Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015012.1 Kokia drynarioides strain JFW-HI SEQ_130056, 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: 316062
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 41 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:242755 original size:23 final size:21
Alignment explanation
Indices: 242711--242752 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
242701 ATAAATTATT
242711 TTTAGGCTTATATATTAGAAA
1 TTTAGGCTTATATATTAGAAA
242732 TTTAGGCTTATATATTAGAAA
1 TTTAGGCTTATATATTAGAAA
242753 AATCCTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (21 bp):
TTTAGGCTTATATATTAGAAA
Found at i:243675 original size:15 final size:16
Alignment explanation
Indices: 243646--243675 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
243636 GAAATACTAT
243646 AAGAGTTTATTTAAAC
1 AAGAGTTTATTTAAAC
243662 AAGAGTTT-TTTAAA
1 AAGAGTTTATTTAAA
243676 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.40
Consensus pattern (16 bp):
AAGAGTTTATTTAAAC
Found at i:244318 original size:19 final size:19
Alignment explanation
Indices: 244287--244379 Score: 58
Period size: 19 Copynumber: 4.9 Consensus size: 19
244277 ACTTAAATAG
244287 TAATACTTT-TATTTATATC
1 TAATA-TTTATATTTATATC
244306 TAATATTTATA--T-TAT-
1 TAATATTTATATTTATATC
244321 TAA-A-TTATATTTCATATTC
1 TAATATTTATATTT-ATA-TC
*
244340 TGTAATATTTATA-TTATATA
1 --TAATATTTATATTTATATC
244360 TATATATTTAATATTTATAT
1 TA-ATATTT-ATATTTATAT
244380 TATTGAATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 26
0.69 0.01 0.30
Matches are distributed among these distances:
13 5 0.08
14 1 0.02
15 4 0.07
16 3 0.05
17 3 0.05
18 6 0.10
19 13 0.22
20 4 0.07
21 12 0.20
22 3 0.05
23 5 0.08
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (19 bp):
TAATATTTATATTTATATC
Found at i:244346 original size:36 final size:36
Alignment explanation
Indices: 244306--244374 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
244296 TATTTATATC
*
244306 TAATATTTATATTATTAAAT-TATATTTCATATTCTG
1 TAATATTTATATTA-TAAATATATATTTAATATTCTG
*
244342 TAATATTTATATTATATATATATATTTAATATT
1 TAATATTTATATTATAAATATATATTTAATATT
244375 TATATTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (36 bp):
TAATATTTATATTATAAATATATATTTAATATTCTG
Found at i:244365 original size:13 final size:14
Alignment explanation
Indices: 244342--244382 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
244332 TCATATTCTG
244342 TAATATTTATATTA
1 TAATATTTATATTA
*
244356 T-ATATATATATT-
1 TAATATTTATATTA
244368 TAATATTTATATTA
1 TAATATTTATATTA
244382 T
1 T
244383 TGAATTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 1 0.04
13 20 0.87
14 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATATTTATATTA
Found at i:244625 original size:19 final size:19
Alignment explanation
Indices: 244601--244640 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
244591 AAAAATTAAT
*
244601 AACAAATTTGATTACGATA
1 AACAAATTTAATTACGATA
244620 AACAAATTTAATTACGATA
1 AACAAATTTAATTACGATA
244639 AA
1 AA
244641 TGACATTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (19 bp):
AACAAATTTAATTACGATA
Found at i:251291 original size:51 final size:51
Alignment explanation
Indices: 251222--251611 Score: 471
Period size: 51 Copynumber: 7.6 Consensus size: 51
251212 CTATAAACGA
* * *
251222 AAAGGTCTGATGTCTAAGTGTCATTGTGAGTAAATGAATCCTATACGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
251273 AAAGGTCTGATGATTAAGTGTCATCGTAAGTAAATGAATCCTTTACGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
251324 AAAGGT-TCGATGACTAAGAGTCATCATGAGTAAATGAATCCTTTATGGATT
1 AAAGGTCT-GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
251375 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGA-G
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
**
251425 AAAGGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * *
251476 AAATGTCTGATGACTAAGTGTCATCGTGAATAAATGAATCCATGATGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * ** * * * **
251527 AAGGGTCCGATGACTTTGTGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
251579 AAGAGGTCCGATGACTACA-TGTCATCGTGAGTA
1 AA-AGGTCTGATGACTA-AGTGTCATCGTGAGTA
251612 TTAAATGAAA
Statistics
Matches: 292, Mismatches: 41, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
50 48 0.16
51 208 0.71
52 10 0.03
53 26 0.09
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (51 bp):
AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:251499 original size:152 final size:152
Alignment explanation
Indices: 251222--251611 Score: 514
Period size: 152 Copynumber: 2.5 Consensus size: 152
251212 CTATAAACGA
* * * * * *
251222 AAAGGTCTGATGTCTAAGTGTCATTGTGAGTAAATGAATCCTATACGGATTAAAGGTCTGATGAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATACGGA-CAAAGGTCCGATGAC
*
251287 TAAGTGTCATCGTAAGTAAATGAATCCTTTACGGATTAAAGGTTCGATGACTAAGAGTCATCATG
65 TAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTTCGATGACTAAGAGTCATCATG
* * *
251352 AGTAAATGAATCCTTTATGGATT
130 AATAAATGAATCCATGATGGATT
* * * *
251375 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGAGAAAGGTCCAATGACT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATACGGACAAAGGTCCGATGACT
* * *
251440 AAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAATG-TCTGATGACTAAGTGTCATCGTG
66 AAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTTC-GATGACTAAGAGTCATCATG
251504 AATAAATGAATCCATGATGGATT
130 AATAAATGAATCCATGATGGATT
* ** * *
251527 AAGGGTCCGATGACTTTGTGTCATCGTGAGTATATGAATTCCTATATGGAACAAGAGGTCCGATG
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTATACGG-ACAA-AGGTCCGATG
251592 ACTACA-TGTCATCGTGAGTA
63 ACTA-AGTGTCATCGTGAGTA
251612 TTAAATGAAA
Statistics
Matches: 207, Mismatches: 25, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
151 2 0.01
152 123 0.59
153 51 0.25
154 3 0.01
155 27 0.13
156 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (152 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATACGGACAAAGGTCCGATGACT
AAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTTCGATGACTAAGAGTCATCATGA
ATAAATGAATCCATGATGGATT
Found at i:258151 original size:12 final size:13
Alignment explanation
Indices: 258117--258157 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
258107 ATTGGAATTT
258117 ATTTTT-GTTTTA
1 ATTTTTAGTTTTA
*
258129 ATTACTTAG-TTTA
1 ATT-TTTAGTTTTA
258142 ATTTTTAGTTTTA
1 ATTTTTAGTTTTA
258155 ATT
1 ATT
258158 AAACCCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 7 0.29
13 16 0.67
14 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (13 bp):
ATTTTTAGTTTTA
Found at i:259656 original size:20 final size:20
Alignment explanation
Indices: 259611--259655 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
259601 CACATAGAAA
* *
259611 TTTTTTATTATTTGCTTTTG
1 TTTTTTATTATCTACTTTTG
259631 TTTTTTATT-TCTACTTTTG
1 TTTTTTATTATCTACTTTTG
259650 TTTTTT
1 TTTTTT
259656 TCTTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.78
Consensus pattern (20 bp):
TTTTTTATTATCTACTTTTG
Found at i:266616 original size:38 final size:38
Alignment explanation
Indices: 266565--266638 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
266555 TCCAAGAAAG
266565 CTTCTTATTCCCTTAACATTTGTTGGTGGTGGCAATAT
1 CTTCTTATTCCCTTAACATTTGTTGGTGGTGGCAATAT
266603 CTTCTTATTCCCTTAACATTTGTTGGTGGTGGCAAT
1 CTTCTTATTCCCTTAACATTTGTTGGTGGTGGCAAT
266639 TTCTCGATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.45
Consensus pattern (38 bp):
CTTCTTATTCCCTTAACATTTGTTGGTGGTGGCAATAT
Found at i:286645 original size:2 final size:2
Alignment explanation
Indices: 286638--286670 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
286628 TACAAAGTTT
286638 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
286671 TTTCACTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:287943 original size:36 final size:36
Alignment explanation
Indices: 287891--287961 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
287881 TAGCATACTA
* *
287891 TCCCAGAAATGGAAAATTATTATTACACAGTAAACC
1 TCCCAGAAATGAAAAATGATTATTACACAGTAAACC
* *
287927 TCCCAGAAATGAAAAATGGTTATTACACGGTAAAC
1 TCCCAGAAATGAAAAATGATTATTACACAGTAAAC
287962 TTCATTAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (36 bp):
TCCCAGAAATGAAAAATGATTATTACACAGTAAACC
Found at i:296781 original size:39 final size:40
Alignment explanation
Indices: 296694--296781 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
296684 TCAGTATTTT
* * * *
296694 AAAAGGATGTTGTCTGAAAGGATATCAAATGGAAAGGTTG
1 AAAAGGATGTTATCCGAAAAGATATCAAATGGAAAGGTCG
296734 AAAAGGATGTTATCCGAAAAGATATC-AAT-GACAAGGTCG
1 AAAAGGATGTTATCCGAAAAGATATCAAATGGA-AAGGTCG
296773 AAAAGGATG
1 AAAAGGATG
296782 GCAATGAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.05
39 18 0.42
40 23 0.53
ACGTcount: A:0.43, C:0.08, G:0.27, T:0.22
Consensus pattern (40 bp):
AAAAGGATGTTATCCGAAAAGATATCAAATGGAAAGGTCG
Found at i:298229 original size:216 final size:215
Alignment explanation
Indices: 297159--301786 Score: 5516
Period size: 216 Copynumber: 21.6 Consensus size: 215
297149 TATGGATAAA
* * * * * *
297159 TTATAACTTCGATTCCTTAAAGTATTTAAGAAGATCCATTCCTTTGATCAATTTGCCGAACATTT
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * * ** **
297224 CAAGCTCGAGAAATCGCACCATTTGGTCTAAATAGTTTGTCACTTTGTAAACATTTTTTGGTCAA
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * * * * * * **
297289 TGAAATGATAACTTATTCATGAGAGAGTTGTTTCTCTCTTGATTTTTGGCCGAACTTTTGAACTT
131 TGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAACTT
297354 GTCAAACTTTTACGAGTTCTT
195 GTCAAACTTTTACGAGTTCTT
* *
297375 TTATAACTTC-AGTTCCTTAAAGTATTCAAGACGATCCATTCCATCGAGCAATTTTTCGAACATT
1 TTATAACTTCGA-TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATT
* * *
297439 CCATGCTC-AAAAATTGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGCTTTTGGTA
65 CCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA-CTTTTGGTC
* * * *
297502 TTTTAATTAAAAACTTATTTACGTGGGAGTTGTTTCTCTCTTAGTTCTTGGCCGAACTTCTGAAC
129 TTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAAC
* *
297567 TTGTCAAACTTTTACAAATTCTT
193 TTGTCAAACTTTTACGAGTTCTT
* * * * *
297590 TTATAACTTCGGTTCCTTAAAGTATTCAAGATGATTCATTCCTTCGAGCAATTTTCCAAACATTA
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* *
297655 CATGCTCGAGAAATCGCATCATTTGGTCTAAAGT-GTTTATCATTTTGTAAACAACTTTTGGTGT
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAA-TAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * * *
297719 TTGAATCAAAAAACTTATTTACATGAGAGTTGATTCTCTCTTGGTTCTTGGCCGAACTTCTGAAC
130 TTGAAT-TAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAAC
*
297784 TTGTCAAACTTTTACGAGTTCTA
193 TTGTCAAACTTTTACGAGTTCTT
* * * * * *
297807 TTATAACTTATG-TTCTTTAAAGTATTCAAGATGATCCATTCCTTCGAGCTATTTTTCGAACACT
1 TTATAACTT-CGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATT
* * * * *
297871 CCATACTCGGGAAATTGTATCATTTGGTCTAAATAG--TGTCTTTTTGTAAACAACTTTTGGTCT
65 CCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * * *
297934 TTGAATTAAAAACTTATTTACATGAGAGTTATTTCCCTCTTGGTTCTTGGCTGAACTTCC-ATAC
130 TTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGC-CAACTTCCGA-AC
*
297998 TTGTCAAGA-TTTTACGAGTTCTA
193 TTGTCAA-ACTTTTACGAGTTCTT
* * * *
298021 TTATAATTTCTATTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTCCAAACATTC
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * *
298086 CATGCTCGAGAAATCGCATCATTTAGTCTAAATAATTTGTCATTTTGTAAACAACATTTGGTCTT
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * * *
298151 TAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAGCTTCCAAACTT
131 TGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCCAA-CTTCCGAACTT
298216 GTCAAACTTTTACGAGTTCTT
195 GTCAAACTTTTACGAGTTCTT
* * * * *
298237 TTATAACTTCGATTCCTTAAATTATTCAAGACGATCCATTCCGTCGTGAAATTTTTCGAACATTC
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * * * *** *
298302 CATGCTTGGGAAATCAG-ATCATTTGTTCTAAATAGTGTGTCATTTTGTAAA-AAAAATTAGTCT
66 CATGCTCGAGAAATC-GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * *
298365 TTGAATT-AAAATTTATTTACGTGACAGTTGTTTCTCTCTTGGTTCTTAGCCAAACTTCCGAACT
130 TTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAACT
298429 TGTCAAACTTTTACGAGTTCTT
194 TGTCAAACTTTTACGAGTTCTT
** * * * * *
298451 TTATATTTTCGATTCCATAAAGTATTCAAGACAATCCATTCCTTTGAACAATTTTTCGAACATTC
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * * * * *
298516 CAAGCTTGGGAAATCGTATCATTTGGTCTAAATAGTTTGTAATTTTGTAAAACAACTTTTAGTCT
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT-AAACAACTTTTGGTCT
* * * *
298581 TTGAATTAAAAAATTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTTTCGAACC
130 TTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAACT
298646 TGTCAAACTTTTACGAGTTCTT
194 TGTCAAACTTTTACGAGTTCTT
* * * *
298668 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCGTCGTGAAATTTTTCGAACATTC
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * * * *
298733 CATGCTTGGGAAATCAG-ATCATTTGTTCTAAATAGTTTGTCATTTTGTAAA-AAATTTTGGTCA
66 CATGCTCGAGAAATC-GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * * *
298796 TTGAATTATAAATTTATTAACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCCAAACTTCCAAACT
130 TTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAACT
298861 TGTCAAACTTTTACGAGTTCTT
194 TGTCAAACTTTTACGAGTTCTT
* * * * *
298883 TTATAACTTCGGTTCCTTAAAGTATTCAAAACGATCCATTCCTTTGACCAA-TTTCTCGAACAAT
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTC-CGAACATT
* * * *
298947 CCATGCTCGAAAAATCGTATCATTTGGTCTAAATACTTTGTCATATTGTAAACAACTTTTGGTCT
65 CCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * *
299012 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGTCGAACTTCCAAACT
130 TTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGG-CCAACTTCCGAACT
299077 TGTCAAACTTTTACGAGTTCTT
194 TGTCAAACTTTTACGAGTTCTT
* * *
299099 TTATAACTTCGATTCCTTAAAGAATTCAAGATGGTCCATTCCTTCGAGCAATTTTCC-AATCATT
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAA-CATT
* * * * * * *
299163 CCAAGCTCGAGAAATCGCGTCATTTCGTCCAAATAGTTTGTCACTTTGTAAACAATTTTTGGTCA
65 CCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * * * * * *
299228 ATGAAATAAAAACTTATTCACATGAGAGTTGTTTCTCCCTTGGTTCTTGGTCGAACTTTCGAACT
130 TTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGG-CCAACTTCCGAACT
299293 TGTCAAACTTTTACGAGTTCTT
194 TGTCAAACTTTTACGAGTTCTT
* * * * *
299315 TTATAACTTCGGTTCCTTAAAGTATTCAAGATGATTCATTCCTTCGAGCAAATTTCCAAACATTC
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* *
299380 CATGCTCGAGAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACATTTGGTCTT
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *
299445 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGCTGAACTTCCGAACTT
131 TGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGC-CAACTTCCGAACTT
*
299510 GTCAAACTTTTACGAGTTCTA
195 GTCAAACTTTTACGAGTTCTT
* * * *
299531 TTATAACTTATG-TTCCTTAAAGTATTCAAGATGATCTATTCCTTCGAGCAATTTTTCGAACATT
1 TTATAACTT-CGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATT
* * *
299595 CCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCTTTTTGTAAACAACTTTTGGTTT
65 CCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * * * *
299660 TTGAATTAAAAACTTATTTACATGAGAGTTGTTTCCCTCTTGGTTCTTAGCTGAACTTTCGAACT
130 TTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGC-CAACTTCCGAACT
* *
299725 TGTCAAGCTTTTACGAGTTCTA
194 TGTCAAACTTTTACGAGTTCTT
*
299747 TTATAACTTCTG-TTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTT-CGAAACAT
1 TTATAACTTC-GATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCG-AACAT
* * * * **
299810 TCCATGCTCGGGAAATCGCAT-AGTTTAGTCTAAGTAGTTTGTCATTTTGTAATCAACAATTGGT
64 TCCATGCTCGAGAAATCGCATCA-TTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGT
* * *
299874 CTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTTTCGAA
128 CTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAA
299939 CTTGTCAAACTTTTACGAGTTCTT
192 CTTGTCAAACTTTTACGAGTTCTT
* * *
299963 TTATAACTTCGATTCCTTAAATTATTCAAGATGATCCATT-CTGTC-ATGAAAATTTT-CGAACA
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCT-TCGA-G-CAATTTTCCGAACA
* * * * * ***
300025 TTCCATACTCGGGAAATCGGATCATTTGTTCTAAATAGTTTGTCATTTTGTAAAAAAAAATTGGT
63 TTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGT
* * * * *
300090 ATTTGAATT-AAAATTTATTTACGTGACAGTTGTTTCTCTCTAGATTCTTGGCCAAACTTCCGAA
128 CTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAA
300154 CTTGTCAAACTTTTACGAGTTCTT
192 CTTGTCAAACTTTTACGAGTTCTT
** * * * * * * *
300178 TTATATTTTCGATTCCATAAAGTATTCAAGACAATCCATTCCTTTGACCAATTTTTCAAACAATC
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * * *
300243 CATGCTCGAGAAATTGTATCATTTGATCTAAATACTTTGTCATTTTGT-AACAACTTTTGGTCTT
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *
300307 TGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAGCTT
131 TGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAACTT
*
300372 GTTAAACTTTTACGAGTTCTT
195 GTCAAACTTTTACGAGTTCTT
*
300393 TTATAACTTCGATTCCTTAAAGTATTCAAGACGGTCCATTCCTTCGAG-AGATTTTCC-AATCAT
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCA-ATTTTCCGAA-CAT
* * * * *
300456 TCCAAGCTCGAGAAATCGCATCATTTCGTCCAAATAGTTTGTCACTTTGTAAACAATTTTTGGTC
64 TCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTC
** * * * * * * * * *
300521 AATGAAATGATAACTTATTCACGGGAGAGTTGTTTCTCTCTTGATTTTTAGCCGAACTTTCGAAC
129 TTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAAC
* *
300586 TTGTTAAACTTTTACAAGTTCTT
193 TTGTCAAACTTTTACGAGTTCTT
* *
300609 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCATCGAGCAATTTTTCGAACATTC
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * *
300674 CATGCTC-AAAAATCGTATCATTTGGTCTAAATAGTTCGTCATTTTGT-AACAACTTTTGGTCTT
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* *
300737 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAGCTT
131 TGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCC-AACTTCCGAACTT
300802 GTCAAACTTTTACGAGTTCTT
195 GTCAAACTTTTACGAGTTCTT
*
300823 TTATAACTTCGATTCCTTAAAGTATTCAAGACGGTCCATTCCTTCGAG-AGATTTTCC-AATCAT
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCA-ATTTTCCGAA-CAT
* ** * * *
300886 TCCAAGCTCGAGAAATCGCATCATTTCATCCAAATAGTTTGTCACTTTGTAAACAATTTTTGGTC
64 TCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTC
** * * ** * * * * * *
300951 AATGAAATGATGACTTATTCACGGGAGAGTTGTTTCTCTCTTGATTTTTGGTCGAACTTTCGAAC
129 TTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGG-CCAACTTCCGAAC
*
301016 TTGTCAAACTTTTACAAGTTCTT
193 TTGTCAAACTTTTACGAGTTCTT
301039 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCA----TTC---C-A---T-CGAACATTC
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * *
301092 CATGCTC-AAAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTATT
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
* * *
301156 TGAATTAAAAACTTATTTACATGAGAGTTGTTTCTCTCTTGGTTCTTGGCTGAACTTCTGAACTT
131 TGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGC-CAACTTCCGAACTT
301221 GTCAAACTTTTACGAGTTCTT
195 GTCAAACTTTTACGAGTTCTT
* * * *
301242 TTATAACTTCGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCGAGCAATTTTTCGAACATTA
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * *
301307 CATGCTCGAGAAATCGCGTCATTTGGTTTAAAGT-GTTTATCATTTTGTAAACAACTTTTGGTCT
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAA-TAGTTTGTCATTTTGTAAACAACTTTTGGTCT
* * * * * *
301371 TTGAATTTAAAACTTATTTACATGGGAGTTGTTTCTTTCTTAGTTCTT-----A--GCCGAACTT
130 TTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCCAACTTCCGAACTT
* * *
301429 -TCGAACTTTTTACGAGTTATA
195 GTCAAAC-TTTTACGAGTTCTT
** ** *
301450 TTATAACTTCTG-TTCCTTAAAGTATTCAAGACGATCCATTCCTTTAAGACAATTTTTTGAATAT
1 TTATAACTTC-GATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAG-CAATTTTCCGAACAT
* * * *
301514 TTCATGCTC-AGGAAATCACATCATTTGGTCTAAATAGTTAGTCTTTTTGTAAACAA--------
64 TCCATGCTCGA-GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGT
* * *
301570 C--TG-------AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGTCGAGCTTCCGAA
128 CTTTGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGG-CCAACTTCCGAA
* *
301626 CATGTCAAACTTTTACGAGTTCTA
192 CTTGTCAAACTTTTACGAGTTCTT
* * * * * * **
301650 TTATAACTTTGATTCCTTAAAGCATTCAAGACGATCAATTCTTTCTAGCAGTTTTCAAAACATTC
1 TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
* * *
301715 CATGCTCGA-AAACCGCATCATTTGGTCTAAATATTTTGTCATTTTGTAAA-AACTTTTTGGTTT
66 CATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAC-TTTTGGTCT
301778 TTGAATTAA
130 TTGAATTAA
301787 GGGTTAAATA
Statistics
Matches: 3817, Mismatches: 488, Indels: 216
0.84 0.11 0.05
Matches are distributed among these distances:
192 33 0.01
197 2 0.00
198 36 0.01
199 21 0.01
200 61 0.02
201 6 0.00
202 1 0.00
203 155 0.04
204 12 0.00
205 3 0.00
207 8 0.00
208 67 0.02
209 59 0.02
210 2 0.00
211 1 0.00
212 3 0.00
213 5 0.00
214 503 0.13
215 830 0.22
216 1651 0.43
217 356 0.09
218 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (215 bp):
TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTC
CATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTT
TGAATTAAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTGGCCAACTTCCGAACTTG
TCAAACTTTTACGAGTTCTT
Found at i:303845 original size:30 final size:31
Alignment explanation
Indices: 303808--303892 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 31
303798 ACTAGTGGAC
303808 GAAAAAAAGTTTAGGTACCAATTTGGGACAA
1 GAAAAAAAGTTTAGGTACCAATTTGGGACAA
* * * * *
303839 -AAAAAAACTATAAGTACCAATCTGGGAGAA
1 GAAAAAAAGTTTAGGTACCAATTTGGGACAA
** * *
303869 GTGAAAAAGTTCAGGTACTAATTT
1 GAAAAAAAGTTTAGGTACCAATTT
303893 TATATTTAAC
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
30 25 0.62
31 15 0.38
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.24
Consensus pattern (31 bp):
GAAAAAAAGTTTAGGTACCAATTTGGGACAA
Found at i:304289 original size:216 final size:216
Alignment explanation
Indices: 303905--305176 Score: 1439
Period size: 216 Copynumber: 5.9 Consensus size: 216
303895 TATTTAACCC
* * * * ** * * **
303905 TTGAATTAAAAACTTATATAC-ATGAGATTTGTTTCTATTTTGAATCATGGCTGAACTTCCAAAC
1 TTGAATTAAAAACTTATTTACGA-GAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAAC
* * * *
303969 TTGTCAATCTTTTACAAGTTCTTTTATAACTTAAGTTACTTAAAGTATTCAAGATGATCCATTCC
65 TTGTCAAACTTTTACGAGTTCTTTTATAACTTAAGTTCCTTAAAGTATTCAAGACGATCCATTCC
* * *
304034 TTCAAGCAATAATTT-GAACATTCCATGCTCTGGAAATCACATCATTTGGTCTAAAAAGTTTGTC
130 TTCAAGCAAT-TTTTCGAACATTCCATGCTCGGGAAATCACATCATTTGGTCTAAATAGTTTGTC
*
304098 ATTTTGTAAACAAGTTTTGGTCT
194 ATTTTGTAAACAACTTTTGGTCT
**
304121 TTGAATTAAAAACTTATTTACGAGAGGGTTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACT
1 TTGAATTAAAAACTTATTTACGAGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACT
* * * * * * *
304186 TGTCAAGCATTTACGAGTTGTTTAATAACTT-TGATTCCTTAAATTATTCAAGATGATCCATTCC
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTAAG-TTCCTTAAAGTATTCAAGACGATCCATTCC
** * *
304250 TTTGAGCAATTTTTCGAACATTCCATCCTCGGAAAATCACATCATTTGGTCTAAATAGTTTGTCA
130 TTCAAGCAATTTTTCGAACATTCCATGCTCGGGAAATCACATCATTTGGTCTAAATAGTTTGTCA
*
304315 TTTT-TAAACAACTTTTGTTCT
195 TTTTGTAAACAACTTTTGGTCT
* ** * *
304336 TTG--------ACTTAATTACGTTAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTAAAAT
1 TTGAATTAAAAACTTATTTACGAGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACT
* * * ** *
304393 TGTCAAACTTTTATGCGTTATTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTAAGTTCCTTAAAGTATTCAAGACGATCCATTCCT
* * * * * * * *
304458 TCGAGCAATTTTCCGAACATTCGAAGCTCGGAAAATCACATTATTTGGTTTAAATAG-TT-TCAC
131 TCAAGCAATTTTTCGAACATTCCATGCTCGGGAAATCACATCATTTGGTCTAAATAGTTTGTCAT
* * *
304521 TTTGTAGACAATTTTTGGTCA
196 TTTGTAAACAACTTTTGGTCT
* * * * * * * *
304542 TTAAAATAAAATCTTATTTATGTGAGTATTGTTTCTCTCTTGGTTCTTGGTCGAACTTCCGAACT
1 TTGAATTAAAAACTTATTTACGAGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACT
* * *
304607 TGTCAAGCTTTTACGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTCAAGACGATCCATTCAT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTAAGTTCCTTAAAGTATTCAAGACGATCCATTCCT
* ** *
304672 TCAAGAAATTTTAT-GAACATTCCATGCTCGGGAAATCGTATCATTTGGTGTAAATAGTTTGTCA
131 TCAAGCAATTTT-TCGAACATTCCATGCTCGGGAAATCACATCATTTGGTCTAAATAGTTTGTCA
*
304736 TTTTATAAACAACTTTTGGTCT
195 TTTTGTAAACAACTTTTGGTCT
* * * * **
304758 TTGAATTAAAAACTTATTTACGTGAGAAATGTTTCTCACTAGGTTCTTGGATGAACTTCTGAACT
1 TTGAATTAAAAACTTATTTACGAGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACT
* * * * ** *
304823 TGACAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCATAAAGTATTTAAGACGAGGCATTTCT
66 TGTCAAACTTTTACGAGTTCTTTTATAACTTAAGTTCCTTAAAGTATTCAAGACGATCCATTCCT
* * *
304888 TCGAGCAATTTTTTGAACA-TCACATGCTTGGGAAATCACATCATTTGGTCTAAATAGTTTGTCA
131 TCAAGCAATTTTTCGAACATTC-CATGCTCGGGAAATCACATCATTTGGTCTAAATAGTTTGTCA
*
304952 TTTTGTAAACAATTTTTGGTCT
195 TTTTGTAAACAACTTTTGGTCT
* * * * * * *
304974 TTGAAATAAGAACTTATTTACGTGAGAAATGTTTCTCTTTTGGTTCTTGGACGAACTTTTGAACT
1 TTGAATTAAAAACTTATTTACGAGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACT
* *
305039 AT-TCAAACATTTACGAGTTCTTTTATAACTTCAA-TTCCTTAAAGTATTCAAGATGATCCATTC
66 -TGTCAAACTTTTACGAGTTCTTTTATAACTT-AAGTTCCTTAAAGTATTCAAGACGATCCATTC
* * *
305102 CTTCAAGCAA-TTTTCTGAACATTCCATTCTTGGGAAATCACATCATTTAGTCTAAATAGTTTGT
129 CTTCAAGCAATTTTTC-GAACATTCCATGCTCGGGAAATCACATCATTTGGTCTAAATAGTTTGT
*
305166 AATTTTGTAAA
193 CATTTTGTAAA
305177 GGGATAATGC
Statistics
Matches: 897, Mismatches: 137, Indels: 44
0.83 0.13 0.04
Matches are distributed among these distances:
205 6 0.01
206 17 0.02
207 150 0.17
208 1 0.00
214 149 0.17
215 31 0.03
216 538 0.60
217 5 0.01
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (216 bp):
TTGAATTAAAAACTTATTTACGAGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACT
TGTCAAACTTTTACGAGTTCTTTTATAACTTAAGTTCCTTAAAGTATTCAAGACGATCCATTCCT
TCAAGCAATTTTTCGAACATTCCATGCTCGGGAAATCACATCATTTGGTCTAAATAGTTTGTCAT
TTTGTAAACAACTTTTGGTCT
Found at i:308829 original size:216 final size:216
Alignment explanation
Indices: 308450--308922 Score: 684
Period size: 216 Copynumber: 2.2 Consensus size: 216
308440 GCATTATCCC
* * *
308450 TTTTGTAAACAACTTTTGGTCTTTGAATTTAAAACTTATTTACATGAGAATTGTTTCTCTTTTGG
1 TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGACAATTGTTTCTCTCTTGG
* * * * * * * *
308515 TTCTTGGACGAACTTTTAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTTTGTAAA
66 TACTCGGACAAACTTTTAAACTTGTCAAACATTTACGAATTCATTTATAACTTAGATTCTGTAAA
* * * * * *
308580 GTATTCAAGACGATCCATTCCTTTGAACAATTTTTCGAACATTCGAAGCTCGAGAAATTGCATCA
131 GTATTCAAGACGATCCATTCCTATCAACAATTTTACGAACATTCCAAGCTCAAGAAATCGCATCA
*
308645 TTTGGTCTAAATAATTTTTCA
196 TTTGGTCTAAATAATTTGTCA
*
308666 TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGACAATTGTTTCTCTCTTGG
1 TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGACAATTGTTTCTCTCTTGG
* *
308731 TACTCGGACAAACTTTTGAACTTGTCAAACATTTACTAATTCATTTATAACTTTAG-TTCCT-TA
66 TACTCGGACAAACTTTTAAACTTGTCAAACATTTACGAATTCATTTATAAC-TTAGATT-CTGTA
*
308794 AAGTATTCAAGACGATCCATTCC-ATCAAGCAATTTTACGAACATTCCATGCTCAAGAAATCGCA
129 AAGTATTCAAGACGATCCATTCCTATCAA-CAATTTTACGAACATTCCAAGCTCAAGAAATCGCA
*
308858 TCATTTGGTCTTAATAATTTGTCA
193 TCATTTGGTCTAAATAATTTGTCA
308882 TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAC-TATTTA
1 TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTA
308923 AACCAAATGA
Statistics
Matches: 231, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
215 9 0.04
216 218 0.94
217 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (216 bp):
TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACATGACAATTGTTTCTCTCTTGG
TACTCGGACAAACTTTTAAACTTGTCAAACATTTACGAATTCATTTATAACTTAGATTCTGTAAA
GTATTCAAGACGATCCATTCCTATCAACAATTTTACGAACATTCCAAGCTCAAGAAATCGCATCA
TTTGGTCTAAATAATTTGTCA
Found at i:309346 original size:216 final size:214
Alignment explanation
Indices: 308973--312480 Score: 3557
Period size: 216 Copynumber: 16.4 Consensus size: 214
308963 AATTTCACTT
* * * *
308973 GTAAAAGTTTGACAAGTTTGGAAGTTCATCCAAAAACAAAGAGAGAAAAAATTCTCACGTAAATA
1 GTAAAAGTTTGAC-AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * ** *
309038 AGATTTTAATTCAAAGACC-AAAGTTGTTTACAAAATGATGAACTATTTAGACCAAATGATGCAA
65 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGCGA
* * *
309102 TTTCACGAGCAT-AATATGTTCGGAAAATTGCTCGAAAGAATGGATCGTCTTAAATACTTTAAGG
129 TTTCCCGAGCATGGA-ATGTTCGGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGG
309166 AACCGAAGTTATAAAAGAACTC
193 AACCGAAGTTATAAAAGAACTC
* * * *
309188 GTAAAAGTTTTACTAGTTCGAAAATTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
1 GTAAAAGTTTGAC-AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * * * * *
309253 AGTTTTTATTTCAAACAACAAAAGTTGTTTACAAAATAACAAACTACTTAGACCAAATGATGTGA
65 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATAA-AAACTATTTAGACCAAATGATGCGA
** * * *
309318 TTTCCAAAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCG-CATTAAATACTTTGAGG
129 TTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCGTC-TTGAATACTTTAAGG
* *
309382 AATCGAAGTTAT-AAAGAACTT
193 AACCGAAGTTATAAAAGAACTC
* * * * * *
309403 GTAAAAGTTTTAAAAGTTTGGAAGTTCGTCCAAGAATC-A-ATAGATACAATTCTCACGTAAATA
1 GTAAAAG-TTTGACAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* *
309466 AGTTTTTAATTTAAAGACCAAAACTTGTTTAAAAAAATGAAAAACTATTTAGACCAAATGATGCG
65 AGTTTTTAATTCAAAGACCAAAACTTGTTT-ACAAAAT-AAAAACTATTTAGACCAAATGATGCG
** ** ** *
309531 ATTTCTTGAGCATGGAAACTTCAAAAAATTGCTC-AAAGGAATGCA-CTGTCTTGAATACTTTAA
128 ATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAA-GAATGGATC-GTCTTGAATACTTTAA
309594 GGAACC-AATGTTATAAAAGAACTC
191 GGAACCGAA-GTTATAAAAGAACTC
* * * *
309618 GTAAAAGTTTGACATGTTTGAAAGTTTGTCCAAGAACCAAGAGAGAAATGATTCTCACATAAATA
1 GTAAAAGTTTGACA-GTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * * * * * * *
309683 AGCTTTTAATTGAAAGAGCAAAACTTGTTTACAAAAT-GACACTTTTTAGA-AAAATGATACGAT
65 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATAAAAACTATTTAGACCAAATGATGCGAT
* * * * * *
309746 TTCTCGAGCATGGAGTGTTCAGAAAATTGCTCGAAGGAAAGGATCGTCTTGAATGCTTTAAGGAA
130 TTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGAA
*
309811 CTGAAGTTATAAAAGAACTC
195 CCGAAGTTATAAAAGAACTC
* * * *
309831 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACC-A-ATAGAAACAATTCTCATGTAAA-A
1 GTAAAAGTTTGAC-AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * * * * *
309893 AGGTTTTTAGTTCAAAGACCAAAACGTGTTTAGAAAATGAAAAACTATTTAGTCAAAAAGATGCG
65 A-GTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGCG
* * * * * *
309958 ATTTCCCGTGCATGGAATGTTTC-GAAAATTGTTTGAAGGAATGTACCGTCTTGAATACTTTAAG
128 ATTTCCCGAGCATGGAATG-TTCGGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
* *
310022 GAATCGAAGTTATAAAATAACTC
192 GAACCGAAGTTATAAAAGAACTC
*
310045 GTAAAAGTTTGACATGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
1 GTAAAAGTTTGACA-GTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * *
310110 AGTTTTTAATTCAAAGACCATAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGA
65 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGCGA
* * * * * *
310175 TTTCCTGAGCATGAAATGTTCGAAAAATTGCTCGAAGGAAGGGA-CGTCTTGAATACTTTAAGAA
129 TTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGA
** *
310239 ATAGAAGTTATAAAGGAACTC
194 ACCGAAGTTATAAAAGAACTC
* * * * *
310260 GTAAAAGTTTTACTAGTTCGGAAGTTCTTCCACGAACCAAGATAGAAATAATTCTCACGTAAATA
1 GTAAAAGTTTGAC-AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * *
310325 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAACTATTTAGACAAAATGATGTGAT
65 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATAAAAACTATTTAGACCAAATGATGCGAT
* * *
310390 TTCCTGAGCATGGAATGTTCAGAAAATTGCTC-AAAGGAATGGATTGTCTTGAATACTTTAAGGA
130 TTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAA-GAATGGATCGTCTTGAATACTTTAAGGA
* *
310454 ATCGAAGTTATAAACGAACTC
194 ACCGAAGTTATAAAAGAACTC
* * * *
310475 GTAAAAGTTTGACATGTTTGGAAGTTTGTCCAAGAACAAAGAGAGAAACAATTCTCATGTAAATA
1 GTAAAAGTTTGACA-GTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * * * * * *
310540 AGTTTTTAGTTCAAAGACCAAAACTTATTAACAATATGACAAACTATTTAGACCAACTGATGTGA
65 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGCGA
* * * * ** * *
310605 TTTCTCGAGCATTGAATGTTTGGAAAATTACTCGATGGAAAGTATCGTCTTGAATACTTTAAGGA
129 TTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGA
*
310670 ACAGAAGTTATAAAAGAACTC
194 ACCGAAGTTATAAAAGAACTC
* * * *
310691 GTAAAAGTTTTACAAGTTCGGAAGTTCATCCAAGAATCAAGAGAGAAAGT-ATTCTCACGTAAAT
1 GTAAAAGTTTGAC-AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAA-TAATTCTCACGTAAAT
* * *
310755 AAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAACGAAAAACTATTTATACCAAATGATGCG
64 AAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA-TAAAAACTATTTAGACCAAATGATGCG
* ** * * *
310820 ATTTCCCGAGCATGAAATGTTTAGAAAATTGCTC-AAAGTAATGTACCATCTTGAATACTTTAAG
128 ATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAG-AATGGATCGTCTTGAATACTTTAAG
*
310884 GAACCGAAGTTATAAAATAACTC
192 GAACCGAAGTTATAAAAGAACTC
* * * * *
310907 ATAAAAGTTTCACATGTTTGGAAGTTCGTCAAAGAACCAAGAGAGACACT-ATTCTCACATAAAT
1 GTAAAAGTTTGACA-GTTTGGAAGTTCGTCCAAGAACCAAGAGAGA-AATAATTCTCACGTAAAT
* *
310971 AATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCG
64 AAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGCG
* * * * *
311036 ATTTCCCAAGCATGAAATGTTCGAAAAATTGCTC-AAAGAAATGGATCATCTTGACTACTTTAAG
128 ATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAG-AATGGATCGTCTTGAATACTTTAAG
*
311100 GAACCAAAGTTATAAAAGAACTC
192 GAACCGAAGTTATAAAAGAACTC
* * * * *
311123 ATAAAAGTTTTACGAATTTGGAAGTTTGTCCAAGAACCAAG-GAGAAACT-ATTCTCACGTAAAA
1 GTAAAAGTTTGAC-AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAA-TAATTCTCACGTAAAT
** * * *
311186 AAGTTATTT-A--CAAA-ATGAAAA-------AC--TATATAGAC-A---A-A--A--TGATGCG
64 AAGTT-TTTAATTCAAAGACCAAAACTTGTTTACAAAATAAAAACTATTTAGACCAAATGATGCG
** * * * *
311229 ATTTTTCGAGCA-GTAAATGTTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATTCTTTAAG
128 ATTTCCCGAGCATG-GAATGTTCGGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
*
311293 GAACCAAAGTTATAAAAGAACTC
192 GAACCGAAGTTATAAAAGAACTC
* * * * *
311316 GTAAAAGTTTGACTAGTTCGGAAGTT-TTCCAAGAACC-A-ATAGAAACAATTCTCATGTAAATA
1 GTAAAAGTTTGAC-AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * * ** * *
311378 AGTTTTTAATTCAAAAACCAAAATTTTTTTACAAAATGGCAAACTATTTAGACCAAATGATTCAA
65 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGCGA
* * * * * * * *
311443 TTTCTCGAGAATGGAATGCTCGAAAAATTGCTCGAAGGAATGG-TCCCCATCTTGTATAATTTAA
129 TTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGAT---CGTCTTGAATACTTTAA
*
311507 GGAACCAAAGTTATAAAAGAACTC
191 GGAACCGAAGTTATAAAAGAACTC
**
311531 GTAAAAGTTTGACATGTTTATAAGATT-GTCCAAGAACCAAGAGAGAAA-AATTTCTCACGTAAA
1 GTAAAAGTTTGACA-GTTTGGAAG-TTCGTCCAAGAACCAAGAGAGAAATAA-TTCTCACGTAAA
* ** * * *
311594 TAAGTTTTTAATTGAAAGGTC-AAAGTTGTTTACAAAATGAAAAACTATTTTGACAAAATGATGC
63 TAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGC
* * * *
311658 AATTTCCCGAGCATGAAATGTTCGAAAAATTGCT--AAAGGAAAT-GATCATCTTGAATACTTTA
127 GATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAA-G-AATGGATCGTCTTGAATACTTTA
* *
311720 CGGAACCAAAGTTATAAAAGAACTC
190 AGGAACCGAAGTTATAAAAGAACTC
* * * * * * * * * **
311745 ATAAAAATTGGACATGTATGGTAGTTCGTCCAAGAACTAAGAGAGAAACAATTCTTAGGTAAGCA
1 GTAAAAGTTTGACA-GTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * * * * *
311810 AGTTTTTAAATAAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAAACCAAATGATGTGA
65 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGCGA
* ** * * * * * *
311875 TTTTCTAAGTATGGAATGTTCGAAAAATTTCTCGAAGGAATGGATCATCTTAAATACTTTAAGGA
129 TTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGA
* **
311940 ACCGAAGTTCTAAAAGAGTTC
194 ACCGAAGTTATAAAAGAACTC
** * * * * *
311961 GTAAAAGTTTGACAAGTGCGGAAGTTCATCCAAGAACCAAGGGAAAAACAATTCTCATGTAAATA
1 GTAAAAGTTTGAC-AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * * * *
312026 AGTTTTTAATTCAAAGACTAAAAACTTGTTTACAAAATGACAAACCATTTAAAACAAATGATGCG
65 AGTTTTTAATTCAAAGAC-CAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGCG
** * * * * *
312091 ATTTCTTGAGCATGTAATGTTCGGAAAATTTCTC-AAAGGAATGGATCATCCTGAATACTTTATG
128 ATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAA-GAATGGATCGTCTTGAATACTTTAAG
*
312155 AAACCGAAGTTATAAAAGAACTC
192 GAACCGAAGTTATAAAAGAACTC
* * * * * *
312178 ATAAATGTTTGACAAGTTTGGAAGTTCATCCAAGAAACAAGAGAGAAACAATTCTCAAGTAAATA
1 GTAAAAGTTTGAC-AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
* * * * * *
312243 AGTTTTTAATTCGAAGACAAAAAGTTGCTTACAAAATGAAAAACTATTAAGACTAAATGATGCGA
65 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-AAAAACTATTTAGACCAAATGATGCGA
* * * * * * ***
312308 TTTCCCGTGCATGAAATGTTCGAAAAATAGCTTGAAAGAATGGATCATCTTGAATACTTTATTTA
129 TTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGA
* *
312373 ACTGAAGTTATAAAAAAACTC
194 ACCGAAGTTATAAAAGAACTC
* * * * * *
312394 GTAAAAGTTTTACATGTTTTGAAGTTCGTCTAAGAAGCAAGAGAGAAACAATTCTCAAGTAAATA
1 GTAAAAGTTTGACA-GTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATA
*
312459 AGTTTTTAATTCAATGACCAAA
65 AGTTTTTAATTCAAAGACCAAA
312481 TGATGCGATT
Statistics
Matches: 2770, Mismatches: 428, Indels: 189
0.82 0.13 0.06
Matches are distributed among these distances:
190 3 0.00
191 24 0.01
192 11 0.00
193 104 0.04
194 8 0.00
195 1 0.00
197 1 0.00
198 1 0.00
201 3 0.00
202 4 0.00
203 4 0.00
204 3 0.00
205 3 0.00
208 1 0.00
209 1 0.00
210 2 0.00
211 48 0.02
212 7 0.00
213 221 0.08
214 383 0.14
215 560 0.20
216 1025 0.37
217 318 0.11
218 34 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (214 bp):
GTAAAAGTTTGACAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATAA
GTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATAAAAACTATTTAGACCAAATGATGCGATT
TCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGAAC
CGAAGTTATAAAAGAACTC
Found at i:310455 original size:430 final size:432
Alignment explanation
Indices: 308973--312480 Score: 3919
Period size: 430 Copynumber: 8.2 Consensus size: 432
308963 AATTTCACTT
* * * * *
308973 GTAAAAGTTTGACAAGTTTGGAAGTTCATCCAAAAACAAAGAGAGAAAAAATTCTCACGTAAATA
1 GTAAAAGTTTTACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * ** * *
309038 AGATTTTAATTCAAAGACC-AAAGTTGTTTACAAAATGATGAACTATTTAGACCAAATGATGCAA
66 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCGA
* *
309102 TTTCAC-GAGCAT-AATATGTTCGGAAAATTGCTCGAAA-GAATGGATCGTCTTAAATACTTTAA
131 TTTC-CTGAGCATGAA-ATGTTCAGAAAATTGCTC-AAAGGAATGGATCGTCTTGAATACTTTAA
* * * *
309164 GGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTTAC-TAGTTCGAAAATTCGTCCAAGAACCAA
193 GGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAT-GTTTGGAAGTTCGTCCAAGAACCAA
* * * * * *
309228 GAGAGAAATAATTCTCACGTAAATAAGTTTTTATTTCAAACAACAAAAGTTGTTTACAAAATAAC
257 GAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAC
* ** *
309293 AAACTACTTAGACCAAATGATGTGATTTCCAAAGCATGGAATGTTCGGAAAATTGCTCGAAGGAA
322 AAACTATTTAGACCAAATGATGTGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAA
* * * * *
309358 TGGATC-GCATTAAATACTTTGAGGAATC-GAAGTTAT-AAAGAACTT
387 TGGATCATC-TTGAATACTTT-AAGAAACAGAAGTTATAAAAGAACTC
* * * *
309403 GTAAAAGTTTTAAAAGTTTGGAAGTTCGTCCAAGAATC-A-ATAGATACAATTCTCACGTAAATA
1 GTAAAAGTTTTACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * *
309466 AGTTTTTAATTTAAAGACCAAAACTTGTTTAAAAAAATGAAAAACTATTTAGACCAAATGATGCG
66 AGTTTTTAATTCAAAGACCAAAACTTGTTT-ACAAAATGAAAAACTATTTAGACAAAATGATGCG
* * * *
309531 ATTTCTTGAGCATGGAAA-CTTCAAAAAATTGCTCAAAGGAATGCA-CTGTCTTGAATACTTTAA
130 ATTTCCTGAGCAT-GAAATGTTCAGAAAATTGCTCAAAGGAATGGATC-GTCTTGAATACTTTAA
* *
309594 GGAACC-AATGTTATAAAAGAACTCGTAAAAGTTTGACATGTTTGAAAGTTTGTCCAAGAACCAA
193 GGAACCGAA-GTTATAAAAGAACTCGTAAAAGTTTGACATGTTTGGAAGTTCGTCCAAGAACCAA
** * * * *
309658 GAGAGAAATGATTCTCACATAAATAAGCTTTTAATTGAAAGAGCAAAACTTGTTTACAAAATGAC
257 GAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAC
* * ** *
309723 --ACTTTTTAGA-AAAATGATACGATTT-CTCGAGCATGGAGTGTTC-AGAAAATTGCTCGAAGG
322 AAACTATTTAGACCAAATGATGTGATTTCCT-GAGCATGGAATGTTCGA-AAAATTGCTCGAAGG
* * * * *
309783 AAAGGATCGTCTTGAATGCTTTAAGGAACTGAAGTTATAAAAGAACTC
385 AATGGATCATCTTGAATACTTTAAGAAACAGAAGTTATAAAAGAACTC
* * * *
309831 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACC-A-ATAGAAACAATTCTCATGTAAA-A
1 GTAAAAGTTTTACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * * *
309893 AGGTTTTTAGTTCAAAGACCAAAACGTGTTTAGAAAATGAAAAACTATTTAGTCAAAAAGATGCG
66 A-GTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCG
* * * * ** * *
309958 ATTTCCCGTGCATGGAATGTTTC-GAAAATTGTTTGAAGGAATGTACCGTCTTGAATACTTTAAG
130 ATTTCCTGAGCATGAAATG-TTCAGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAG
* *
310022 GAATCGAAGTTATAAAATAACTCGTAAAAGTTTGACATGTTTGGAAGTTCGTCCAAGAACCAAGA
194 GAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACATGTTTGGAAGTTCGTCCAAGAACCAAGA
*
310087 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCATAACTTGTTTACAAAATGACAA
259 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAA
* *
310152 ACTATTTAGACCAAATGATGTGATTTCCTGAGCATGAAATGTTCGAAAAATTGCTCGAAGGAAGG
324 ACTATTTAGACCAAATGATGTGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATG
* * *
310217 GA-CGTCTTGAATACTTTAAGAAATAGAAGTTATAAAGGAACTC
389 GATCATCTTGAATACTTTAAGAAACAGAAGTTATAAAAGAACTC
* * * * * *
310260 GTAAAAGTTTTACTAGTTCGGAAGTTCTTCCACGAACCAAGATAGAAATAATTCTCACGTAAATA
1 GTAAAAGTTTTACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
*
310325 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATG-AAAACTATTTAGACAAAATGATGTGA
66 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCGA
* *
310389 TTTCCTGAGCATGGAATGTTCAGAAAATTGCTCAAAGGAATGGATTGTCTTGAATACTTTAAGGA
131 TTTCCTGAGCATGAAATGTTCAGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGA
* * * *
310454 ATCGAAGTTATAAACGAACTCGTAAAAGTTTGACATGTTTGGAAGTTTGTCCAAGAACAAAGAGA
196 ACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACATGTTTGGAAGTTCGTCCAAGAACCAAGAGA
* * * * *
310519 GAAACAATTCTCATGTAAATAAGTTTTTAGTTCAAAGACCAAAACTTATTAACAATATGACAAAC
261 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAAC
* * * * * * * *
310584 TATTTAGACCAACTGATGTGATTT-CTCGAGCATTGAATGTTTGGAAAATTACTCGATGGAAAGT
326 TATTTAGACCAAATGATGTGATTTCCT-GAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGG
* *
310648 ATCGTCTTGAATACTTTAAGGAACAGAAGTTATAAAAGAACTC
390 ATCATCTTGAATACTTTAAGAAACAGAAGTTATAAAAGAACTC
* * * **
310691 GTAAAAGTTTTACAAGTTCGGAAGTTCATCCAAGAATCAAGAGAGAAAGTATTCTCACGTAAATA
1 GTAAAAGTTTTACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * *
310756 AGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAACGAAAAACTATTTATACCAAATGATGCGA
66 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCGA
* * * * * *
310821 TTTCCCGAGCATGAAATGTTTAGAAAATTGCTCAAAGTAATGTACCATCTTGAATACTTTAAGGA
131 TTTCCTGAGCATGAAATGTTCAGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGA
* * * *
310886 ACCGAAGTTATAAAATAACTCATAAAAGTTTCACATGTTTGGAAGTTCGTCAAAGAACCAAGAGA
196 ACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACATGTTTGGAAGTTCGTCCAAGAACCAAGAGA
* * * * * *
310951 GACACTATTCTCACATAAATAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAAC
261 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAAC
* ** * * *
311016 TATTTAGACCAAATGATGCGATTTCCCAAGCATGAAATGTTCGAAAAATTGCTCAAAGAAATGGA
326 TATTTAGACCAAATGATGTGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGA
* *
311081 TCATCTTGACTACTTTAAGGAACCA-AAGTTATAAAAGAACTC
391 TCATCTTGAATACTTTAA-GAAACAGAAGTTATAAAAGAACTC
* * *
311123 ATAAAAGTTTTACGAA-TTTGGAAGTTTGTCCAAGAACCAAG-GAGAAACTATTCTCACG----T
1 GTAAAAGTTTTAC-AAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
* *
311182 -A------AA---AAAG--------TTATTTACAAAATGAAAAACTATATAGACAAAATGATGCG
65 AAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCG
* ** * *
311229 ATTT-TTCGAGCA-GTAAATGTTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATTCTTTAA
130 ATTTCCT-GAGCATG-AAATGTTCAGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAA
* * *
311292 GGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGAC-TAGTTCGGAAGTT-TTCCAAGAACC-A
193 GGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAT-GTTTGGAAGTTCGTCCAAGAACCAA
* * * * * *
311354 -ATAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAAATTTTTTTACAAAATGGC
257 GAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAC
* * *
311418 AAACTATTTAGACCAAATGAT-TCAATTT-CTCGAGAATGGAATGCTCGAAAAATTGCTCGAAGG
322 AAACTATTTAGACCAAATGATGT-GATTTCCT-GAGCATGGAATGTTCGAAAAATTGCTCGAAGG
* * *
311481 AATGG-TCCCCATCTTGTATAATTTAAGGAACCA-AAGTTATAAAAGAACTC
385 AATGGAT---CATCTTGAATACTTTAA-GAAACAGAAGTTATAAAAGAACTC
* * **
311531 GTAAAAGTTTGACATGTTTATAAGATT-GTCCAAGAACCAAGAGAGAAA-AATTTCTCACGTAAA
1 GTAAAAGTTTTACAAGTTTGGAAG-TTCGTCCAAGAACCAAGAGAGAAACAA-TTCTCACGTAAA
* ** * *
311594 TAAGTTTTTAATTGAAAGGTC-AAAGTTGTTTACAAAATGAAAAACTATTTTGACAAAATGATGC
64 TAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGC
* * *
311658 AATTTCCCGAGCATGAAATGTTC-GAAAAATTGCT-AAAGGAAAT-GATCATCTTGAATACTTTA
129 GATTTCCTGAGCATGAAATGTTCAG-AAAATTGCTCAAAGG-AATGGATCGTCTTGAATACTTTA
* * * * * * * *
311720 CGGAACCAAAGTTATAAAAGAACTCATAAAAATTGGACATGTATGGTAGTTCGTCCAAGAACTAA
192 AGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACATGTTTGGAAGTTCGTCCAAGAACCAA
* * ** * * *
311785 GAGAGAAACAATTCTTAGGTAAGCAAGTTTTTAAATAAAAGACTAAAACTTGTTTACAAAATGAC
257 GAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAC
* * * * *
311850 AAACTATTTAAACCAAATGATGTGATTTTCTAAGTATGGAATGTTCGAAAAATTTCTCGAAGGAA
322 AAACTATTTAGACCAAATGATGTGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAA
* * * * **
311915 TGGATCATCTTAAATACTTTAAGGAACCGAAGTTCTAAAAGAGTTC
387 TGGATCATCTTGAATACTTTAAGAAACAGAAGTTATAAAAGAACTC
* ** * * * *
311961 GTAAAAGTTTGACAAGTGCGGAAGTTCATCCAAGAACCAAGGGAAAAACAATTCTCATGTAAATA
1 GTAAAAGTTTTACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * *
312026 AGTTTTTAATTCAAAGACTAAAAACTTGTTTACAAAATGACAAACCATTTA-AAACAAATGATGC
66 AGTTTTTAATTCAAAGAC-CAAAACTTGTTTACAAAATGAAAAACTATTTAGACA-AAATGATGC
* * * * * * *
312090 GATTTCTTGAGCATGTAATGTTCGGAAAATTTCTCAAAGGAATGGATCATCCTGAATACTTTATG
129 GATTTCCTGAGCATGAAATGTTCAGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAG
* * * * * *
312155 AAACCGAAGTTATAAAAGAACTCATAAATGTTTGACAAGTTTGGAAGTTCATCCAAGAAACAAGA
194 GAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACATGTTTGGAAGTTCGTCCAAGAACCAAGA
* * * * * *
312220 GAGAAACAATTCTCAAGTAAATAAGTTTTTAATTCGAAGACAAAAAGTTGCTTACAAAATGAAAA
259 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAA
* * * * * * * * *
312285 ACTATTAAGACTAAATGATGCGATTTCCCGTGCATGAAATGTTCGAAAAATAGCTTGAAAGAATG
324 ACTATTTAGACCAAATGATGTGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATG
*** * *
312350 GATCATCTTGAATACTTTATTTAACTGAAGTTATAAAAAAACTC
389 GATCATCTTGAATACTTTAAGAAACAGAAGTTATAAAAGAACTC
* * * * *
312394 GTAAAAGTTTTACATGTTTTGAAGTTCGTCTAAGAAGCAAGAGAGAAACAATTCTCAAGTAAATA
1 GTAAAAGTTTTACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
*
312459 AGTTTTTAATTCAATGACCAAA
66 AGTTTTTAATTCAAAGACCAAA
312481 TGATGCGATT
Statistics
Matches: 2609, Mismatches: 382, Indels: 172
0.82 0.12 0.05
Matches are distributed among these distances:
405 2 0.00
406 109 0.04
407 2 0.00
408 81 0.03
409 145 0.06
413 1 0.00
414 1 0.00
417 4 0.00
420 4 0.00
423 4 0.00
426 9 0.00
427 255 0.10
428 142 0.05
429 169 0.06
430 680 0.26
431 213 0.08
432 487 0.19
433 301 0.12
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (432 bp):
GTAAAAGTTTTACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCGA
TTTCCTGAGCATGAAATGTTCAGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGA
ACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACATGTTTGGAAGTTCGTCCAAGAACCAAGAGA
GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAAC
TATTTAGACCAAATGATGTGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGA
TCATCTTGAATACTTTAAGAAACAGAAGTTATAAAAGAACTC
Found at i:311323 original size:193 final size:190
Alignment explanation
Indices: 310991--311385 Score: 549
Period size: 193 Copynumber: 2.1 Consensus size: 190
310981 TTCAAAGACC
* *
310991 AAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGAAATGT
1 AAAAGTT-TTTACAAAATGAAAAACTATATAGACAAAATGATGCGATTTCCCAAGCATGAAATGT
*
311056 TCGAAAAATTGCTCAAAGAAATGGATCATCTTGACTACTTTAAGGAACCAAAGTTATAAAAGAAC
65 TCGAAAAATTGCTCAAAGAAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAAC
* * *
311121 TCATAAAAGTTTTACGAATTTGGAAGTTTGTCCAAGAACCAAGGAGAAACTATTCTCACGTAA
130 TCATAAAAGTTTGACGAATTCGGAAGTTT-TCCAAGAACCAA-GAGAAACAATTCTCACGTAA
** *
311184 AAAAGTTATTTACAAAATGAAAAACTATATAGACAAAATGATGCGATTTTTCGAGCA-GTAAATG
1 AAAAGTT-TTTACAAAATGAAAAACTATATAGACAAAATGATGCGATTTCCCAAGCATG-AAATG
* * * * * *
311248 TTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATTCTTTAAGGAACCAAAGTTATAAAAGAA
64 TTCGAAAAATTGCTCAAAGAAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAA
* * * * *
311313 CTCGTAAAAGTTTGACTAGTTCGGAAGTTTTCCAAGAACCAATAGAAACAATTCTCATGTAA
129 CTCATAAAAGTTTGACGAATTCGGAAGTTTTCCAAGAACCAAGAGAAACAATTCTCACGTAA
*
311375 ATAAGTTTTTA
1 AAAAGTTTTTA
311386 ATTCAAAAAC
Statistics
Matches: 179, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
190 4 0.02
191 23 0.13
192 13 0.07
193 139 0.78
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (190 bp):
AAAAGTTTTTACAAAATGAAAAACTATATAGACAAAATGATGCGATTTCCCAAGCATGAAATGTT
CGAAAAATTGCTCAAAGAAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACT
CATAAAAGTTTGACGAATTCGGAAGTTTTCCAAGAACCAAGAGAAACAATTCTCACGTAA
Found at i:312893 original size:216 final size:214
Alignment explanation
Indices: 312508--312965 Score: 585
Period size: 216 Copynumber: 2.1 Consensus size: 214
312498 CATGAAGAAA
* *
312508 TGCTCGAAGGAATGGATCGTCTTGATTACTTTAAGGAAACAAAGTTATAAAAGAATTCATAAAAG
1 TGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAACAAAGTTATAAAAGAACTCATAAAAG
* * * *
312573 ATTCACAAAATGAAAGTTCGTCAAGAACCAAGAGAGAAAATATTCCCACGTAATTAAGTTTTTAA
66 ATTCACAAAATGAAAGTTCGTCAAGAACCAAGAAAGAAAATATTCCCACGCAAATAAATTTTTAA
* *
312638 CTCAAACATCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCGATTTCCCA-A
131 CTCAAACACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCGATTT-CCAGA
*
312702 GCATGAAATGTTAAGAAAAT
195 GCATGAAATATTAAGAAAAT
* * * * * *
312722 TGCTCGAAGGAATGTATCGACTTAAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAG
1 TGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAACAAAGTTATAAAAGAACTCATAAAAG
* * *** * * * * * * *
312787 TTTGACATGTTTGGATGTTCATTCAAGAACTAAGAAAGACACTATTCTCACGCAAATAAATTTTT
66 ATTCACA-AAATGAAAGTTC-GTCAAGAACCAAGAAAGAAAATATTCCCACGCAAATAAATTTTT
* * * * *
312852 AATTCAAAGACCAAACCTTGTTTACAAAATGAAAAACTATTTAGACCAAATTATGCGATTTCCAG
129 AACTCAAACACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCGATTTCCAG
*
312917 AGCATGAAATATTCAGAAAAT
194 AGCATGAAATATTAAGAAAAT
312938 TGCTCGAAGGAATGGATCGTCTTGAATA
1 TGCTCGAAGGAATGGATCGTCTTGAATA
312966 GATATGAGTC
Statistics
Matches: 205, Mismatches: 36, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
214 62 0.30
215 10 0.05
216 133 0.65
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (214 bp):
TGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAACAAAGTTATAAAAGAACTCATAAAAG
ATTCACAAAATGAAAGTTCGTCAAGAACCAAGAAAGAAAATATTCCCACGCAAATAAATTTTTAA
CTCAAACACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACAAAATGATGCGATTTCCAGAG
CATGAAATATTAAGAAAAT
Done.