Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014815.1 Kokia drynarioides strain JFW-HI SEQ_129857, 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: 90506
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 331 characters in sequence are not A, C, G, or T
Found at i:414 original size:20 final size:22
Alignment explanation
Indices: 375--415 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
365 TAAAATGAAT
375 TTTTAAACAAAAAGAAAAGGGC
1 TTTTAAACAAAAAGAAAAGGGC
*
397 TTTTAAA-AGAAA-AAAAGGG
1 TTTTAAACAAAAAGAAAAGGG
416 AAAGTGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.20
Consensus pattern (22 bp):
TTTTAAACAAAAAGAAAAGGGC
Found at i:1214 original size:30 final size:28
Alignment explanation
Indices: 1178--1281 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 28
1168 TAGAGGTCCT
1178 TAAACTTTTCCAAAATTATATTTTGACCCC
1 TAAAC-TTTCCAAAATTATATTTT-ACCCC
* * *
1208 TAAACTTCTCTAAAATTATATTTTAACCT
1 TAAACTT-TCCAAAATTATATTTTACCCC
* * *
1237 TGAACTTTCTAAAAATTACATTTTACCCC
1 TAAACTTTC-CAAAATTATATTTTACCCC
*
1266 CAAACTTTCCAAAATT
1 TAAACTTTCCAAAATT
1282 CCATTTTCGA
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 8 0.13
29 33 0.54
30 20 0.33
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (28 bp):
TAAACTTTCCAAAATTATATTTTACCCC
Found at i:1317 original size:30 final size:28
Alignment explanation
Indices: 1189--1323 Score: 112
Period size: 29 Copynumber: 4.6 Consensus size: 28
1179 AAACTTTTCC
* *
1189 AAAATTATATTTTGACCCCTAAACTTCTCT-
1 AAAATTACATTTT-AACCC-AAACTT-TCTA
* **
1219 AAAATTATATTTTAACCTTGAACTTTCTA
1 AAAATTACATTTTAACC-CAAACTTTCTA
* *
1248 AAAATTACATTTTACCCCCAAACTTTC-C
1 AAAATTACATTTTA-ACCCAAACTTTCTA
*
1276 AAAATTCCATTTTCGAACCCAAACTTTCTA
1 AAAATTACATTTT--AACCCAAACTTTCTA
*
1306 AAAATTACATTTTTACCC
1 AAAATTACATTTTAACCC
1324 TCGAACTTCC
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
28 19 0.22
29 39 0.45
30 28 0.33
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (28 bp):
AAAATTACATTTTAACCCAAACTTTCTA
Found at i:1331 original size:30 final size:30
Alignment explanation
Indices: 1210--1621 Score: 227
Period size: 29 Copynumber: 14.0 Consensus size: 30
1200 TTGACCCCTA
* * *
1210 AACTTCTCT-AAAATTATA-TTTTAACCTTG
1 AACTT-TCTAAAAATTACATTTTTACCCTCG
* *
1239 AACTTTCTAAAAATTACA-TTTTACCCCCA
1 AACTTTCTAAAAATTACATTTTTACCCTCG
* * * * *
1268 AACTTTC-CAAAATTCCATTTTCGAACC-CA
1 AACTTTCTAAAAATTACATTTT-TACCCTCG
1297 AACTTTCTAAAAATTACATTTTTACCCTCG
1 AACTTTCTAAAAATTACATTTTTACCCTCG
** * *
1327 AAC-TTCCCAAAATTTCATTTTTGA-CATCG
1 AACTTTCTAAAAATTACATTTTT-ACCCTCG
* * *
1356 -ATTTTCCCAAAAATTACATTTTTGACCCT-A
1 AACTTT-CTAAAAATTACATTTTT-ACCCTCG
* * * *
1386 AACTTTTTGAAAATTACATTTTTGCCCCTTG
1 AACTTTCTAAAAATTACATTTTT-ACCCTCG
* * * **
1417 ATCTTTC-CAAAATTCCATTTTTGA-CCTTA
1 AACTTTCTAAAAATTACATTTTT-ACCCTCG
*
1446 AACTTT-TCAAAAATAACATTTTTACCCTCG
1 AACTTTCT-AAAAATTACATTTTTACCCTCG
* *
1476 AACTTCCT-AAAATTCCATTTTTTA-CCTCG
1 AACTTTCTAAAAATTACA-TTTTTACCCTCG
* ** *
1505 -ATTTTCCCAAAATTACATTTTTGACCCT-A
1 AACTTTCTAAAAATTACATTTTT-ACCCTCG
* *
1534 AAC-TCCCAAAAATTACATTTTTACCCTCG
1 AACTTTCTAAAAATTACATTTTTACCCTCG
* *
1563 AAC-TTCCAAAAATTCCATTTTTGACCC-CG
1 AACTTTCTAAAAATTACATTTTT-ACCCTCG
1592 AAACTTTC-AAAAATTACCA-TTTTACCCTCG
1 -AACTTTCTAAAAATTA-CATTTTTACCCTCG
1622 GATGTCCAAA
Statistics
Matches: 301, Mismatches: 56, Indels: 51
0.74 0.14 0.12
Matches are distributed among these distances:
28 26 0.09
29 138 0.46
30 120 0.40
31 17 0.06
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (30 bp):
AACTTTCTAAAAATTACATTTTTACCCTCG
Found at i:1346 original size:29 final size:30
Alignment explanation
Indices: 1248--1621 Score: 247
Period size: 30 Copynumber: 12.7 Consensus size: 30
1238 GAACTTTCTA
* * *
1248 AAAATTACA-TTTT-ACCCCCAAACTTTCC
1 AAAATTACATTTTTGACCCTCGAACTTCCC
* * * * **
1276 AAAATTCCATTTTCGAACC-CAAACTTTCTA
1 AAAATTACATTTTTGACCCTCGAAC-TTCCC
1306 AAAATTACATTTTT-ACCCTCGAACTTCCC
1 AAAATTACATTTTTGACCCTCGAACTTCCC
* * **
1335 AAAATTTCATTTTTGA-CATCGATTTTCCC
1 AAAATTACATTTTTGACCCTCGAACTTCCC
* ***
1364 AAAAATTACATTTTTGACCCT-AAACTTTTTG
1 -AAAATTACATTTTTGACCCTCGAAC-TTCCC
* * * *
1395 AAAATTACATTTTTGCCCCTTGATCTTTCC
1 AAAATTACATTTTTGACCCTCGAACTTCCC
* ** * *
1425 AAAATTCCATTTTTGA-CCTTAAACTTTTCA
1 AAAATTACATTTTTGACCCTCGAAC-TTCCC
* *
1455 AAAATAACATTTTT-ACCCTCGAACTTCCT
1 AAAATTACATTTTTGACCCTCGAACTTCCC
* * **
1484 AAAATTCCATTTTTTA-CCTCGATTTTCCC
1 AAAATTACATTTTTGACCCTCGAACTTCCC
*
1513 AAAATTACATTTTTGACCCT-AAAC-TCCC
1 AAAATTACATTTTTGACCCTCGAACTTCCC
*
1541 AAAAATTACATTTTT-ACCCTCGAACTTCCA
1 -AAAATTACATTTTTGACCCTCGAACTTCCC
* * *
1571 AAAATTCCATTTTTGACCC-CGAAACTTTCA
1 AAAATTACATTTTTGACCCTCG-AACTTCCC
1601 AAAATTACCA-TTTT-ACCCTCG
1 AAAATTA-CATTTTTGACCCTCG
1622 GATGTCCAAA
Statistics
Matches: 271, Mismatches: 55, Indels: 38
0.74 0.15 0.10
Matches are distributed among these distances:
28 17 0.06
29 120 0.44
30 126 0.46
31 8 0.03
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTTGACCCTCGAACTTCCC
Found at i:1346 original size:59 final size:59
Alignment explanation
Indices: 1239--1621 Score: 268
Period size: 59 Copynumber: 6.5 Consensus size: 59
1229 TTTAACCTTG
* * * * *
1239 AACTTTCTAAAAATTACA-TTTTACCCCCAAACTTTCCAAAATTCCATTTTCGAACCC-A
1 AACTTTCTAAAAATTACATTTTTACCCTCGAACTTCCCAAAATTACATTTTTG-ACCCTA
* * *
1297 AACTTTCTAAAAATTACATTTTTACCCTCGAACTTCCCAAAATTTCATTTTTGA-CATC
1 AACTTTCTAAAAATTACATTTTTACCCTCGAACTTCCCAAAATTACATTTTTGACCCTA
* * * * *** * *
1355 GATTTTCCCAAAAATTACATTTTTGACCCT-AAACTTTTTGAAAATTACATTTTTGCCCCTTG
1 AACTTT-CTAAAAATTACATTTTT-ACCCTCGAAC-TTCCCAAAATTACATTTTTGACCC-TA
* * * ** * * * *
1417 ATCTTTC-CAAAATTCCATTTTTGA-CCTTAAACTTTTCAAAAATAACATTTTT-ACCCTCG
1 AACTTTCTAAAAATTACATTTTT-ACCCTCGAAC-TTCCCAAAATTACATTTTTGACCCT-A
* * **
1476 AACTTCCT-AAAATTCCATTTTTTA-CCTCGATTTTCCCAAAATTACATTTTTGACCCTA
1 AACTTTCTAAAAATTACA-TTTTTACCCTCGAACTTCCCAAAATTACATTTTTGACCCTA
* * * * *
1534 AAC-TCCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGA
1 AACTTTCTAAAAATTACATTTTTACCCTCGAACTTCCCAAAATTACATTTTTGA-CCCTA
1593 AACTTTC-AAAAATTACCA-TTTTACCCTCG
1 AACTTTCTAAAAATTA-CATTTTTACCCTCG
1622 GATGTCCAAA
Statistics
Matches: 263, Mismatches: 45, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
57 10 0.04
58 76 0.29
59 105 0.40
60 66 0.25
61 2 0.01
62 4 0.02
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (59 bp):
AACTTTCTAAAAATTACATTTTTACCCTCGAACTTCCCAAAATTACATTTTTGACCCTA
Found at i:1630 original size:59 final size:58
Alignment explanation
Indices: 1239--1682 Score: 222
Period size: 59 Copynumber: 7.5 Consensus size: 58
1229 TTTAACCTTG
* * *
1239 AACTTTCTAAAAATTA-CATTTTACCCCCAAACTTTCC-AAAATTCCATTTTCGAACCC-A
1 AACTTTC-AAAAATTACCATTTTACCCTCGAAC-TTCCAAAAATTCCATTTTTG-ACCCGA
* * *
1297 AACTTTCTAAAAATTA-CATTTTTACCCTCGAACTTCCCAAAATTTCATTTTTGACATCG-
1 AACTTTC-AAAAATTACCA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGAC-CCGA
* * *** * *
1356 -ATTTTCCCAAAAATTA-CATTTTTGACCCT-AAACTTTTTGAAAATTACATTTTTGCCCCTTG-
1 AACTTT--CAAAAATTACCA-TTTT-ACCCTCGAAC-TTCCAAAAATTCCATTTTTGACCC--GA
* * ** * **
1417 ATCTTTCCAAAATT-CCATTTTTGA-CCTTAAACTTTTCAAAAATAACATTTTT-ACCCTCG-
1 AACTTTCAAAAATTACCA-TTTT-ACCCTCGAAC-TTCCAAAAATTCCATTTTTGA-CC-CGA
* * ** * * *
1476 AACTTCCTAAAATT-CCATTTTTTA-CCTCGATTTTCCCAAAATTACATTTTTGACCCTA
1 AACTTTCAAAAATTACCA--TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCGA
**
1534 AACTCCCAAAAATTA-CATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGA
1 AACTTTCAAAAATTACCA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCCGA
* *
1593 AACTTTCAAAAATTACCATTTTACCCTCGGA-TGTCCAAAAATTCCGTTTTTGATCCCGA
1 AACTTTCAAAAATTACCATTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGA-CCCGA
*** *
1652 TTTTTTCTAAAAGTTACCATTTTACCC-CGAA
1 AACTTTC-AAAAATTACCATTTTACCCTCGAA
1683 TGTTTAAAGT
Statistics
Matches: 314, Mismatches: 48, Indels: 47
0.77 0.12 0.11
Matches are distributed among these distances:
57 7 0.02
58 86 0.27
59 129 0.41
60 87 0.28
61 2 0.01
62 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (58 bp):
AACTTTCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCGA
Found at i:6030 original size:22 final size:21
Alignment explanation
Indices: 5999--6039 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5989 AAGACAAATG
*
5999 GAGGAAAAATATAGGCGATTA
1 GAGGAAAAATAGAGGCGATTA
*
6020 GAGGAGAAAATCGAGGCGAT
1 GAGGA-AAAATAGAGGCGAT
6040 ACAAGGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.44, C:0.07, G:0.34, T:0.15
Consensus pattern (21 bp):
GAGGAAAAATAGAGGCGATTA
Found at i:14609 original size:183 final size:188
Alignment explanation
Indices: 13887--14845 Score: 940
Period size: 183 Copynumber: 4.9 Consensus size: 188
13877 ATCCACAAAT
* * * * * * *
13887 AGTGAGACGGTCATCTTCTTAATGAAATACAAAGAAGTATATCAACTCGAGGCTCAATACGAGCA
1 AGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAATGCGAGCA
* *
13952 AATCTTCGAACCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
66 AATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
* * *
14017 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGTGGATT
131 TTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTT-CT--T--GAT---GAGAAG-AGATT
14082 GAAACA
187 ---A-A
* * * * * * * * *
14088 AGCGATGCGGTCACCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACTC-ACGCTCAATC
1 AGTGAGGCGGTCATCTTCCTGATGAGATA--CAG-AGAAG--TATA-CCAACTCGAGGCTCAATG
*
14152 CGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG-GGGTCGAAGCAATAAAATG
60 CGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATG
* * * * *
14216 GTCAACTTCCTAATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTAATCAGATACAGAGAAG
125 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTT-CT--T--GAT---GAGAAG
14281 CAGATTGAAA
182 -AGATT--AA
* * * *
14291 CAGCGACGCAGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAATGCGAGT
1 -AGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAATGCGAGC
* * *
14356 AAATCTTCGAACCCCAGCTTCCTGATGAGATACCGAGAAGC-GGATCGACGCAATAAAATGGTCA
65 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGG-TCGAAGCAATAAAATGGTTA
* *
14420 GCTTCCTGATGAGATACTAAGAGGTGGACCAAATTTGTCTTCTTGATGAG-A-A-A-T-A
129 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCTTGATGAGAAGAGATTAA
* *
14475 AGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTCGAGGCTCAATTCGAGCA
1 AGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAATGCGAGCA
* *
14540 AATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGAAATAAAATGGTTAGC
66 AATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
*
14605 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGGTACAGAGAAGAGGATT
131 TTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTC-T--TGA--T---GAGAAGA-GATT
14670 GAAACA
187 ---A-A
* * *
14676 AGTGAGGCGGTCATCTTCTTGATGAGATACAGGGAAGTATACCAACTC-A----C--TGCGAACA
1 AGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAATGCGAGCA
* * ** *
14734 AATCTTCGAACGCCAGCTTCCTGATGAGATAGTGAGAAGCAAATCGAAGCAATAAAGTGGTTAGC
66 AATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
* * *
14799 TTCCTGATGAGATACGGAGAAGTGAACCAAATTTGTCTTCCTGATGA
131 TTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCTTGATGA
14846 AACACAGAGA
Statistics
Matches: 656, Mismatches: 73, Indels: 73
0.82 0.09 0.09
Matches are distributed among these distances:
183 153 0.23
184 4 0.01
186 5 0.01
187 1 0.00
188 2 0.00
189 2 0.00
191 7 0.01
192 4 0.01
193 1 0.00
194 101 0.15
195 4 0.01
196 2 0.00
197 1 0.00
198 6 0.01
199 57 0.09
200 57 0.09
201 73 0.11
202 2 0.00
203 2 0.00
204 33 0.05
205 81 0.12
206 53 0.08
207 5 0.01
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (188 bp):
AGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAATGCGAGCA
AATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
TTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCTTGATGAGAAGAGATTAA
Found at i:14810 original size:194 final size:197
Alignment explanation
Indices: 14469--14898 Score: 560
Period size: 194 Copynumber: 2.2 Consensus size: 197
14459 TTCTTGATGA
* * *
14469 GAAATAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTCGAGGCTCAATT
1 GAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGA-G--C-ATG
* **
14534 CGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGAAATAAAATG
62 CGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAATCGAAGAAATAAAATG
* * * ***
14599 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGGTACAGAGAAG
127 GTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAAACACAGAGAAG
*
14664 AGGATT
192 AGGATC
* *
14670 GAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACAGGGAAGTATACCAACTC-A-C-TGCGAA
1 GAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGCATGCGAA
* * * * *
14732 CAAATCTTCGAACGCCAGCTTCCTGATGAGATAGTGAGAAGCAAATCGAAGCAATAAAGTGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAATCGAAGAAATAAAATGGTTA
* *
14797 GCTTCCTGATGAGATACGGAGAAGTGAACCAAATTTGTCTTCCTGATGAAACACAGAGAAGTGGA
131 GCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAAACACAGAGAAGAGGA
14862 TC
196 TC
* * * * *
14864 AAAACAAGTGATGCAGTCGTCTTCCTAATGAGATA
1 GAAACAAGTGAGGCGGTCATCTTCCTGATGAGATA
14899 TTGAGAAGAA
Statistics
Matches: 201, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
194 149 0.74
196 1 0.00
200 1 0.00
201 50 0.25
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (197 bp):
GAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGCATGCGAA
CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAATCGAAGAAATAAAATGGTTA
GCTTCCTGATGAGATACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAAACACAGAGAAGAGGA
TC
Found at i:15301 original size:6 final size:6
Alignment explanation
Indices: 15273--15369 Score: 67
Period size: 6 Copynumber: 16.3 Consensus size: 6
15263 TTAGATTAGT
* * **
15273 TTTAGA TTT-AA TTCTAAA TTTAAA TTTAAA TTCATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
15321 TTT-AG TTTAAA TTTGAAA --TAAT TTTAAA CTTAAA CTTTAAA ATTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA
15368 TT
1 TT
15370 CAAAGTTCAT
Statistics
Matches: 69, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
4 2 0.03
5 8 0.12
6 47 0.68
7 12 0.17
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:15345 original size:35 final size:35
Alignment explanation
Indices: 15291--15359 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
15281 TAATTCTAAA
* *
15291 TTTAAATTTAAATTCATTTTTAAATTTAAA-TTTAG
1 TTTAAATTTAAATT-AATTTTAAACTTAAACTTTAG
15326 TTTAAATTTGAAA-TAATTTTAAACTTAAACTTTA
1 TTTAAATTT-AAATTAATTTTAAACTTAAACTTTA
15360 AAATTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 13 0.43
35 14 0.47
36 3 0.10
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (35 bp):
TTTAAATTTAAATTAATTTTAAACTTAAACTTTAG
Found at i:15346 original size:17 final size:17
Alignment explanation
Indices: 15262--15354 Score: 71
Period size: 18 Copynumber: 5.4 Consensus size: 17
15252 TACTTTTGAG
* * *
15262 TTTAGATTAGTTTTAGA
1 TTTAAATTAATTTTAAA
* *
15279 TTTAATTCTAAATTTAAA
1 TTTAAAT-TAATTTTAAA
*
15297 TTTAAATTCATTTTTAAA
1 TTTAAATT-AATTTTAAA
* *
15315 TTTAAATTTAGTTTAAA
1 TTTAAATTAATTTTAAA
15332 TTTGAAA-TAATTTTAAA
1 TTT-AAATTAATTTTAAA
*
15349 CTTAAA
1 TTTAAA
15355 CTTTAAAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
16 3 0.05
17 25 0.42
18 31 0.53
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTAAATTAATTTTAAA
Found at i:16934 original size:58 final size:58
Alignment explanation
Indices: 16830--17252 Score: 301
Period size: 58 Copynumber: 7.2 Consensus size: 58
16820 CCAAAATAAT
* * * *
16830 ATTTTGACCCCCGAAC-TTCTCTAAAATTATATTTTGACCCTCAAACTTTTTAAAAATTAC
1 ATTTTTACCCCC-AACTTTC-CAAAAATTACATTTTGACCCTCAAAC-TTTCAAAAATTAC
*
16890 ATTTTTACCCCCAACTTTCC-AAAATTCCATTTTCGACCCT-AAACTTTCTAAAAATTAC
1 ATTTTTACCCCCAACTTTCCAAAAATTACATTTT-GACCCTCAAACTTTC-AAAAATTAC
* * * * * * *
16948 A-TTTTACCCTCGAAC-TTCCTAGAATTCCATTTTTGA-CCTC-GATTTTCCCAAAAAATAC
1 ATTTTTACCC-CCAACTTTCCAAAAATTACA-TTTTGACCCTCAAACTTT--CAAAAATTAC
* * ** * * *
17006 ATTTTTGACCTCGAACTTTTTAAAAATTACATTTTTACCCCTCAAACTTTCCAAAATTCC
1 ATTTTT-ACCCCCAACTTTCCAAAAATTACATTTTGA-CCCTCAAACTTTCAAAAATTAC
* * * * *
17066 ATTTTTACCCCAAACTTTCCAAAAATTACATTTTTACCCTCAAACTTCCCAAAATTCC
1 ATTTTTACCCCCAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCAAAAATTAC
** * * * * * **
17124 ATTTTTAAACTCTATTTTCCCAAAAATTACATTTTGACCCTGACACTTTTGAAAATTAC
1 ATTTTTACCCCCAACTTT-CCAAAAATTACATTTTGACCCTCAAACTTTCAAAAATTAC
* * *
17183 A-TTTTACCCCTAAAC-TTCCAAAAAATCCATTTTTGA-CCTCGAAACTTTCAAAAATTACC
1 ATTTTTACCCC-CAACTTTCCAAAAATTACA-TTTTGACCCTC-AAACTTTCAAAAATTA-C
17242 A-TTTTACCCCC
1 ATTTTTACCCCC
17253 GGATGTCCAA
Statistics
Matches: 291, Mismatches: 52, Indels: 42
0.76 0.14 0.11
Matches are distributed among these distances:
57 35 0.12
58 108 0.37
59 101 0.35
60 39 0.13
61 4 0.01
62 4 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (58 bp):
ATTTTTACCCCCAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCAAAAATTAC
Found at i:17114 original size:29 final size:29
Alignment explanation
Indices: 16843--17250 Score: 246
Period size: 30 Copynumber: 13.9 Consensus size: 29
16833 TTGACCCCCG
* * *
16843 AACTTCTCTAAAATTATATTTTGACCCTCA
1 AACTTC-CAAAAATTACATTTTTACCCTCA
** *
16873 AACTTTTTAAAAATTACATTTTTACCC-CC
1 AAC-TTCCAAAAATTACATTTTTACCCTCA
* *
16902 AACTTTCC-AAAATTCCATTTTCGACCCT-A
1 AAC-TTCCAAAAATTACATTTT-TACCCTCA
* *
16931 AACTTTCTAAAAATTACA-TTTTACCCTCG
1 AAC-TTCCAAAAATTACATTTTTACCCTCA
* * * *
16960 AACTTCCTAGAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTACATTTTT-ACCCTCA
** * *
16989 ATTTTCCCAAAAAATACATTTTTGA-CCTCG
1 AACTT-CCAAAAATTACATTTTT-ACCCTCA
**
17019 AACTTTTTAAAAATTACATTTTTACCCCTCA
1 AAC-TTCCAAAAATTACATTTTTA-CCCTCA
*
17050 AACTTTCC-AAAATTCCATTTTTACCC-CA
1 AAC-TTCCAAAAATTACATTTTTACCCTCA
17078 AACTTTCCAAAAATTACATTTTTACCCTCA
1 AAC-TTCCAAAAATTACATTTTTACCCTCA
* * ** *
17108 AACTTCCCAAAATTCCATTTTTAAACTCT
1 AACTTCCAAAAATTACATTTTTACCCTCA
** * *
17137 ATTTTCCCAAAAATTACATTTTGACCCTGA
1 AACTT-CCAAAAATTACATTTTTACCCTCA
* ***
17167 CACTTTTGAAAATTACA-TTTTACCC-CTA
1 AACTTCCAAAAATTACATTTTTACCCTC-A
* *
17195 AACTTCCAAAAAATCCATTTTTGA-CCTCGA
1 AACTTCCAAAAATTACATTTTT-ACCCTC-A
*
17225 AACTTTCAAAAATTACCA-TTTTACCC
1 AACTTCCAAAAATTA-CATTTTTACCC
17251 CCGGATGTCC
Statistics
Matches: 291, Mismatches: 67, Indels: 40
0.73 0.17 0.10
Matches are distributed among these distances:
28 56 0.19
29 97 0.33
30 122 0.42
31 16 0.05
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCA
Found at i:17235 original size:87 final size:87
Alignment explanation
Indices: 17087--17250 Score: 201
Period size: 87 Copynumber: 1.9 Consensus size: 87
17077 AAACTTTCCA
* * * *
17087 AAAATTACATTTTTACCCTCAAACTTCCCAAAATTCCATTTTTAAACTCTATTTTCCCAAAAATT
1 AAAATTACATTTTTACCCTCAAACTTCCAAAAAATCCATTTTTAAACTCAACTTT-CCAAAAATT
17152 A-CATTTTGACCCTGACACTTTTG
65 ACCATTTT-ACCCTGACACTTTTG
* *
17175 AAAATTACA-TTTTACCC-CTAAACTTCCAAAAAATCCATTTTTGACCTCGAAACTTT-CAAAAA
1 AAAATTACATTTTTACCCTC-AAACTTCCAAAAAATCCATTTTTAAACTC--AACTTTCCAAAAA
17237 TTACCATTTTACCC
63 TTACCATTTTACCC
17251 CCGGATGTCC
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
86 1 0.02
87 46 0.70
88 15 0.23
89 4 0.06
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (87 bp):
AAAATTACATTTTTACCCTCAAACTTCCAAAAAATCCATTTTTAAACTCAACTTTCCAAAAATTA
CCATTTTACCCTGACACTTTTG
Found at i:17275 original size:59 final size:58
Alignment explanation
Indices: 17143--17392 Score: 165
Period size: 59 Copynumber: 4.3 Consensus size: 58
17133 CTCTATTTTC
* * ** ***
17143 CCAAAAATTACA-TTTTGACCCTGACACTTTTGAAAATTA-CATTTTACCCCTAAACT-T
1 CCAAAAATTCCATTTTTGA-CCTGAAACTTTCAAAAATTACCATTTTACCCCCGGA-TGT
*
17200 CCAAAAAATCCATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTACCCCCGGATGT
1 CCAAAAATTCCATTTTTGACCT-GAAACTTTCAAAAATTACCATTTTACCCCCGGATGT
* * *** *
17259 CCAAAAATTCCGTTTTTGATCCTTATTTTTTTCTAAAAGTTACCATTTTA-CCCCGGATGT
1 CCAAAAATTCCATTTTTGA-CCTGA-AACTTTC-AAAAATTACCATTTTACCCCCGGATGT
* * * * * * *
17319 -CTAAAGTTTCATTTTTAACCT-AGAACTTTCCCAAAATTACCGTTTTGCCCCCGAGA-GT
1 CCAAAAATTCCATTTTTGACCTGA-AACTTT-CAAAAATTACCATTTTACCCCCG-GATGT
17377 CC-AAAATTACCATTTT
1 CCAAAAATT-CCATTTT
17393 GCCCCCGAGT
Statistics
Matches: 151, Mismatches: 30, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
57 29 0.19
58 37 0.25
59 53 0.35
60 17 0.11
61 15 0.10
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (58 bp):
CCAAAAATTCCATTTTTGACCTGAAACTTTCAAAAATTACCATTTTACCCCCGGATGT
Found at i:17392 original size:28 final size:28
Alignment explanation
Indices: 17349--17410 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
17339 TAGAACTTTC
*
17349 CCAAAATTACCGTTTTGCCCCCGAG-AGT
1 CCAAAATTACCATTTTGCCCCCGAGTA-T
17377 CCAAAATTACCATTTTGCCCCCGAGTAT
1 CCAAAATTACCATTTTGCCCCCGAGTAT
17405 CCAAAA
1 CCAAAA
17411 AGTCTCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.31, C:0.32, G:0.13, T:0.24
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGTAT
Found at i:18331 original size:24 final size:26
Alignment explanation
Indices: 18304--18351 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
18294 AGAGAAATGT
18304 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
18328 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
18352 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:18462 original size:25 final size:23
Alignment explanation
Indices: 18434--18486 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
18424 AGCACGTTTC
18434 GTGCCCTATGTTATTAGCACTTCGT
1 GTGCCCTATG--ATTAGCACTTCGT
* * *
18459 GTGCCCTCTGATTAGTACTTTGT
1 GTGCCCTATGATTAGCACTTCGT
18482 GTGCC
1 GTGCC
18487 TTCTGTTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.64
25 9 0.36
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GTGCCCTATGATTAGCACTTCGT
Found at i:18472 original size:23 final size:23
Alignment explanation
Indices: 18446--18491 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18436 GCCCTATGTT
18446 ATTAGCACTTCGTGTGCCCTCTG
1 ATTAGCACTTCGTGTGCCCTCTG
* * *
18469 ATTAGTACTTTGTGTGCCTTCTG
1 ATTAGCACTTCGTGTGCCCTCTG
18492 TTACCCAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (23 bp):
ATTAGCACTTCGTGTGCCCTCTG
Found at i:33300 original size:6 final size:6
Alignment explanation
Indices: 33285--33314 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
33275 TTTTCACCTA
*
33285 TTTTAT TTTTAC TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
33315 GTATCCTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:35323 original size:31 final size:29
Alignment explanation
Indices: 35283--35357 Score: 123
Period size: 31 Copynumber: 2.5 Consensus size: 29
35273 ACTGATGTGG
35283 TATTAAAATTATTTTTTAAAATATAAAAT
1 TATTAAAATTATTTTTTAAAATATAAAAT
*
35312 TAATTTAAAATTAATTTTTAAAATATAAAAT
1 T-A-TTAAAATTATTTTTTAAAATATAAAAT
35343 TATTAAAATTATTTT
1 TATTAAAATTATTTT
35358 AAATTTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 13 0.31
30 2 0.05
31 27 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TATTAAAATTATTTTTTAAAATATAAAAT
Found at i:35360 original size:20 final size:20
Alignment explanation
Indices: 35283--35365 Score: 52
Period size: 20 Copynumber: 4.2 Consensus size: 20
35273 ACTGATGTGG
35283 TATTAAAATTATTTTTTAAAA-
1 TATTAAAATTA--TTTTAAAAT
*
35304 TA-TAAAATTAATTTAAAAT
1 TATTAAAATTATTTTAAAAT
35323 TAATTTTTAAAA-TA---TAAAAT
1 T-A---TTAAAATTATTTTAAAAT
*
35343 TATTAAAATTATTTTAAATT
1 TATTAAAATTATTTTAAAAT
35363 TAT
1 TAT
35366 AATCATCATC
Statistics
Matches: 50, Mismatches: 2, Indels: 21
0.68 0.03 0.29
Matches are distributed among these distances:
16 6 0.12
17 2 0.04
18 7 0.14
19 2 0.04
20 24 0.48
21 2 0.04
23 2 0.04
24 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTAAAATTATTTTAAAAT
Found at i:37298 original size:30 final size:29
Alignment explanation
Indices: 37264--37455 Score: 194
Period size: 30 Copynumber: 6.5 Consensus size: 29
37254 TTTAACACCC
*
37264 AAACTTTCCAAAAATTTAAATTTGACCCCT
1 AAACTTTCTAAAAATTT-AATTTGACCCCT
* * *
37294 AAACTTTCTAAAAATTTCATTTTAACCCT
1 AAACTTTCTAAAAATTTAATTTGACCCCT
* * *
37323 AAACTTTCTAAAAATTCAAATTTTACCCTT
1 AAACTTTCTAAAAATT-TAATTTGACCCCT
*
37353 AAACTTTCTAAAAATTGTATTTTGA-CCCT
1 AAACTTTCTAAAAATT-TAATTTGACCCCT
*
37382 CAAACTTT-TAAAAATTTCAATTTAACACCC-
1 -AAACTTTCTAAAAATTT-AATTTGAC-CCCT
*
37412 AAACTTTCTAAAAATTTCATTTTGA-CCCT
1 AAACTTTCTAAAAATTT-AATTTGACCCCT
*
37441 AAACTTTCTGAAAAT
1 AAACTTTCTAAAAAT
37456 CATATTTTAA
Statistics
Matches: 137, Mismatches: 18, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
28 4 0.03
29 62 0.45
30 68 0.50
31 3 0.02
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (29 bp):
AAACTTTCTAAAAATTTAATTTGACCCCT
Found at i:37322 original size:29 final size:29
Alignment explanation
Indices: 37252--37455 Score: 218
Period size: 29 Copynumber: 6.9 Consensus size: 29
37242 TTAAAACTAT
* * *
37252 ATTTTAACACCCAAACTTTCCAAAAATTTAA
1 ATTTTAAC-CCTAAACTTTCTAAAAATTT-C
* *
37283 ATTTGACCCCTAAACTTTCTAAAAATTTC
1 ATTTTAACCCTAAACTTTCTAAAAATTTC
37312 ATTTTAACCCTAAACTTTCTAAAAA-TTC
1 ATTTTAACCCTAAACTTTCTAAAAATTTC
37340 AAATTTT-ACCCTTAAACTTTCTAAAAATTGT-
1 --ATTTTAACCC-TAAACTTTCTAAAAATT-TC
*
37371 ATTTTGACCCTCAAACTTT-TAAAAATTTC
1 ATTTTAACCCT-AAACTTTCTAAAAATTTC
* *
37400 AATTTAACACCCAAACTTTCTAAAAATTTC
1 ATTTTAAC-CCTAAACTTTCTAAAAATTTC
* *
37430 ATTTTGACCCTAAACTTTCTGAAAAT
1 ATTTTAACCCTAAACTTTCTAAAAAT
37456 CATATTTTAA
Statistics
Matches: 149, Mismatches: 14, Indels: 22
0.81 0.08 0.12
Matches are distributed among these distances:
28 4 0.03
29 70 0.47
30 67 0.45
31 7 0.05
32 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (29 bp):
ATTTTAACCCTAAACTTTCTAAAAATTTC
Found at i:37336 original size:59 final size:59
Alignment explanation
Indices: 37252--37455 Score: 261
Period size: 59 Copynumber: 3.4 Consensus size: 59
37242 TTAAAACTAT
* * *
37252 ATTTTAACACCCAAACTTTCCAAAAATTTAAATTTGACCCCTAAACTTTCTAAAAATTTC
1 ATTTTAAC-CCTAAACTTTCTAAAAATTTAAATTTAACCCCTAAACTTTCTAAAAATTTC
* * *
37312 ATTTTAACCCTAAACTTTCTAAAAATTCAAATTTTACCCTTAAACTTTCTAAAAATTGT-
1 ATTTTAACCCTAAACTTTCTAAAAATTTAAATTTAACCCCTAAACTTTCTAAAAATT-TC
* *
37371 ATTTTGACCCTCAAACTTT-TAAAAATTTCAATTTAACACCC-AAACTTTCTAAAAATTTC
1 ATTTTAACCCT-AAACTTTCTAAAAATTTAAATTTAAC-CCCTAAACTTTCTAAAAATTTC
* *
37430 ATTTTGACCCTAAACTTTCTGAAAAT
1 ATTTTAACCCTAAACTTTCTAAAAAT
37456 CATATTTTAA
Statistics
Matches: 128, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
58 8 0.06
59 102 0.80
60 18 0.14
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (59 bp):
ATTTTAACCCTAAACTTTCTAAAAATTTAAATTTAACCCCTAAACTTTCTAAAAATTTC
Found at i:37465 original size:59 final size:58
Alignment explanation
Indices: 37260--37478 Score: 243
Period size: 59 Copynumber: 3.7 Consensus size: 58
37250 ATATTTTAAC
* * * * *
37260 ACCC-AAACTTTCCAAAAATTTAAATTTGACCCCTAAACTTTCTAAAAATTTCATTTTA
1 ACCCTAAACTTTCTAAAAATTCAATTTTAACCCC-AAACTTTCTAAAAATTTCATTTTG
*
37318 ACCCTAAACTTTCTAAAAATTCAAATTTT-ACCCTTAAACTTTCTAAAAATTGT-ATTTTG
1 ACCCTAAACTTTCTAAAAATTC-AATTTTAACCC-CAAACTTTCTAAAAATT-TCATTTTG
37377 ACCCTCAAACTTT-TAAAAATTTCAA-TTTAACACCCAAACTTTCTAAAAATTTCATTTTG
1 ACCCT-AAACTTTCTAAAAA-TTCAATTTTAAC-CCCAAACTTTCTAAAAATTTCATTTTG
* *
37436 ACCCTAAACTTTCTGAAAA-TCATATTTTAACTGCCAAACTTTC
1 ACCCTAAACTTTCTAAAAATTCA-ATTTTAAC-CCCAAACTTTC
37479 CAATATTTTG
Statistics
Matches: 140, Mismatches: 9, Indels: 23
0.81 0.05 0.13
Matches are distributed among these distances:
57 3 0.02
58 16 0.11
59 103 0.74
60 18 0.13
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (58 bp):
ACCCTAAACTTTCTAAAAATTCAATTTTAACCCCAAACTTTCTAAAAATTTCATTTTG
Found at i:37636 original size:2 final size:2
Alignment explanation
Indices: 37629--37660 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
37619 ATTTTAATCC
37629 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
37661 AATTTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39171 original size:16 final size:15
Alignment explanation
Indices: 39150--39203 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
39140 TTTTAAAATA
39150 ATTTTAACAATTTTAT
1 ATTTTAA-AATTTTAT
**
39166 ATTTTAAAA-AATAT
1 ATTTTAAAATTTTAT
39180 -TTTTAATAATTTTAT
1 ATTTTAA-AATTTTAT
39195 ATTTTAAAA
1 ATTTTAAAA
39204 AATAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
13 6 0.19
14 5 0.16
15 7 0.23
16 13 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTAAAATTTTAT
Found at i:39190 original size:29 final size:28
Alignment explanation
Indices: 39144--39218 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 28
39134 TTATAATTTT
39144 AAAATAATTTTAACAATTTTATATTTTAA
1 AAAATAATTTTAA-AATTTTATATTTTAA
*
39173 AAAATATTTTTAATAATTTTATATTTTAA
1 AAAATAATTTTAA-AATTTTATATTTTAA
39202 AAAATAATTTTAAAATT
1 AAAATAATTTTAAAATT
39219 ATTTGCTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
28 4 0.09
29 39 0.91
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
AAAATAATTTTAAAATTTTATATTTTAA
Found at i:39595 original size:2 final size:2
Alignment explanation
Indices: 39588--39613 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39578 GTTATCACTT
39588 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
39614 TCACCATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:46355 original size:2 final size:2
Alignment explanation
Indices: 46348--46373 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46338 GTAATCACTT
46348 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
46374 TATCACCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:50580 original size:9 final size:9
Alignment explanation
Indices: 50566--50617 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
50556 GCAAATGATT
50566 TTAAAATTA
1 TTAAAATTA
50575 TTAAAATTA
1 TTAAAATTA
50584 TT----TT-
1 TTAAAATTA
50588 TTAAAA-TA
1 TTAAAATTA
50596 -TAAAATTA
1 TTAAAATTA
50604 TTAAAATTA
1 TTAAAATTA
50613 TTAAA
1 TTAAA
50618 TAATTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
7 6 0.17
8 2 0.06
9 24 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:50586 original size:20 final size:20
Alignment explanation
Indices: 50558--50626 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
50548 TCAAGTCAGC
*
50558 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
50578 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
50598 AAATTA--TTAAAATTATT-
1 AAATTATTTTAAAATTATTA
*
50615 AAATAATTTTAA
1 AAATTATTTTAA
50627 TTTTCAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
16 6 0.15
17 7 0.17
18 1 0.02
19 4 0.10
20 13 0.32
21 2 0.05
22 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:52187 original size:20 final size:20
Alignment explanation
Indices: 52137--52189 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
52127 TACAGTCTAC
52137 AACTTAGTTGT-TCCGGTAG
1 AACTTAGTTGTATCCGGTAG
* *
52156 AAGTATACTTGTAT-CGGTAG
1 AACT-TAGTTGTATCCGGTAG
52176 AACTGTAGTTGTAT
1 AACT-TAGTTGTAT
52190 TAGTAGAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.11
20 23 0.85
21 1 0.04
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (20 bp):
AACTTAGTTGTATCCGGTAG
Found at i:52457 original size:20 final size:20
Alignment explanation
Indices: 52406--52457 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
52396 GTCTTCAAGG
* * *
52406 TATCGGTAGAACTGTAGTTG
1 TATCGGTAGAAGTGGAGTTC
*
52426 TATCGATAGAAGTGGAGTTC
1 TATCGGTAGAAGTGGAGTTC
52446 TATCGGTAGAAG
1 TATCGGTAGAAG
52458 CCTCACTGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.31
Consensus pattern (20 bp):
TATCGGTAGAAGTGGAGTTC
Found at i:55314 original size:20 final size:21
Alignment explanation
Indices: 55268--55316 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
55258 GTCTGCAGCT
*
55268 TAGTTGT-TCCGGTAAAAGTA
1 TAGTTGTATCCGGTAAAACTA
* *
55288 TACTTGTAT-CGGTAAAACTG
1 TAGTTGTATCCGGTAAAACTA
55308 TAGTTGTAT
1 TAGTTGTAT
55317 TAGTAGAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (21 bp):
TAGTTGTATCCGGTAAAACTA
Found at i:55754 original size:20 final size:20
Alignment explanation
Indices: 55696--55762 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
55686 GATTAAAATA
55696 TTAAAATAAATTTAATAATT
1 TTAAAATAAATTTAATAATT
**
55716 TTATATTTTAAA---AATTAATT
1 TTA-A-AATAAATTTAA-TAATT
55736 TTAAAATAAATTTAATAATT
1 TTAAAATAAATTTAATAATT
55756 TTAAAAT
1 TTAAAAT
55763 TATTTGTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 23 0.62
21 3 0.08
22 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAATAAATTTAATAATT
Found at i:65783 original size:3 final size:3
Alignment explanation
Indices: 65769--65798 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
65759 ACATCGTCAT
*
65769 CAA CAT CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
65799 TAATAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.33, G:0.00, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:66906 original size:6 final size:6
Alignment explanation
Indices: 66895--66942 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
66885 GTGTTGCACG
* *
66895 CATCAC CATCAC CACTTCCAT CATCAT CATCAC CATCAC CATCAC CAT
1 CATCAC CATCAC CA--T-CAC CATCAC CATCAC CATCAC CATCAC CAT
66943 GATCCCCATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 31 0.84
7 1 0.03
8 1 0.03
9 4 0.11
ACGTcount: A:0.31, C:0.46, G:0.00, T:0.23
Consensus pattern (6 bp):
CATCAC
Found at i:66936 original size:21 final size:21
Alignment explanation
Indices: 66895--66967 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
66885 GTGTTGCACG
* *
66895 CATCACCATCACCA-CTTCCAT
1 CATCATCATCACCATC-ACCAT
66916 CATCATCATCACCATCACCAT
1 CATCATCATCACCATCACCAT
* * * * *
66937 CACCATGATCCCCATCATCTT
1 CATCATCATCACCATCACCAT
*
66958 CATCTTCATC
1 CATCATCATC
66968 TTCATCTTCA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.27, C:0.44, G:0.01, T:0.27
Consensus pattern (21 bp):
CATCATCATCACCATCACCAT
Found at i:66952 original size:27 final size:27
Alignment explanation
Indices: 66895--66953 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
66885 GTGTTGCACG
* *
66895 CATCACCATCACCACTTCCATCATCAT
1 CATCACCATCACCACTACCATCATCAC
* *
66922 CATCACCATCACCA-TCACCATGATCCC
1 CATCACCATCACCACT-ACCATCATCAC
66949 CATCA
1 CATCA
66954 TCTTCATCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.31, C:0.46, G:0.02, T:0.22
Consensus pattern (27 bp):
CATCACCATCACCACTACCATCATCAC
Found at i:66960 original size:6 final size:6
Alignment explanation
Indices: 66951--66991 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
66941 ATGATCCCCA
66951 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATC
66992 ATAAACAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (6 bp):
TCATCT
Found at i:80720 original size:39 final size:39
Alignment explanation
Indices: 80651--80854 Score: 182
Period size: 39 Copynumber: 5.3 Consensus size: 39
80641 ATAACCTGGT
* * * * * *
80651 AGTGTTTATAGTGTCACTACCACTTTAGTATAGCATTAC
1 AGTGTTTACAATGTCACTGCCAGTTCAGTATAGCATTGC
* *
80690 GGTGTTTACAATGTCA-TCGCCAATTCAGTATTA-CATTGC
1 AGTGTTTACAATGTCACT-GCCAGTTCAGTA-TAGCATTGC
* * * *
80729 AATGTTTACAGA-GTCACCGCTAGTTCAGTATATCATTGC
1 AGTGTTTACA-ATGTCACTGCCAGTTCAGTATAGCATTGC
* * * *
80768 AGTGTTTATAGTGTCACTTCCAGTTCAGTGTAGCATTGC
1 AGTGTTTACAATGTCACTGCCAGTTCAGTATAGCATTGC
* *
80807 AGTCTTTACAGTGTCACTG-CAGTTCAGTATAGCATTGC
1 AGTGTTTACAATGTCACTGCCAGTTCAGTATAGCATTGC
*
80845 AGTGCTTACA
1 AGTGTTTACA
80855 GTGTTACTAA
Statistics
Matches: 133, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
38 29 0.22
39 101 0.76
40 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (39 bp):
AGTGTTTACAATGTCACTGCCAGTTCAGTATAGCATTGC
Found at i:80783 original size:78 final size:77
Alignment explanation
Indices: 80677--80858 Score: 206
Period size: 78 Copynumber: 2.4 Consensus size: 77
80667 CTACCACTTT
* * * * *
80677 AGTATAGCATTACGGTGTTTACAATGTCA-TCGCCAATTCAGTATTA-CATTGCAATGTTTACAG
1 AGTATAGCATTGCAGTGTTTACAGTGTCACT-GCCAATTCAGT-GTAGCATTGCAATCTTTACAG
80740 AGTCACCGCTAGTTC
64 AGTCACCGC-AGTTC
* * * * * *
80755 AGTATATCATTGCAGTGTTTATAGTGTCACTTCCAGTTCAGTGTAGCATTGCAGTCTTTACAGTG
1 AGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAATTCAGTGTAGCATTGCAATCTTTACAGAG
*
80820 TCACTGCAGTTC
66 TCACCGCAGTTC
*
80832 AGTATAGCATTGCAGTGCTTACAGTGT
1 AGTATAGCATTGCAGTGTTTACAGTGT
80859 TACTAACGAT
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
77 31 0.36
78 55 0.63
79 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (77 bp):
AGTATAGCATTGCAGTGTTTACAGTGTCACTGCCAATTCAGTGTAGCATTGCAATCTTTACAGAG
TCACCGCAGTTC
Found at i:81363 original size:21 final size:21
Alignment explanation
Indices: 81339--81391 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
81329 CTTGTGATAG
81339 TTCTACCGATACAAGT-ATGAC
1 TTCTACCGATACAAGTCATG-C
* *
81360 TTCTACCGAAACAATTCATGC
1 TTCTACCGATACAAGTCATGC
*
81381 TTCTATCGATA
1 TTCTACCGATA
81392 TAACAAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGC
Found at i:81838 original size:21 final size:21
Alignment explanation
Indices: 81814--81865 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
81804 GTGTAGATTC
81814 CTACCGATACAAGTGAC-T-CTT
1 CTACCGATACAAGT--CTTACTT
*
81835 CTACTGATACAAGTCTTACTT
1 CTACCGATACAAGTCTTACTT
81856 CTACCGATAC
1 CTACCGATAC
81866 TAAAAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 25 0.93
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (21 bp):
CTACCGATACAAGTCTTACTT
Found at i:88308 original size:29 final size:30
Alignment explanation
Indices: 88275--88343 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
88265 TACATTAGTA
88275 GTCACCCAACTATTAGTAAATTT-T-TTTTT-
1 GTCACCCAACTATT--TAAATTTGTCTTTTTG
* *
88304 GTCACCTAACTATTTAATTTTGTCTTTTTG
1 GTCACCCAACTATTTAAATTTGTCTTTTTG
88334 GTCACCCAAC
1 GTCACCCAAC
88344 GATGACAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 6 0.18
28 1 0.03
29 18 0.53
30 9 0.26
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.45
Consensus pattern (30 bp):
GTCACCCAACTATTTAAATTTGTCTTTTTG
Found at i:89726 original size:21 final size:20
Alignment explanation
Indices: 89659--89726 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
89649 TTAACAATTA
*
89659 AAGATTAATTAAATA-AATT
1 AAGATTAATTAAATATAAAT
*
89678 AAAATTAATTAAA-ACTAAAAT
1 AAGATTAATTAAATA-T-AAAT
*
89699 ATGATTAATTAAATATAAAT
1 AAGATTAATTAAATATAAAT
89719 AAGTATTA
1 AAG-ATTA
89727 TGAAATAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 12 0.31
20 6 0.15
21 19 0.49
22 1 0.03
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (20 bp):
AAGATTAATTAAATATAAAT
Done.