAAAAAA-ATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAATT
* * * *
254382 ATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAA
130 ATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGTGTCAATTTTTGCAAA
* ** * * ** ** * *
254447 ATTTTA-TC--TTTCGGGTCATTTTCCATCACAGTTTTAAAC-TAAAAAAGCGTTCCGGGGCCCC
195 ATTTTAGCCAAAATCGTGT-AATAACCATCACAGTTTTAGGCTTAAAAACGCGTTTCGGGGCCCC
*** * * *
254508 GACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTTGAAATATTTATATTTATCTAACT-AAA
259 GACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAA-TAAAA
254572 TGTCAGCC-A
323 TGTCAGCCGA
* * * * *
254581 CATTGGATTTAAGGATTTGA-TTTTATGACCATCTGAATCATGTTTCGATTTTATTTGAAATTAA
1 -ATTGGATTTAAGGATTT-ATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * * *
254645 TTCAGAAAAAATTGGAAAAACGATATTAGAAGCCTTAAGAGCCCTTCAATCTTTTT-GTCTTTG-
64 TTCAGAAAAAAAT-GAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGT-GTTGA
* * * * **
254708 A--AT-TA-----TATGAGAATTTTGGCCAAAAAGTGAGGAAAAAT-TTTCCGAATCAATTTTTG
127 ATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTT-CGTGTCAATTTTTG
* * ** **** * * * *
254764 CAAAATTTTAGTCGAAATCGTGTGCTTTTAATCACGGTTTTAAGC-TAAAAACACGTTTCGAGGC
191 CAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTAGGCTTAAAAACGCGTTTCGGGGC
* * * *
254828 CCC-AGCTCAATTTTGCATGATTTTTGGCACGAAGACTCAC-TCAAATATCTATATTCATCT
256 CCCGA-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTC-CTTGAAATATCTATATTCATCT
254888 GACCAAATTT
Statistics
Matches: 1057, Mismatches: 204, Indels: 80
0.79 0.15 0.06
Matches are distributed among these distances:
320 3 0.00
321 50 0.05
322 3 0.00
323 81 0.08
324 6 0.01
326 33 0.03
327 66 0.06
328 6 0.01
329 28 0.03
330 171 0.16
331 192 0.18
332 145 0.14
333 185 0.18
334 11 0.01
335 1 0.00
336 14 0.01
337 62 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (332 bp):
ATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
CAGAAAAAAATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTA
TATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGTGTCAATTTTTGCAAAA
TTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTAGGCTTAAAAACGCGTTTCGGGGCCCCGA
CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATAAAATGT
CAGCCGA
Found at i:255375 original size:531 final size:522
Alignment explanation
Indices: 254466--255426 Score: 1302
Period size: 531 Copynumber: 1.8 Consensus size: 522
254456 TTCGGGTCAT
* *
254466 TTTCCATCACAGTTTTAAACTAAAAAAGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTG
1 TTTCCATCACAGCTTTAAACTAAAAAAGCGTTCCGGGACCCCGACTCAGTTTTGCATGATTTTTG
* * * * *
254531 GCAAGAAGACTTCTTGAAATATTTATATTTATCTAACTAAATGTCAGCCACATTGGATTTAAGGA
66 GCAAGAAGAATCCTTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGA
* * * **
254596 TTTGATTTTATGACCATCTGAATCATGTTTCGATTTTATTTGAAATTAATTCAGAAAAAATTGGA
131 TTTGATTTTACGACCATCTGAATAATGTTTCGATTTAATTCAAAATTAATTCAGAAAAAATTGGA
* * * * * *
254661 AAAACGATATTAGAAGCCTTAAGAGCCCTTCAATCTTTTTGTCTTTGAATTATATGAGAATTTTG
196 AAAACGATATTAAAAGCCTGAAAAACCCTTCAAGCTTTTTGTCTTTGAATTATATGAGAATTGTG
* ** *
254726 GCCAAAAAGTGAGGAAAAATTTTCCGAATCAATTTTTGCAAAATTTTAGTCGAAATCGTGTGCTT
261 GCCAAAAAGTGAGGAAAAATTTTCCGAATCAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTA
* * *
254791 TTAATCACGGTTTTAAGCTAAAAACACGTTTCGAGGCCCCAGCTCAATTTTGCATGATTTTTGGC
326 TCAATCACGATTTTAAGCTAAAAACACATTTCGAGGCCCCAGCTCAATTTTGCATGATTTTTGGC
254856 ACGAAGACTCAC-TCAAATATCTATATTCATCTGACCAAATTTTTTTGGCAACGAATTATATATT
391 ACGAAGACTC-CTTCAAATATCTATATTCATCTGACCAAATTTTTTTGGCAACGAATTATATATT
254920 TTTTTATGAGAGTTGTGCCAAAAATTTTCCGGATCAATTTTTCTAAAATGTTAGCCGAAATCGTA
455 TTTTTATGAGAGTTGTGCCAAAAATTTTCCGGATCAATTTTTCTAAAATGTTAGCCGAAATCGTA
254985 TAC
520 TAC
* * ** *
254988 TTTCCATCA-AGACTTTAAGCTAAAAACGCGTTTTGGGACTCCGACTCAGTTTTGCAT-ATTTTT
1 TTTCCATCACAG-CTTTAAACTAAAAAAGCGTTCCGGGACCCCGACTCAGTTTTGCATGATTTTT
* * *
255051 TGCACGAAGAATCCTTGAAATATTTATATTCATCTGACCAAATCTCAGCCACATTGGATTTAAGG
65 GGCAAGAAGAATCCTTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGG
* * * * *
255116 -TTTGTTTTTACGAGCATTTGTATAATGTTTCTATTTAATTCAAAATTAATTCAGGAAAAAATTG
130 ATTTGATTTTACGACCATCTGAATAATGTTTCGATTTAATTCAAAATTAATTCA-GAAAAAATTG
* * * *
255180 GAAAAATGATTTTAAAAGTCTGAAAAACCCTTCAAGCTTTTTCTTCTTTGAATTATATATTGACT
194 GAAAAACGATATTAAAAGCCTGAAAAACCCTTCAAGCTTTTT-GTCTTTG------A-ATT-A-T
* *
255245 ATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGA
249 ATGAGAATTGTGGCCAAAAAGTGAGGAAAAATTTTCCGAATCAATTTTTGCAAAATTTTAGCCGA
* * *
255310 AATCGTGCACTATCCATCACGATTTTAAGCTAAAAACGCATTTCGAGGCCCC-GACTCAGTTTTG
314 AATCGTGCACTATCAATCACGATTTTAAGCTAAAAACACATTTCGAGGCCCCAG-CTCAATTTTG
* * * *
255374 CATGATTTTTGGCACGCAGACTCCTTGAACTATCTATATTCATCTGACTAAAT
378 CATGATTTTTGGCACGAAGACTCCTTCAAATATCTATATTCATCTGACCAAAT
255427 CTCAGCCACT
Statistics
Matches: 374, Mismatches: 51, Indels: 19
0.84 0.11 0.04
Matches are distributed among these distances:
520 43 0.11
521 109 0.29
522 53 0.14
528 1 0.00
529 3 0.01
530 3 0.01
531 162 0.43
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (522 bp):
TTTCCATCACAGCTTTAAACTAAAAAAGCGTTCCGGGACCCCGACTCAGTTTTGCATGATTTTTG
GCAAGAAGAATCCTTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGA
TTTGATTTTACGACCATCTGAATAATGTTTCGATTTAATTCAAAATTAATTCAGAAAAAATTGGA
AAAACGATATTAAAAGCCTGAAAAACCCTTCAAGCTTTTTGTCTTTGAATTATATGAGAATTGTG
GCCAAAAAGTGAGGAAAAATTTTCCGAATCAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTA
TCAATCACGATTTTAAGCTAAAAACACATTTCGAGGCCCCAGCTCAATTTTGCATGATTTTTGGC
ACGAAGACTCCTTCAAATATCTATATTCATCTGACCAAATTTTTTTGGCAACGAATTATATATTT
TTTTATGAGAGTTGTGCCAAAAATTTTCCGGATCAATTTTTCTAAAATGTTAGCCGAAATCGTAT
AC
Found at i:255985 original size:334 final size:332
Alignment explanation
Indices: 254939--256040 Score: 1604
Period size: 334 Copynumber: 3.3 Consensus size: 332
254929 GAGTTGTGCC
* ** * * *
254939 AAAAATTTTCCGGATCAATTTTT-CTAAAATGTTAGCCGAAATCGTATACTTTCCATCAAGACTT
1 AAAAATTTTCCGGATCAATTTTTGC-AAAATTTTAGCCGAAATCGTGCACTATCCATCACGATTT
* *
255003 TAAGCTAAAAACGCGTTTTG-GGACTCCGACTCAGTTTTGCAT-ATTTTTTGCACGAAGA-ATCC
65 TAAGCTAAAAACGCGTTTCGAGG-CCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACA-CC
* * * *
255065 TTGAAATATTTATATTCATCTGACCAAATCTCAGCCACATTGGATTTAAGG-TTTGTTTTTACGA
128 TTGAACTATCTATATTCATCTGACTAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGA
* * *
255129 GCATTTGTATAATGTTTCTATTTAATTCAAAATTAATTCAGGAA-AAAATTGGAAAAATGATTTT
193 GCATTTGTATCATGTTTCTATTTAATTCAAAATTAATT-A-GAATAAAATTGGAAAAACGATATT
*
255193 AAAAGTCTGAAAAACCCTTCAAGCTTTTTCTTCTTTGAATTATATATTGACTATGAGAATTGTGG
256 AAAAGTCTGAAAAACCCTTCAAGCTTTTT-TTCTTTGAATTATATATTGTCTATGAGAATTGTGG
255258 CCAAAAATTGAGG
320 CCAAAAATTGAGG
255271 AAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTATCCATCACGATTTT
1 AAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTATCCATCACGATTTT
* * * *
255336 AAGCTAAAAACGCATTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCACGCAGACTCCTTG
66 AAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACACCTTG
255401 AACTATCTATATTCATCTGACTAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCA
131 AACTATCTATATTCATCTGACTAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCA
* *
255466 TCTGTATCATGTTTCTATTTAATTCAAAATTAA-T----T----CTGGAAAAACGATATTAAAAG
196 TTTGTATCATGTTTCTATTTAATTCAAAATTAATTAGAATAAAATTGGAAAAACGATATTAAAAG
* * * *
255522 CCTGAAAAACCCTTCAAGCTTTTTTTATTTGAATTATATAGTGTCTATGAGAATTATGGCCAAAA
261 TCTGAAAAACCCTTCAAGCTTTTTTTCTTTGAATTATATATTGTCTATGAGAATTGTGGCCAAAA
255587 ATTGAGG
326 ATTGAGG
** *
255594 AAAAATTTTCTAGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTGTCCATCACGATTTT
1 AAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTATCCATCACGATTTT
255659 AAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTTTGCACGAAGACACCTT
66 AAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTTTGCATGA-TTTTTTGCACGAAGACACCTT
*
255724 GAACTATCTATATTCATCTGACTAAATCTCAGCCACTTTGGATTTAAGGATTTATTTTTACGAGC
130 GAACTATCTATATTCATCTGACTAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGC
*
255789 ATTTGTATCATGTTTCTACTTAATTCAAAATTAATTAAGAATAAAATTGGAAAAACGATATTAAA
195 ATTTGTATCATGTTTCTATTTAATTCAAAATTAATT-AGAATAAAATTGGAAAAACGATATTAAA
* * * * * * *
255854 AGTCTGAAAAACCTTTCAAGCCTTTTGTCTTTGAGTTATATATTTTCGATGAGAATTGTGGCAAA
259 AGTCTGAAAAACCCTTCAAGCTTTTTTTCTTTGAATTATATATTGTCTATGAGAATTGTGGCCAA
*
255919 AAATTAAGG
324 AAATTGAGG
* * * * *
255928 AAAAATATTCCGGCTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTT
1 AAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTATCCATCACGATTTT
* * *
255993 AAGTTAAAAACGCGTTTCGAGGCCCTGACTCAGTTTTTCATGATTTTT
66 AAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTT
256041 AGC
Statistics
Matches: 693, Mismatches: 60, Indels: 33
0.88 0.08 0.04
Matches are distributed among these distances:
323 148 0.21
324 155 0.22
325 1 0.00
330 1 0.00
332 92 0.13
333 72 0.10
334 224 0.32
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (332 bp):
AAAAATTTTCCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGCACTATCCATCACGATTTT
AAGCTAAAAACGCGTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTTGCACGAAGACACCTTG
AACTATCTATATTCATCTGACTAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCA
TTTGTATCATGTTTCTATTTAATTCAAAATTAATTAGAATAAAATTGGAAAAACGATATTAAAAG
TCTGAAAAACCCTTCAAGCTTTTTTTCTTTGAATTATATATTGTCTATGAGAATTGTGGCCAAAA
ATTGAGG
Done.