Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011850.1 Kokia drynarioides strain JFW-HI SEQ_126846, 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: 97776
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:529 original size:95 final size:93
Alignment explanation
Indices: 423--1291 Score: 1247
Period size: 95 Copynumber: 9.3 Consensus size: 93
413 TGGTTTCGAC
* *
423 AATAATATTTTTTATTTAAATAATTTTAAATTTTGAATTTGGTAAAAAAGGAATTGTAAAATCAA
1 AATAAT-TTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAAAAA-GAATTGTCAAATCAA
*
488 CATATTATTTGATAAAAATTAAAATATTAT
64 CACATTATTTGATAAAAATTAAAATATTAT
* * * *
518 AATAACTTTTTTATTTAAATAATTTTAAAATTTGAATTTAGTAAATAATGTATTGTCAAATCAAC
1 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAA-AAAGAATTGTCAAATCAAC
*
583 ACATTATTTGATAAAAATTGAAATATTAT
65 ACATTATTTGATAAAAATTAAAATATTAT
*
612 AATAA-TTTTTTATTTAAATAATTTTAAAATTTGAATTTGGT-AAAAA-AATTATCAAATCAACA
1 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAAAAAGAATTGTCAAATCAACA
*
674 CATTATTTGATAAAAATTATAATATTAT
66 CATTATTTGATAAAAATTAAAATATTAT
* *
702 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGATAAAGAAAGAATTGTCAAATCAAT
1 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAA-AAAGAATTGTCAAATCAAC
* *
767 ATATTATTTGATAAAAATTGAAATATTAT
65 ACATTATTTGATAAAAATTAAAATATTAT
* * * *
796 AATAA-TTTTTTATTTAAATACTTTTAAATTTTGAATTTGGTAAATAATGTATTGTCAAATCAAC
1 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAA-AAAGAATTGTCAAATCAAC
860 ACATTATTTGATAAAAATTAAAATATTAT
65 ACATTATTTGATAAAAATTAAAATATTAT
889 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAGAAAAAGAATTGTCAAATCAA
1 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGT-A-AAAAAGAATTGTCAAATCAA
* *
954 CACATCATTTGATAAAAATTGAAATATTAT
64 CACATTATTTGATAAAAATTAAAATATTAT
* * *
984 AATAATTTTTTTATTTAAATAATTATAAAATTTGAATTTGATGAAAAAA-AATTTTATCAAATCA
1 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGT-AAAAAAGAA--TTGTCAAATCA
*
1048 ACACATTATTCGATAAAAATTAAAATA-T-T
63 ACACATTATTTGATAAAAATTAAAATATTAT
* * *
1077 -ATAA---TTTTATTTAAATAATTTTAAATTTTGAATTTGATAAAAAAAGAATTGTTAAATCAAC
1 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGT-AAAAAAGAATTGTCAAATCAAC
*
1138 ACATTATTTGATAAAAATTTAAATATTAT
65 ACATTATTTGATAAAAATTAAAATATTAT
***
1167 AATAATCTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAATAATTTATTGTCAAATCAA
1 AATAAT-TTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAA-AAAGAATTGTCAAATCAA
1232 CACATTATTTGATAAAAATTAAAATATTAT
64 CACATTATTTGATAAAAATTAAAATATTAT
*
1262 AATAATTGTTTTTATTTAAATAATGTTAAA
1 AATAATT-TTTTTATTTAAATAATTTTAAA
1292 TTAATTTTAA
Statistics
Matches: 697, Mismatches: 57, Indels: 40
0.88 0.07 0.05
Matches are distributed among these distances:
88 34 0.05
89 39 0.06
90 48 0.07
91 41 0.06
92 8 0.01
93 125 0.18
94 171 0.25
95 229 0.33
96 2 0.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (93 bp):
AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAAAAAGAATTGTCAAATCAACA
CATTATTTGATAAAAATTAAAATATTAT
Found at i:759 original size:184 final size:185
Alignment explanation
Indices: 424--1291 Score: 1286
Period size: 184 Copynumber: 4.7 Consensus size: 185
414 GGTTTCGACA
* *
424 ATAAT-ATTTTTTATTTAAATAATTTTAAATTTTGAATTTGGTAAAAAAGGAATTGTAAAATCAA
1 ATAATAATTTTTTATTTAAATAATTTTAAAATTTGAATTTGGT-AAAAA-GAATTGTCAAATCAA
* *
488 CATATTATTTGATAAAAATTAAAATATTATAATAACTTTTTTATTTAAATAATTTTAAAATTTGA
64 CACATTATTTGATAAAAATTAAAATATTATAATAATTTTTTTATTTAAATAATTTTAAAATTTGA
* * *
553 ATTT-AGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATT
129 ATTTGA-TAAAAAAAGAATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATT
*
610 ATAATAATTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAAAA-AATTATCAAATCAACA
1 ATAATAATTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAAAAGAATTGTCAAATCAACA
*
674 CATTATTTGATAAAAATTATAATATTATAATAATTTTTTTATTTAAATAATTTTAAAATTTGAAT
66 CATTATTTGATAAAAATTAAAATATTATAATAATTTTTTTATTTAAATAATTTTAAAATTTGAAT
* * *
739 TTGATAAAGAAAGAATTGTCAAATCAATATATTATTTGATAAAAATTGAAATATT
131 TTGATAAAAAAAGAATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATT
* * *
794 ATAATAATTTTTTATTTAAATACTTTTAAATTTTGAATTTGGTAAATAATGTATTGTCAAATCAA
1 ATAATAATTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAA-AA-GAATTGTCAAATCAA
859 CACATTATTTGATAAAAATTAAAATATTATAATAATTTTTTTATTTAAATAATTTTAAAATTTGA
64 CACATTATTTGATAAAAATTAAAATATTATAATAATTTTTTTATTTAAATAATTTTAAAATTTGA
* *
924 ATTTGGTAAGAAAAAGAATTGTCAAATCAACACATCATTTGATAAAAATTGAAATATT
129 ATTTGATAA-AAAAAGAATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATT
* * * *
982 ATAATAATTTTTTTATTTAAATAATTATAAAATTTGAATTTGATGAAAAAAAATTTTATCAAATC
1 ATAATAA-TTTTTTATTTAAATAATTTTAAAATTTGAATTTGGT-AAAAAGAA--TTGTCAAATC
* *
1047 AACACATTATTCGATAAAAATTAAAATA-T-T-ATAA---TTTTATTTAAATAATTTTAAATTTT
62 AACACATTATTTGATAAAAATTAAAATATTATAATAATTTTTTTATTTAAATAATTTTAAAATTT
* *
1106 GAATTTGATAAAAAAAGAATTGTTAAATCAACACATTATTTGATAAAAATTTAAATATT
127 GAATTTGATAAAAAAAGAATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATT
**
1165 ATAATAATCTTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAATAATTTATTGTCAAATC
1 ATAATAA--TTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAA-AA-GAATTGTCAAATC
*
1230 AACACATTATTTGATAAAAATTAAAATATTATAATAATTGTTTTTATTTAAATAATGTTAAA
62 AACACATTATTTGATAAAAATTAAAATATTATAATAATT-TTTTTATTTAAATAATTTTAAA
1292 TTAATTTTAA
Statistics
Matches: 620, Mismatches: 42, Indels: 36
0.89 0.06 0.05
Matches are distributed among these distances:
183 91 0.15
184 239 0.39
185 5 0.01
186 14 0.02
187 124 0.20
188 53 0.09
189 35 0.06
190 59 0.10
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (185 bp):
ATAATAATTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAAAAGAATTGTCAAATCAACA
CATTATTTGATAAAAATTAAAATATTATAATAATTTTTTTATTTAAATAATTTTAAAATTTGAAT
TTGATAAAAAAAGAATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATT
Found at i:925 original size:278 final size:276
Alignment explanation
Indices: 423--1291 Score: 1302
Period size: 278 Copynumber: 3.1 Consensus size: 276
413 TGGTTTCGAC
* * *
423 AATAATATTTTTTATTTAAATAATTTTAAATTTTGAATTTGGTAAAAAAGGAATTGTAAAATCAA
1 AATAAT-TTTTTTATTTAAATAATTTTAAAATTTGAATTTGATAAAAAA-GAATTGTCAAATCAA
*
488 CATATTATTTGATAAAAATTAAAATATTATAATAACTTTTTTATTTAAATAATTTTAAAATTTGA
64 CATATTATTTGATAAAAATT-AAATATTATAATAA-TTTTTTATTTAAATAATTTTAAATTTTGA
* *
553 ATTTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAA-
127 ATTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATAAT
*
617 TTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAAAA-AATTATCAAATCAACACATTATT
192 TTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAAAATAATTGTCAAATCAACACATTATT
681 TGATAAAAATTATAATATTAT
257 TGATAAAAATTA-AATATTAT
*
702 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGATAAAGAAAGAATTGTCAAATCAAT
1 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGATAAA-AAAGAATTGTCAAATCAAC
*
767 ATATTATTTGATAAAAATTGAAATATTATAATAATTTTTTATTTAAATACTTTTAAATTTTGAAT
65 ATATTATTTGATAAAAATT-AAATATTATAATAATTTTTTATTTAAATAATTTTAAATTTTGAAT
832 TTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATAATTT
129 TTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATAATTT
* *
897 TTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAGAAAAAGAATTGTCAAATCAACACATCAT
194 TTTTATTTAAATAATTTTAAAATTTGAATTTGGT---AAAAATAATTGTCAAATCAACACATTAT
962 TTGATAAAAATTGAAATATTAT
256 TTGATAAAAATT-AAATATTAT
* *
984 AATAATTTTTTTATTTAAATAATTATAAAATTTGAATTTGATGAAAAAA-AATTTTATCAAATCA
1 AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGAT-AAAAAAGAA--TTGTCAAATCA
* * *
1048 ACACATTATTCGATAAAAATTAAA-A-TATTATAA--TTTTATTTAAATAATTTTAAATTTTGAA
63 ACATATTATTTGATAAAAATTAAATATTATAATAATTTTTTATTTAAATAATTTTAAATTTTGAA
* * * * * *
1109 TTTGATAAAAAAAGAATTGTTAAATCAACACATTATTTGATAAAAATTTAAATATTATAATAATC
128 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATAAT-
*
1174 TTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAATAATTTATTGTCAAATCAACACATTA
192 TTTTTTATTTAAATAATTTTAAAATTTGAATTTGGTAAA-AA-TAATTGTCAAATCAACACATTA
1239 TTTGATAAAAATTAAAATATTAT
255 TTTGATAAAAATT-AAATATTAT
*
1262 AATAATTGTTTTTATTTAAATAATGTTAAA
1 AATAATT-TTTTTATTTAAATAATTTTAAA
1292 TTAATTTTAA
Statistics
Matches: 546, Mismatches: 30, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
276 3 0.01
277 91 0.17
278 253 0.46
279 65 0.12
280 7 0.01
281 8 0.01
282 87 0.16
283 32 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (276 bp):
AATAATTTTTTTATTTAAATAATTTTAAAATTTGAATTTGATAAAAAAGAATTGTCAAATCAACA
TATTATTTGATAAAAATTAAATATTATAATAATTTTTTATTTAAATAATTTTAAATTTTGAATTT
GGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATAATTTTT
TTATTTAAATAATTTTAAAATTTGAATTTGGTAAAAATAATTGTCAAATCAACACATTATTTGAT
AAAAATTAAATATTAT
Found at i:1310 original size:12 final size:11
Alignment explanation
Indices: 1276--1313 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1266 ATTGTTTTTA
1276 TTTAAA-TAAT
1 TTTAAATTAAT
*
1286 GTTAAATTAAT
1 TTTAAATTAAT
1297 TTTAAATGTAAT
1 TTTAAAT-TAAT
1309 TTTAA
1 TTTAA
1314 TTTCAACTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 5 0.21
11 10 0.42
12 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (11 bp):
TTTAAATTAAT
Found at i:5373 original size:58 final size:58
Alignment explanation
Indices: 5264--5375 Score: 131
Period size: 58 Copynumber: 1.9 Consensus size: 58
5254 AATTTGTTTC
* * *
5264 TTTTATCAGATAAATAAGGTGGTGTCGACCAAACAATGACCAACACCCAAAAAAATAT
1 TTTTATCAGATAAATAAGCTGGTGTCAACCAAACAATGACCAACACACAAAAAAATAT
* *
5322 TTTTATCTGATAAATAAATGCTGGTGTCAACCAATGC-ATGA-CAA-ACACAAAAAA
1 TTTTATCAGATAAAT-AA-GCTGGTGTCAACCAA-ACAATGACCAACACACAAAAAA
5376 GTTGAACTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
58 23 0.50
59 5 0.11
60 17 0.37
61 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (58 bp):
TTTTATCAGATAAATAAGCTGGTGTCAACCAAACAATGACCAACACACAAAAAAATAT
Found at i:5525 original size:57 final size:57
Alignment explanation
Indices: 5442--5604 Score: 197
Period size: 57 Copynumber: 2.8 Consensus size: 57
5432 AAAATTTTTG
* * * * *
5442 CATTTTTTATTATACAAAAAGGTGGTGTCGGCCAA-GCAATGATCAACAAAAAAAAAAT
1 CATTTTTTATTAGATAAAAATGTGGTGTCGACCAATGC-ATGACCAAC-AAAAAAAAAT
*
5500 -ATTTTTTATCTA-ATAAAAATGTGGTGTCGACCAATGCATGACCAACACAAAAAAAT
1 CATTTTTTAT-TAGATAAAAATGTGGTGTCGACCAATGCATGACCAACAAAAAAAAAT
* *
5556 CATTTTTTATTAGATAAAAAATGTGGTGTCGATCAATGCATGGCCAACA
1 CATTTTTTATTAGAT-AAAAATGTGGTGTCGACCAATGCATGACCAACA
5605 TCAATTTTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
56 11 0.12
57 47 0.51
58 35 0.38
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (57 bp):
CATTTTTTATTAGATAAAAATGTGGTGTCGACCAATGCATGACCAACAAAAAAAAAT
Found at i:5580 original size:58 final size:57
Alignment explanation
Indices: 5155--5604 Score: 256
Period size: 62 Copynumber: 7.5 Consensus size: 57
5145 GAAAGGAGAG
* * **
5155 AAAGTTGGTGTCGACTAATAAATGACC-ACATCAAAAAAATTTATTTTTTTAATCT-GATTAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACA-CAAAAAAA--TA-TTTTTT-AT-TAGA-TAAA
* ** * * *
5217 AAAGGTGGTGTCGACCAATGTATGGTCAACACCAAAAAATTTGTTTCTTTTATCAGATAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACA-CAAAAAA-AT-ATT-TTTTATTAGATAAA
* *
5278 TAAGGTGGTGTCGACCAA-ACAATGACCAACACCCAAAAAAATA-TTTTTATCT-GATAAA
1 AAAGGTGGTGTCGACCAATGC-ATGACCAACA--CAAAAAAATATTTTTTAT-TAGATAAA
* * * * * *
5336 TAAATGCTGGTGTCAACCAATGCATGACAAACACAAAAAAGTTGAACTTTTTATCAGATAAA
1 -AAA-GGTGGTGTCGACCAATGCATGACCAACACAAAAAA-AT--ATTTTTTATTAGATAAA
* * * ** * *
5398 AAAGGCGATATCGGTCAA-GCAATGGCCAACACAAAAAATTTTTGCATTTTTTATT--ATACAA
1 AAAGGTGGTGTCGACCAATGC-ATGACCAACACAAAAAA---AT--ATTTTTTATTAGATA-AA
* * *
5459 AAAGGTGGTGTCGGCCAA-GCAATGATCAACAAAAAAAAAATATTTTTTATCTA-AT-AA
1 AAAGGTGGTGTCGACCAATGC-ATGACCAAC-ACAAAAAAATATTTTTTAT-TAGATAAA
*
5516 AAATGTGGTGTCGACCAATGCATGACCAACACAAAAAAATCATTTTTTATTAGATAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACAAAAAAAT-ATTTTTTATTAGATAAA
* * *
5574 AAATGTGGTGTCGATCAATGCATGGCCAACA
1 AAAGGTGGTGTCGACCAATGCATGACCAACA
5605 TCAATTTTTT
Statistics
Matches: 309, Mismatches: 52, Indels: 58
0.74 0.12 0.14
Matches are distributed among these distances:
56 11 0.04
57 46 0.15
58 53 0.17
59 9 0.03
60 48 0.16
61 61 0.20
62 67 0.22
63 14 0.05
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (57 bp):
AAAGGTGGTGTCGACCAATGCATGACCAACACAAAAAAATATTTTTTATTAGATAAA
Found at i:23809 original size:44 final size:45
Alignment explanation
Indices: 23760--23849 Score: 173
Period size: 44 Copynumber: 2.0 Consensus size: 45
23750 TTGAATTAAT
23760 TAAGTTATTCGAATTAACTCAAAT-AAAAAAATTAAATTTTTTGG
1 TAAGTTATTCGAATTAACTCAAATAAAAAAAATTAAATTTTTTGG
23804 TAAGTTATTCGAATTAACTCAAATAAAAAAAATTAAATTTTTTGG
1 TAAGTTATTCGAATTAACTCAAATAAAAAAAATTAAATTTTTTGG
23849 T
1 T
23850 TTAACTCGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 24 0.53
45 21 0.47
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (45 bp):
TAAGTTATTCGAATTAACTCAAATAAAAAAAATTAAATTTTTTGG
Found at i:24740 original size:30 final size:30
Alignment explanation
Indices: 24706--24852 Score: 115
Period size: 29 Copynumber: 5.0 Consensus size: 30
24696 TATGTTTCAC
* *
24706 CCCTTAACTTTTTAAAAATTACATTTTGAA
1 CCCTAAACTTTTCAAAAATTACATTTTGAA
* * *
24736 CCCTTAAC-TTTCCAAAATTATA-TTTG-A
1 CCCTAAACTTTTCAAAAATTACATTTTGAA
* * *
24763 CACTCGAACTTTCCAAAAATTACATTTT-AA
1 CCCT-AAACTTTTCAAAAATTACATTTTGAA
* * *
24793 CCCCTAAAATTTTTCTAGAATTACATTTT-AA
1 -CCCT-AAACTTTTCAAAAATTACATTTTGAA
* *
24824 CCCTAAACTTTTCCAAAATTATATTTTGA
1 CCCTAAACTTTTCAAAAATTACATTTTGA
24853 CCTCGAACTC
Statistics
Matches: 92, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
27 4 0.04
28 7 0.08
29 41 0.45
30 17 0.18
31 23 0.25
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.40
Consensus pattern (30 bp):
CCCTAAACTTTTCAAAAATTACATTTTGAA
Found at i:24760 original size:29 final size:28
Alignment explanation
Indices: 24670--24850 Score: 105
Period size: 29 Copynumber: 6.1 Consensus size: 28
24660 TATAATCGCG
* * *
24670 TTTTAACCCTTAAACTGTCCAAAA-AATA
1 TTTTAACCCTT-AACTTTCCAAAATTACA
* **
24698 TGTTTCACCCCTTAACTTTTTAAAAATTACA
1 T-TTT-AACCCTTAAC-TTTCCAAAATTACA
*
24729 TTTTGAACCCTTAACTTTCCAAAATTATA
1 TTTT-AACCCTTAACTTTCCAAAATTACA
* * *
24758 -TTTGACACTCGAACTTTCCAAAAATTACA
1 TTTTAACCCT-TAACTTTCC-AAAATTACA
* * * *
24787 TTTTAACCCCTAAAATTTTTCTAGAATTACA
1 TTTTAA-CCCT-TAA-CTTTCCAAAATTACA
* *
24818 TTTTAACCCTAAACTTTTCCAAAATTATA
1 TTTTAACCCTTAAC-TTTCCAAAATTACA
24847 TTTT
1 TTTT
24851 GACCTCGAAC
Statistics
Matches: 117, Mismatches: 26, Indels: 19
0.72 0.16 0.12
Matches are distributed among these distances:
27 4 0.03
28 12 0.10
29 43 0.37
30 32 0.27
31 22 0.19
32 4 0.03
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTTAACCCTTAACTTTCCAAAATTACA
Found at i:24861 original size:29 final size:29
Alignment explanation
Indices: 24711--24888 Score: 100
Period size: 29 Copynumber: 6.1 Consensus size: 29
24701 TTCACCCCTT
** *
24711 AACTTTTTAAAAATTACATTTTGAACC-CTT
1 AACTTTTCCAAAATTACATTTTG-ACCTC-G
*
24741 AAC-TTTCCAAAATTATA-TTTGACACTCG
1 AACTTTTCCAAAATTACATTTTGAC-CTCG
* **
24769 AAC-TTTCCAAAAATTACATTTTAACCCCTAA
1 AACTTTTCC-AAAATTACATTTTGA--CCTCG
* * * * *
24800 AATTTTTCTAGAATTACATTTTAACC-CTA
1 AACTTTTCCAAAATTACATTTTGACCTC-G
*
24829 AACTTTTCCAAAATTATATTTTGACCTCG
1 AACTTTTCCAAAATTACATTTTGACCTCG
*
24858 AACTCTCTT--AAAATTACATTTTGGCCTCG
1 AACT-T-TTCCAAAATTACATTTTGACCTCG
24887 AA
1 AA
24889 ATTCTTCGAA
Statistics
Matches: 117, Mismatches: 20, Indels: 23
0.73 0.12 0.14
Matches are distributed among these distances:
27 2 0.02
28 13 0.11
29 68 0.58
30 9 0.08
31 20 0.17
32 5 0.04
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (29 bp):
AACTTTTCCAAAATTACATTTTGACCTCG
Found at i:32940 original size:17 final size:16
Alignment explanation
Indices: 32911--32955 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
32901 AAAATAAATA
32911 AAAAGAAAGAAAAAAGG
1 AAAA-AAAGAAAAAAGG
32928 AAAAAAAGTAAAAAA-G
1 AAAAAAAG-AAAAAAGG
*
32944 TAAAAAAGAAAA
1 AAAAAAAGAAAA
32956 GGAGAGGTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 4 0.15
16 12 0.46
17 10 0.38
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAAAAAAGG
Found at i:34157 original size:49 final size:48
Alignment explanation
Indices: 34055--34162 Score: 110
Period size: 49 Copynumber: 2.2 Consensus size: 48
34045 AATGTAATGG
* * * * *
34055 GAAAGGTTGAGACCGTAACGGCGAACTTGGTACTATGAAGATTTGAAGG
1 GAAAGGTTGAGACCGTAACAGCGAACCTGGTACTAGGAACA-TTGAAGA
* *
34104 GAAAGGTTGAGGCCGTAACAGCGAACCTGGTACCTTAGGAACA-TGACGA
1 GAAAGGTTGAGACCGTAACAGCGAACCTGGTA-C-TAGGAACATTGAAGA
*
34153 GAAAGATTGA
1 GAAAGGTTGA
34163 AGCCTCAACG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
49 42 0.86
50 1 0.02
51 6 0.12
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.19
Consensus pattern (48 bp):
GAAAGGTTGAGACCGTAACAGCGAACCTGGTACTAGGAACATTGAAGA
Found at i:34458 original size:39 final size:39
Alignment explanation
Indices: 34377--34881 Score: 413
Period size: 39 Copynumber: 13.0 Consensus size: 39
34367 GTTACGTCAT
* ** * *
34377 CATCCAATCTCTTACCCCAATCAT-GGGCATTTTACAGT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * *
34415 CATCCATTCTCTTACCCCGATCATGGGGCAGGTTACAGC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * *
34454 CATCCAATCGCTTACGCCGATCATGGGGCAGATTGTATC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * *
34493 CATCCCATCTCTAACCCCAATCATGGGGCAGATTGTAGC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * * * * **
34532 CACCCGATCTTTTACCCTGATCATAGGGCAGATTGTATT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* *
34571 CATCCCATCTCTTACCCCGATCATGGGGCAGATTGTAGC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * * * *
34610 CACCCGATCTTTTACCCTGATCATGGGGCAGATTACAAC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* *
34649 CATCCAATCTCTTACCCCGATCATGAGGCAGATTGCAAC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * ** * * * *
34688 CACCCGATCTTTTACCCTAATCATAGGGCATATTACAAC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * *
34727 CATCCAATCTCTTACCTCGATCATGAGGCAAATTGCAAC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * **
34766 CATTCAATCTTTTACCCCGATCATAAGGCAGATTAG-AGC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATT-GCAGC
** * * * * * * * *
34805 CA-CTTGATTTTTTACGCCAATCATGAGGTAAATTGCAGT
1 CATC-CAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
*
34844 CATCCAATCTCTTACCCCGATCACGGGGCAGATTGCAG
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAG
34882 TCATATGAAG
Statistics
Matches: 370, Mismatches: 92, Indels: 9
0.79 0.20 0.02
Matches are distributed among these distances:
38 23 0.06
39 345 0.93
40 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (39 bp):
CATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
Found at i:35168 original size:160 final size:160
Alignment explanation
Indices: 34904--35252 Score: 459
Period size: 160 Copynumber: 2.2 Consensus size: 160
34894 ATAAAGTGGT
** * * * **
34904 CATCTTCCTGACGAGATGCAGAGAAGTGAACCAAA-TCTATCTTTTTGATGAGATACAAAGAAGT
1 CATCTTCCTGATAAGATACAGAGAAGTGGACCAAATTC-GTCTTCCTGATGAGATACAAAGAAGT
* * * * *
34968 GGATTGAAACAATGAGACGGTTATCTTTCTGATGAGATACAAAGAAGTAGACCAAATCAATGAAG
65 GGATTGAAACAATGAGACAGTCATCTTTCTAATGAGATACAAAGAAGTAGACCAAATCAATAAAA
*
35033 CAAAGCTCAATACGAATGAGACTTCAAACCC
130 CAAAGCTCAATACGAATGAAACTTCAAACCC
* *
35064 CATCTTCTTGATAAGATACAGATAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTG
1 CATCTTCCTGATAAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTG
* * * *
35129 GATTGAAACAATGAGGCAGTCATCCTTT-TAATGAGATACAGATAAGTAGACCAAATTAATAAAA
66 GATTGAAACAATGAGACAGTCAT-CTTTCTAATGAGATACAAAGAAGTAGACCAAATCAATAAAA
* * *
35193 CGAAGCTCAATACGAATGAAACTTCAAGCCT
130 CAAAGCTCAATACGAATGAAACTTCAAACCC
*
35224 CATCTTCCTGATGAGATACAGAGAAGTGG
1 CATCTTCCTGATAAGATACAGAGAAGTGG
35253 GTCAAAACAA
Statistics
Matches: 162, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
160 156 0.96
161 6 0.04
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (160 bp):
CATCTTCCTGATAAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTG
GATTGAAACAATGAGACAGTCATCTTTCTAATGAGATACAAAGAAGTAGACCAAATCAATAAAAC
AAAGCTCAATACGAATGAAACTTCAAACCC
Found at i:35327 original size:208 final size:207
Alignment explanation
Indices: 35064--35928 Score: 1111
Period size: 207 Copynumber: 4.2 Consensus size: 207
35054 CTTCAAACCC
* * *
35064 CATCTTCTTGATAAGATACAGATAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTG
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTG
* * * *
35129 GATTGAAA-CAATGAGGC-AGTCATCCTT-TTAATGAGATACAGATAAGTAGACCAAATTAATAA
66 GATT-AAATCAATGAGGCGA-TCAT-CTTCCTAATAAGA-ACAGAGAAGTAGACCAAATCAATAA
* * * *
35191 AACGAAGCTCAATACGAATGAAACTTC-AAGCCTCATCTTCCTGATGAGATACAGAGAAGTGGGT
127 AGCAAAGCTCAATACGAATGAAACTTCGAA-CCTCATCTTCCTGATAAGATACAAAGAAGTGGGT
*
35255 CAAAACAATAAAGCGAT
191 CAAAGCAATAAAGCGAT
* * *
35272 CATCTTCTTGATGAGATACAAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAAAGAAGTG
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTG
*
35337 GATTGAAA-CAATGAGACGATCATCTTCCTAATAAGATACAGAGAAGTAGACCAAATCAATAAAG
66 GATT-AAATCAATGAGGCGATCATCTTCCTAATAAGA-ACAGAGAAGTAGACCAAATCAATAAAG
* * * *
35401 CAAAACTCAATACAAATGAAACTTC-ATACCTCATCTTCCTGATGAGATACAAAGAAGTGGGTTA
129 CAAAGCTCAATACGAATGAAACTTCGA-ACCTCATCTTCCTGATAAGATACAAAGAAGTGGGTCA
*
35465 AAGCAATAAAACGAT
193 AAGCAATAAAGCGAT
* * * * * *
35480 CATCTTCCTGATGAGATACAGAGAAGTAGACAAAATCCGCCTTCCTGCTGAGATACGGAA-AAGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC-AAAGAAGT
* * * * *
35544 GGATTAAATCAATGAGGCGATCATCTTCTTGATAAGAACAGAGAAGTGGACCAAATCAATGAAGT
65 GGATTAAATCAATGAGGCGATCATCTTCCTAATAAGAACAGAGAAGTAGACCAAATCAATAAAGC
* * * * *
35609 GAAGCTCAATACGAATGAGACTTCGAACCCCATCTTCCTGATAAGATATAGAGAAGTGGGTCAAA
130 AAAGCTCAATACGAATGAAACTTCGAACCTCATCTTCCTGATAAGATACAAAGAAGTGGGTCAAA
* *
35674 GCAATAAAGTGGT
195 GCAATAAAGCGAT
* * * *
35687 CATCTTCCTAATGAGATACAGAGAAGTGGACCAAA-TCTGCCTTCCTAATGAGATACAGAGAAGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAATTC-GTCTTCCTGATGAGATACAAAGAAGT
* *
35751 GGATTAAATCAATGAGGC-ATTCATCTTCCTAATAAGACCAGAGAAGTAGACCAAATCAATGAAG
65 GGATTAAATCAATGAGGCGA-TCATCTTCCTAATAAGAACAGAGAAGTAGACCAAATCAATAAAG
* *
35815 CAAAGCTCAATACGAATGAGACTTCGAACCTCATCTTCTTGATAAGATACAAAGAAGTGGGTCAA
129 CAAAGCTCAATACGAATGAAACTTCGAACCTCATCTTCCTGATAAGATACAAAGAAGTGGGTCAA
*
35880 AGCAATAAAGCGGT
194 AGCAATAAAGCGAT
* *
35894 CATCTTCCTGATGA-AAACAGAGAAGTAGACCAAAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAT
35929 CAATAAAGCA
Statistics
Matches: 581, Mismatches: 66, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
206 21 0.04
207 290 0.50
208 266 0.46
209 4 0.01
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.23
Consensus pattern (207 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTG
GATTAAATCAATGAGGCGATCATCTTCCTAATAAGAACAGAGAAGTAGACCAAATCAATAAAGCA
AAGCTCAATACGAATGAAACTTCGAACCTCATCTTCCTGATAAGATACAAAGAAGTGGGTCAAAG
CAATAAAGCGAT
Found at i:35374 original size:85 final size:85
Alignment explanation
Indices: 35223--35392 Score: 234
Period size: 85 Copynumber: 2.0 Consensus size: 85
35213 ACTTCAAGCC
* * * * *
35223 TCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATAAAGCGATCATCTTCTTGATGAGA
1 TCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTAATAAGA
*
35288 TACAAAGAAGTGGACCAAAT
66 TACAAAGAAGTAGACCAAAT
** *
35308 TCATCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAAT-GAGACGATCATCTTCCTAATAAG
1 TCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATAAAG-CGATCATCTTCCTAATAAG
*
35372 ATACAGAGAAGTAGACCAAAT
65 ATACAAAGAAGTAGACCAAAT
35393 CAATAAAGCA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 2 0.03
85 72 0.97
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (85 bp):
TCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTAATAAGA
TACAAAGAAGTAGACCAAAT
Found at i:35565 original size:85 final size:84
Alignment explanation
Indices: 35435--35600 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 84
35425 CATACCTCAT
* *
35435 CTTCCTGATGAGATACAAAGAAGTGGGTTAAAGCAATAAAACGATCATCTTCCTGATGAGATACA
1 CTTCCTGATGAGATACAAAGAAGTGGATTAAAGCAATAAAACGATCATCTTCCTGATAAGA-ACA
35500 GAGAAGTAGACAAAATCCGC
65 GAGAAGTAGACAAAATCCGC
* * * * ** *
35520 CTTCCTGCTGAGATACGGAA-AAGTGGATTAAATCAATGAGGCGATCATCTTCTTGATAAGAACA
1 CTTCCTGATGAGATAC-AAAGAAGTGGATTAAAGCAATAAAACGATCATCTTCCTGATAAGAACA
* *
35584 GAGAAGTGGACCAAATC
65 GAGAAGTAGACAAAATC
35601 AATGAAGTGA
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
84 18 0.26
85 49 0.71
86 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (84 bp):
CTTCCTGATGAGATACAAAGAAGTGGATTAAAGCAATAAAACGATCATCTTCCTGATAAGAACAG
AGAAGTAGACAAAATCCGC
Found at i:35954 original size:122 final size:122
Alignment explanation
Indices: 35737--36050 Score: 391
Period size: 122 Copynumber: 2.6 Consensus size: 122
35727 CTTCCTAATG
* * * * * * *
35737 AGATACAGAGAAGTGGATTAAATCAATGAGGC-ATTCATCTTCCTAAT-AAGACCAGAGAAGTAG
1 AGATACAAAGAAGTGGATCAAAACAATAAAGCGA-TCATCTTCCTGATGAA-AACAGAGAAGTAG
* * *
35800 ACCAAATCAATGAAGCAAAGCTCAATACGAATGAGACTTCGAA-CCTCATCTTCTTGATA
64 ACCAAATCAATAAAGCAAAGCTCAATACGAATGAGACTTCAAACCCT-ATCTTCATGATA
* * *
35859 AGATACAAAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAAAACAGAGAAGTAGAC
1 AGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTGATGAAAACAGAGAAGTAGAC
* *
35924 CAAATCAATAAAGCAAAGCTCAATACGAATGAGACTTTAAACCCTATCTTCATGATG
66 CAAATCAATAAAGCAAAGCTCAATACGAATGAGACTTCAAACCCTATCTTCATGATA
* * * * *
35981 AGATACAGAGAAGTGGATCAAAACAATAAAGTGATCATCTTTCTGATGAGATACAGAGAAGTGGA
1 AGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTGATGA-AAACAGAGAAGTAGA
36046 CCAAA
65 CCAAA
36051 AGATGAAGTT
Statistics
Matches: 166, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
122 143 0.86
123 23 0.14
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (122 bp):
AGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTGATGAAAACAGAGAAGTAGAC
CAAATCAATAAAGCAAAGCTCAATACGAATGAGACTTCAAACCCTATCTTCATGATA
Found at i:36900 original size:14 final size:14
Alignment explanation
Indices: 36883--36910 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36873 ATTAATACTT
36883 GCATATATATATAG
1 GCATATATATATAG
36897 GCATATATATATAG
1 GCATATATATATAG
36911 ATATACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
GCATATATATATAG
Found at i:37786 original size:58 final size:58
Alignment explanation
Indices: 37724--37833 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
37714 CCCTAAAATG
37724 TCCAAAAAATATA-TTTAACCCCAAACTTTTTA-AAAATTACATTTTAAACCCTTAGCTT
1 TCCAAAAAATATATTTTAACCCCAAA-TTTTTATAAAATTACATTTT-AACCCTTAGCTT
* **
37782 TCCAAAAATTATATTTTAACCCTTAATTTTTATAAAATTACATTTTAACCCT
1 TCCAAAAAATATATTTTAACCCCAAATTTTTATAAAATTACATTTTAACCCT
37834 CGAACTTTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
58 24 0.51
59 23 0.49
ACGTcount: A:0.40, C:0.19, G:0.01, T:0.40
Consensus pattern (58 bp):
TCCAAAAAATATATTTTAACCCCAAATTTTTATAAAATTACATTTTAACCCTTAGCTT
Found at i:37789 original size:30 final size:29
Alignment explanation
Indices: 37724--37887 Score: 127
Period size: 30 Copynumber: 5.6 Consensus size: 29
37714 CCCTAAAATG
* * **
37724 TCCAAAAAATATA-TTTAACCCCAAACTT
1 TCCAAAAATTACATTTTAACCCTTAACTT
** *
37752 TTTAAAAATTACATTTTAAACCCTTAGCTT
1 TCCAAAAATTACATTTT-AACCCTTAACTT
*
37782 TCCAAAAATTATATTTTAACCCTTAA-TT
1 TCCAAAAATTACATTTTAACCCTTAACTT
** *
37810 TTTATAAAATTACATTTTAACCCTCGAACTTT
1 TCCA-AAAATTACATTTTAACCCT-TAAC-TT
* * *
37842 TCC-AAAATTATATTTTGACCCTTGAACTC
1 TCCAAAAATTACATTTTAACCCTT-AACTT
*
37871 TCCCAAAATTACATTTT
1 TCCAAAAATTACATTTT
37888 GGCCCCGAAA
Statistics
Matches: 106, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
28 13 0.12
29 33 0.31
30 57 0.54
32 3 0.03
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (29 bp):
TCCAAAAATTACATTTTAACCCTTAACTT
Found at i:37827 original size:59 final size:60
Alignment explanation
Indices: 37724--37887 Score: 176
Period size: 59 Copynumber: 2.8 Consensus size: 60
37714 CCCTAAAATG
* ** * *
37724 TCCAAAAAATATA-TTTAACCCCAAACTTTTTAAAAATTACATTTTAAACCCT-TAGC-TT
1 TCCAAAAATTATATTTTAACCCTTAACTTTTTAAAAATTACATTTT-AACCCTCGAACTTT
37782 TCCAAAAATTATATTTTAACCCTTAA-TTTTTATAAAATTACATTTTAACCCTCGAACTTT
1 TCCAAAAATTATATTTTAACCCTTAACTTTTTA-AAAATTACATTTTAACCCTCGAACTTT
* * ***
37842 TCC-AAAATTATATTTTGACCCTTGAACTCTCCCAAAATTACATTTT
1 TCCAAAAATTATATTTTAACCCTT-AACTTTTTAAAAATTACATTTT
37888 GGCCCCGAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
58 24 0.27
59 44 0.49
60 20 0.22
61 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (60 bp):
TCCAAAAATTATATTTTAACCCTTAACTTTTTAAAAATTACATTTTAACCCTCGAACTTT
Found at i:37888 original size:30 final size:30
Alignment explanation
Indices: 37815--37896 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
37805 TAATTTTTAT
* * *
37815 AAAATTACATTTTAACCCTCGAACTTTTCC
1 AAAATTACATTTTGACCCTCGAACTCTCCC
* *
37845 AAAATTATATTTTGACCCTTGAACTCTCCC
1 AAAATTACATTTTGACCCTCGAACTCTCCC
*
37875 AAAATTACATTTTGGCCC-CGAA
1 AAAATTACATTTTGACCCTCGAA
37897 ATTTTTCGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 3 0.07
30 41 0.93
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTCGAACTCTCCC
Found at i:39482 original size:29 final size:30
Alignment explanation
Indices: 39398--39483 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 30
39388 ATTTCTTACT
* * *
39398 TTTTCAATTCTCTCTCAACTTTCTCTCAAG
1 TTTTCAATCCTCTCTCAACTCTCACTCAAG
**
39428 TCATTCTCAATCCTCTCTCAGTTCTCACTCAA-
1 T--TT-TCAATCCTCTCTCAACTCTCACTCAAG
39460 TTTTCAATCCTCTCTCAACTCTCA
1 TTTTCAATCCTCTCTCAACTCTCA
39484 TTTTTTAGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
29 19 0.41
30 3 0.07
32 3 0.07
33 21 0.46
ACGTcount: A:0.21, C:0.35, G:0.02, T:0.42
Consensus pattern (30 bp):
TTTTCAATCCTCTCTCAACTCTCACTCAAG
Found at i:39685 original size:25 final size:26
Alignment explanation
Indices: 39633--39689 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
39623 AAATGGTAAG
*
39633 ATTTT-TTATTATATTTAATCTAATT
1 ATTTTGTTATTATATTAAATCTAATT
39658 ATTTTGTTATTATATTGAAAT-TAA-T
1 ATTTTGTTATTATATT-AAATCTAATT
39683 ATTTTGT
1 ATTTTGT
39690 ATCTTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 13 0.45
26 13 0.45
27 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (26 bp):
ATTTTGTTATTATATTAAATCTAATT
Found at i:47556 original size:21 final size:21
Alignment explanation
Indices: 47532--47584 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
47522 TGGACCCATA
47532 AAATTTTCCTTTTATGGGCAG
1 AAATTTTCCTTTTATGGGCAG
47553 AAATTTTCCTTTTATGGGCAG
1 AAATTTTCCTTTTATGGGCAG
47574 AAATTTTCCTT
1 AAATTTTCCTT
47585 AAATATCCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (21 bp):
AAATTTTCCTTTTATGGGCAG
Found at i:51235 original size:18 final size:19
Alignment explanation
Indices: 51193--51249 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 19
51183 TTTGAATTCT
* *
51193 AAAAAAAAATTCTAAAGATA
1 AAAAAAAAATT-TATATATA
*
51213 TAAAAAAAATTTAT-TATA
1 AAAAAAAAATTTATATATA
**
51231 AAAAATTAATTTATATATA
1 AAAAAAAAATTTATATATA
51250 TTATAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 14 0.47
19 6 0.20
20 10 0.33
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAAAAAATTTATATATA
Found at i:60503 original size:41 final size:43
Alignment explanation
Indices: 60264--60510 Score: 301
Period size: 42 Copynumber: 5.9 Consensus size: 43
60254 TCACTTGGTG
* * *
60264 TAAATGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGTA
1 TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
* *
60307 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTA
1 TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
* * *
60350 TAAA-AGAAGACTCAT-ATCTCGGGATAAGCATGAG-TTATGTA
1 TAAATGGAAGACTCATGA-CTCGGAATGAGCATGAGATTATGTA
*
60391 TAAATGGAAGACTCATGACTCGAAATGAGCATGAGATTATGT-
1 TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
* * *
60433 TTAA-GGAAGACTCGTGACTCGGAATGAGCATGAGATTATGTT
1 TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
* * *
60475 TAAAT-GAAGACTTATGACTCGGTA-GAGCATAAGATT
1 TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATT
60511 GTTTAAAAAG
Statistics
Matches: 182, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
41 57 0.31
42 72 0.40
43 53 0.29
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (43 bp):
TAAATGGAAGACTCATGACTCGGAATGAGCATGAGATTATGTA
Found at i:60525 original size:41 final size:42
Alignment explanation
Indices: 60264--60538 Score: 202
Period size: 41 Copynumber: 6.5 Consensus size: 42
60254 TCACTTGGTG
* * * * * *
60264 TAAATGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGTA
1 TAAA-GGAAGACTTATGACTCGGTATGAGCATAAGATTATGTT
* * * * *
60307 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTA
1 TAAA-GGAAGACTTATGACTCGGTATGAGCATAAGATTATGTT
* * * * * *
60350 TAAAAGAAGACTCAT-ATCTCGGGATAAGCATGAG-TTATGTA
1 TAAAGGAAGACTTATGA-CTCGGTATGAGCATAAGATTATGTT
* ** *
60391 TAAATGGAAGACTCATGACTCGAAATGAGCATGAGATTATGTT
1 TAAA-GGAAGACTTATGACTCGGTATGAGCATAAGATTATGTT
** * *
60434 T-AAGGAAGACTCGTGACTCGGAATGAGCATGAGATTATGTT
1 TAAAGGAAGACTTATGACTCGGTATGAGCATAAGATTATGTT
*
60475 TAAATGAAGACTTATGACTCGGTA-GAGCATAAGA-T-TGTT
1 TAAAGGAAGACTTATGACTCGGTATGAGCATAAGATTATGTT
* *
60514 TAAAAAGGAAGATTTACGACTCGGT
1 T--AAAGGAAGACTTATGACTCGGT
60539 TGTTAAATGT
Statistics
Matches: 206, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
39 5 0.02
40 1 0.00
41 76 0.37
42 70 0.34
43 54 0.26
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (42 bp):
TAAAGGAAGACTTATGACTCGGTATGAGCATAAGATTATGTT
Found at i:62796 original size:22 final size:23
Alignment explanation
Indices: 62753--62797 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
62743 AAATAATTTT
**
62753 AATAATTTTATATTTTTTTAAAA
1 AATAATTTTATATAATTTTAAAA
62776 AATAATTTT-TATAATTTTAAAA
1 AATAATTTTATATAATTTTAAAA
62798 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATAATTTTATATAATTTTAAAA
Found at i:73715 original size:21 final size:22
Alignment explanation
Indices: 73691--73732 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
73681 TAATTGTATC
73691 TAATTAAAT-TTTAAAATATTT
1 TAATTAAATATTTAAAATATTT
* *
73712 TAATTATATATTTAAATTATT
1 TAATTAAATATTTAAAATATT
73733 GATGTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTAAATATTTAAAATATTT
Found at i:74664 original size:32 final size:30
Alignment explanation
Indices: 74614--74674 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
74604 AAATTGATAA
74614 AAATAAAATTACATTTTAATCCTCTTTAAAAT
1 AAATAAAATTACATTTTAAT-CT-TTTAAAAT
*
74646 AAATAAAATTATGA-TTTAATCTTTTAAAA
1 AAATAAAATTA-CATTTTAATCTTTTAAAA
74675 ATTATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 7 0.26
31 2 0.07
32 17 0.63
33 1 0.04
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (30 bp):
AAATAAAATTACATTTTAATCTTTTAAAAT
Found at i:84786 original size:15 final size:16
Alignment explanation
Indices: 84752--84783 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
84742 AATGCAAACA
84752 TTAAATATATGTATTT
1 TTAAATATATGTATTT
84768 TTAAATAT-T-TATTT
1 TTAAATATATGTATTT
84782 TT
1 TT
84784 TAACAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTAAATATATGTATTT
Found at i:90601 original size:29 final size:29
Alignment explanation
Indices: 90496--90759 Score: 238
Period size: 28 Copynumber: 9.2 Consensus size: 29
90486 TCAATTAAAG
* *
90496 GAAGCCTTTGTGGTGATCTTTGTTAAAAA
1 GAAGCCTTTGTGGTTATCTCTGTTAAAAA
* * * *
90525 GAAAGTCTTTGTGGTTATCTCGGTT-GAAG
1 G-AAGCCTTTGTGGTTATCTCTGTTAAAAA
* *
90554 GAAACCTTTGTGGTGATCTCTGTTAAAAA
1 GAAGCCTTTGTGGTTATCTCTGTTAAAAA
* *
90583 GAAGCCTTTATGGTTATCT-TAGTT-AAAG
1 GAAGCCTTTGTGGTTATCTCT-GTTAAAAA
* **
90611 GAAGCTTTTGTGGCAATCTCTGTTAAAAA
1 GAAGCCTTTGTGGTTATCTCTGTTAAAAA
* **
90640 GAAGCTTTTGTGGCAATCTCTGTTAAAAA
1 GAAGCCTTTGTGGTTATCTCTGTTAAAAA
* ** *
90669 GAAGCCTTTGTGGCTATCTCAATT-AAAG
1 GAAGCCTTTGTGGTTATCTCTGTTAAAAA
* *
90697 GAAGCC-TTGTGGCTATCTCTGTTAAAAG
1 GAAGCCTTTGTGGTTATCTCTGTTAAAAA
90725 GAAGCC-TTGT-GTCTATCTCTGTT-AAAA
1 GAAGCCTTTGTGGT-TATCTCTGTTAAAAA
90752 GCAAGCCT
1 G-AAGCCT
90760 CGTGGCGATC
Statistics
Matches: 196, Mismatches: 30, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
27 20 0.10
28 79 0.40
29 78 0.40
30 19 0.10
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (29 bp):
GAAGCCTTTGTGGTTATCTCTGTTAAAAA
Found at i:90630 original size:57 final size:57
Alignment explanation
Indices: 90451--90759 Score: 279
Period size: 57 Copynumber: 5.4 Consensus size: 57
90441 TGGTAGATCA
* * ** * **
90451 GGCGATCTCAGTTAAAGA-AAGTTTTTGTGTCTATCTCAATTAAAGGAAGCCTTTGT
1 GGCGATCTCTGTTAAAAAGAAGCCTTTGTGGCTATCTCTGTTAAAGGAAGCCTTTGT
* * * * * * *
90507 GGTGATCTTTGTTAAAAAGAAAGTCTTTGTGGTTATCTCGGTTGAAGGAAACCTTTGT
1 GGCGATCTCTGTTAAAAAG-AAGCCTTTGTGGCTATCTCTGTTAAAGGAAGCCTTTGT
* * * *
90565 GGTGATCTCTGTTAAAAAGAAGCCTTTATGGTTATCT-TAGTTAAAGGAAGCTTTTGT
1 GGCGATCTCTGTTAAAAAGAAGCCTTTGTGGCTATCTCT-GTTAAAGGAAGCCTTTGT
* * * *
90622 GGCAATCTCTGTTAAAAAGAAGCTTTTGTGGCAATCTCTGTTAAAAAGAAGCCTTTGT
1 GGCGATCTCTGTTAAAAAGAAGCCTTTGTGGCTATCTCTGTT-AAAGGAAGCCTTTGT
* ** *
90680 GGCTATCTCAATT-AAAGGAAGCC-TTGTGGCTATCTCTGTTAAAAGGAAGCC-TTGT
1 GGCGATCTCTGTTAAAAAGAAGCCTTTGTGGCTATCTCTGTT-AAAGGAAGCCTTTGT
* *
90735 GTCTATCTCTGTT-AAAAGCAAGCCT
1 GGCGATCTCTGTTAAAAAG-AAGCCT
90760 CGTGGCGATC
Statistics
Matches: 209, Mismatches: 37, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
55 18 0.09
56 45 0.22
57 73 0.35
58 73 0.35
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (57 bp):
GGCGATCTCTGTTAAAAAGAAGCCTTTGTGGCTATCTCTGTTAAAGGAAGCCTTTGT
Found at i:90650 original size:86 final size:84
Alignment explanation
Indices: 90559--90759 Score: 253
Period size: 86 Copynumber: 2.4 Consensus size: 84
90549 TGAAGGAAAC
* * * * *
90559 CTTTGTGGTGATCTCTGTTAAAAAGAAGCCTTTATGGTTATCTTAGTTAAAGGAAGCTTTTGTGG
1 CTTTGTGGTAATCTCTGTTAAAAAGAAGCCTTTATGGCTATCTCAATTAAAGGAAGC-CTTGTGG
90624 CAATCTCTGTTAAAAAGAAG
65 CAATCTCTGTTAAAAAGAAG
* *
90644 CTTTTGTGGCAATCTCTGTTAAAAAGAAGCCTTTGTGGCTATCTCAATTAAAGGAAGCCTTGTGG
1 C-TTTGTGGTAATCTCTGTTAAAAAGAAGCCTTTATGGCTATCTCAATTAAAGGAAGCCTTGTGG
* *
90709 CTATCTCTGTTAAAAGGAAG
65 CAATCTCTGTTAAAAAGAAG
* *
90729 CCTTGT-GTCTATCTCTGTT-AAAAGCAAGCCT
1 CTTTGTGGT-AATCTCTGTTAAAAAG-AAGCCT
90760 CGTGGCGATC
Statistics
Matches: 101, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
83 6 0.06
84 19 0.19
85 26 0.26
86 50 0.50
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (84 bp):
CTTTGTGGTAATCTCTGTTAAAAAGAAGCCTTTATGGCTATCTCAATTAAAGGAAGCCTTGTGGC
AATCTCTGTTAAAAAGAAG
Found at i:91948 original size:6 final size:6
Alignment explanation
Indices: 91937--91961 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
91927 AAATAATAGG
91937 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
91962 TTTTTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Done.