Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020387.1 Corchorus olitorius cultivar O-4 contig20420, 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: 33916
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1180 original size:2 final size:2
Alignment explanation
Indices: 1175--1217 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1165 AACACGTGTG
1175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1217 T
1 T
1218 TACATATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1484 original size:57 final size:58
Alignment explanation
Indices: 1390--1508 Score: 195
Period size: 57 Copynumber: 2.1 Consensus size: 58
1380 AATTATCCGT
* *
1390 TTCTTGTCACATAATAAATGTTATAATAAATCATATCCCCCCTATTTCTACTTAATTA
1 TTCTTGTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTA
* *
1448 TTCTT-TCACACAATAAATGTTATAATAAATCCTATCCCCTCTATCTCTACTTAATTA
1 TTCTTGTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTA
1505 TTCT
1 TTCT
1509 ACATAATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 52 0.91
58 5 0.09
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (58 bp):
TTCTTGTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTA
Found at i:1633 original size:42 final size:42
Alignment explanation
Indices: 1574--1654 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
1564 TAAGGATCAG
1574 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
1616 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
1655 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:2619 original size:2 final size:2
Alignment explanation
Indices: 2612--2641 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2602 ATATGAAACC
2612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2642 GTGTGTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10670 original size:2 final size:2
Alignment explanation
Indices: 10619--10656 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
10609 TACTAGAGTC
10619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10657 CCTACTACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13225 original size:325 final size:327
Alignment explanation
Indices: 11265--14340 Score: 2068
Period size: 325 Copynumber: 9.4 Consensus size: 327
11255 ATTCTTTACA
* * * * *
11265 TCATCTAA-CTAAATCTCAGCAACATTGGATTTAAGAATTTGTTTTTAAGAGCATCTGAATCTTG
1 TCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTA
* * * * * *
11329 TTTCAATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACAATATTAAAAGCGT-AAAAAGC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAA-T
* * * * *
11393 CCTCCAATCTTTTTGGCGTTA-AATTATATATT-TTTATGAGTATTTTAGCCAAAAATTGAGAAG
129 CCTTCAATATTTTTGGC-ATAGAATTATATATTATTTTTGAGTATTTTAGCAAAAAATTGA-AA-
* * * *
11456 AAATCTTTCATGTCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTAACAAACCATTACGGTT
191 AAATC--TC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT----AACCATCATGGTT
** * * * * * * *
11521 TTTTGCTAAAAACACGTT-CTGGGAACCCGACTCAATTTTGCATGATTTCTGGCTCCGAGACTAC
249 TTTTGCTAAAAATGCGTTCCAGGG-CCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
*
11585 TAGAAATATCTATAT
313 TTGAAATATCTATAT
* * * * * *
11600 TCATCTGATCAAATCTCACCCACATTAGATTTAAGGATTTGTCTTTACGAGCATCTAAATTTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTAT
* * ** * * ** **
11665 TTCGATTTGATTAAAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAACGCCAAAAGCCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAATCC
* * *
11730 TTCAATATTTTTGGCATTA-AGTTATATATT-TTTTATGAGTATTTTAGCCAAAATTTGAGGAAA
131 TTCAATATTTTTGGCA-TAGAATTATATATTATTTT-TGAGTATTTTAGCAAAAAATTGA--AAA
* * * * ** *
11793 TATCTTTCGGGTCAATTTTTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTTGG
192 AATC--TC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTTG
* * *** *
11858 ATAAAAAAGCGTTTTGTGGGCCCAG-CTCAGCTTTT-CATGATTTTTGGCGCCAAGACTCCTTGA
254 CTAAAAATGCG-TTCCAGGGCCCCGACTCAG-TTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
*
11921 GATATCTATAT
317 AATATCTATAT
** * * *
11932 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTTTTTTTACAAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTAT
* * * ** * ** *
11997 TTCGATTTAATTAAAAATTAATACAG-AAAAATATGAAAAATGATATTAAAAGTTTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAATCC
* * * * * *
12061 TCCAATCTTTTTGCCATTA-AATTATATA-TATTTTAGGAGTATTTTATCCAAAAATT-AAGGAA
131 TTCAATATTTTTGGCA-TAGAATTATATATTATTTT-TGAGTATTTTAGCAAAAAATTGAA--AA
* * * * * *
12123 ATTTTTTTCGGGTC-TTTTTTAACAAAATTTTAGCCAAAATC--G-------CATCACGG-TTTT
192 A---ATCTC-GGTCAATTTTT-GCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTT
* * * * * * * *
12177 TGCTACAAACGCGTTTCGGGGCACC-AGCTCAGTTTTGCATGATTTTTGACGCCGACACTCCTTG
252 TGCTAAAAATGCGTTCCAGGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG
*
12241 AAATAACTATAT
316 AAATATCTATAT
* * * **
12253 TCATCTAATAAAATCTTAGCCAAATTTCATTTAA-GATTCTTTTTTTTTGTTTTTAACGAGCATC
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGA---------TTTGTTTTT-ACGAGCATC
* * * * * * * *
12317 TGAAT-TATGTTTCGATTTAACTATAAATTAATTTAG-AAAAATACGAAAAACGATATTAAAAGC
56 TAAATCT-TATTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGC
* ** * * * * * * *
12380 GTCAAAAGCCCTTCAATCTTTTTGACGTTGAATTATATATT-TTTTATGAGTATTATGGCTAAAA
120 GTGAAAAATCCTTCAATATTTTTGGCATAGAATTATATATTATTTT-TGAGTATTTTAGCAAAAA
** * * * * *
12444 ACCGAGGAAATATCTTTTGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTAATAATCATCA
184 ATTGA--AAAAATC---TCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
* * * * * * *
12509 CGGTTTTTTTTTTG-TAAAAACGCGTACC-GGGGCCC-ATTTCAGTTTTGAATGA-TTCTGGCGC
244 TGG----TTTTTTGCTAAAAATGCGTTCCAGGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCGC
* *
12570 CGAGACTCCTTGAAGTATCTATAT
304 CAAGACTCCTTGAAATATCTATAT
* * * * * *
12594 TCATCTAATCAAATCCCAG-C-C-----A-TT---G--TT-TTTATA--AGCATTTGAATCATCT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTAT
* * * * * *
12643 TCCGTTTTAATTAGAATTTCATTCAGAAAAAATAGGAAAAACGATATTAGAAGCGT-AAAAAGCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAA-TC
* * * * * * * *
12707 CTTCAATCTTTTTGGCGTTA-AATTATATATT-TTTATAATTATTGT-GACTAAAAGTT------
130 CTTCAATATTTTTGGC-ATAGAATTATATATTATTTTTGAGTATTTTAG-CAAAAAATTGAAAAA
* * * * *
12763 A-C-GGGTC-ATTTATTGCAAAATATTAGCCGAAAT--TGTGC-AA-CATCACGATTTGTTTTTG
193 ATCTCGGTCAATTT-TTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATG--GT-TTTTTG
* * ** * *
12821 CTAAAAACGCGTTCCAGGACCCCGGGTCAGTATTGCATGATTTTTGGCGCCAAGACTCCTTGAAT
254 CTAAAAATGCGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
12886 TATCTATAT
319 TATCTATAT
* * *
12895 TCATCTAATCAAATATCAGCCACATTGGATTTTAGGATTTGTTTTTACGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTAT
* * ** * *
12960 TTCGATTTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAATGATATTAGAAGTGT-AAAAATAC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAATCC
* *
13024 TTCAGTATTTTTGGCATAGAATTATATATTATTTTTGA-TAATTTAGCAAAAAAATTGAAAAAAT
131 TTCAATATTTTTGGCATAGAATTATATATTATTTTTGAGTATTTTAGC-AAAAAATTGAAAAAAT
* * * *
13088 C-CGGTCAATTTTTGAAAAATTTTAACCGAAATCGTGTGA-TAATCATCATGGTTTTTTGCTACA
195 CTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ACTAACCATCATGGTTTTTTGCTAAA
** * * * *
13151 AATGCGTTCCAGGGCCCCGTGTCAGTTTTGCATGATTTTTGGCGCTAAGACTACTTGAGATATCC
259 AATGCGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCT
13216 ATAT
324 ATAT
** *
13220 TCATCTAATCAAATCTCATACACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTAT
* * * * * **
13285 TTCGATTTAATTAGAACTTAATTCAGAAAAAATATGAAAAACAATATGAAAATCGTGAAATGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAATCC
* * ** *
13350 TCCAATCTTTTTGGCATTA-AATTATATA-TATTCCATGAGTATTTTAGCCAAAAATTGAGGAAA
131 TTCAATATTTTTGGCA-TAGAATTATATATTATT-TTTGAGTATTTTAGCAAAAAATT---GAAA
* * * *
13413 AAATTTTCTGGTC-ATTTTCTGCAAAACTTTAGGCGAAATCGTGTACTAACCATCATAGTTTTTT
191 AAA-TCTC-GGTCAATTTT-TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAT-G-----G
* * * * *** *
13477 TTTTTTATCTGAAAATGCGTTTC-GGGATCCCGACTCAGTTTTGCATGATTTTTGGTATCGAGAC
247 TTTTTT-GCTAAAAATGCGTTCCAGGG-CCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGAC
*
13541 TCCTTGAAATATATATAT
310 TCCTTGAAATATCTATAT
* * *** *
13559 CCATCTAATCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTGTACGAATTTCTAAATCATA
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT-TACGAGCATCTAAATCTTA
* * *
13624 TTTCGATTTAATCAGAAATAAACTT-TGAAATAAAATAGGAAAAACAATATTAGAAGCGTGAAAA
65 TTTCGATTTAATTAGAAATTAA-TTCAG-AA-AAAATAGGAAAAACAATATTAGAAGCGTGAAAA
* * * ** * * ** *
13688 AGGCTTTCAATTTTTTTGGTGTTGAATTATTTATT-TTTTATGAGTATTTTCATTAGAAAACA-A
127 A-TCCTTCAATATTTTTGGCATAGAATTATATATTATTTT-TGAGTATTTT-AGCA-AAAA-ATT
* * *
13751 G-AAAAATCTTTCGGCTCAATTTTTGCAAAA-TTTAGCCGAAATCGTGTTCTAACCTTCACGGTT
187 GAAAAAATC--TCGG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTT
** * *
13814 TTCGGCTAAAAATGCGTTTCC-GGG---CGACTCAGTTTTGCATGATTTTTGGTGCCAAAACTCC
249 TTTTGCTAAAAATGCG-TTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
*
13875 TTGAAATATTTATAT
313 TTGAAATATCTATAT
* * * * * * *
13890 TCATCTAACCAAATCTCAGTCATATTAGATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTT-A
* **
13955 TTTC-ATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAATC
** * * * *
14019 CTTCAATATTTTTGATATCGAACT-T-T-TTA----TGAGTATTTTAGCCAAAAATTGAGGAAAT
130 CTTCAATATTTTTGGCATAGAATTATATATTATTTTTGAGTATTTTAGCAAAAAATTGA--AAAA
* ** *
14077 ATCTTTCAGGTCAATTTTTGCAAAATATTAGTTGAAATCGTGTACTAACCATCATGGTTTTTGGC
193 ATC--TC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTTGC
* * * * * * * * *
14142 TGAAAACGCGTTACAGGGCCACGACTCTGTTTTGCATGACTTTTGGTGCCGAGACTCTTTGAAAT
255 TAAAAATGCGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
*
14207 ATCTTTAT
320 ATCTATAT
* * * * * *
14215 TGATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTATGTGCATCTGAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTAT
* * * * *
14280 TTCGATTTAATTAGAAATTAATTCTGAAAAAATATGAAAAATAATATTAAAATCGTGAAAA
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAA
14341 GCCCTCCAAT
Statistics
Matches: 2201, Mismatches: 392, Indels: 306
0.76 0.14 0.11
Matches are distributed among these distances:
297 1 0.00
298 6 0.00
299 20 0.01
300 19 0.01
301 50 0.02
302 5 0.00
303 25 0.01
307 1 0.00
308 2 0.00
309 2 0.00
312 1 0.00
314 2 0.00
315 8 0.00
316 78 0.04
317 136 0.06
318 7 0.00
319 5 0.00
320 25 0.01
321 109 0.05
322 52 0.02
323 1 0.00
324 29 0.01
325 335 0.15
326 42 0.02
327 31 0.01
328 40 0.02
329 22 0.01
330 170 0.08
331 210 0.10
332 173 0.08
333 14 0.01
334 15 0.01
335 141 0.06
336 68 0.03
337 3 0.00
338 9 0.00
339 104 0.05
340 38 0.02
341 80 0.04
342 60 0.03
343 49 0.02
344 8 0.00
345 4 0.00
346 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (327 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTAT
TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAATCC
TTCAATATTTTTGGCATAGAATTATATATTATTTTTGAGTATTTTAGCAAAAAATTGAAAAAATC
TCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTTGCTAAAAA
TGCGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTAT
AT
Found at i:17397 original size:27 final size:27
Alignment explanation
Indices: 17360--17434 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
17350 TTCCGGCATT
*
17360 CAAGGGCAAAACTGTAATTTAGTCAAC
1 CAAGGGCAAAACTGTAATTTAGCCAAC
* * *
17387 CAGGGGTAAAA-TGGTAATTTTAGCCGAC
1 CAAGGGCAAAACT-GTAA-TTTAGCCAAC
*
17415 CAAGGGCAAAACAGTAATTT
1 CAAGGGCAAAACTGTAATTT
17435 TGACATCTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
26 1 0.03
27 16 0.42
28 21 0.55
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (27 bp):
CAAGGGCAAAACTGTAATTTAGCCAAC
Found at i:20515 original size:141 final size:142
Alignment explanation
Indices: 20279--20553 Score: 374
Period size: 141 Copynumber: 1.9 Consensus size: 142
20269 GCATATAGTC
* * * *
20279 AATCAATCAATGAATTATAACTTTGATTGGCAAATTTAATTAACGACTAATGGATTCATTTATTT
1 AATCAATCAATCAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAATGGATTCATTTATCT
* * * *
20344 AGCTAGCATGTTCAATCAATTGATTTTTTTGCTAACATAATTACTAATTGATTGATTGATTTATG
66 AGCTAGCATGTGCAATCAATTAATTGTTTTGCTAACATAATCACTAATTGATTGATTGATTTATG
20409 GTAAAATTAAAT
131 GTAAAATTAAAT
* * * *
20421 AATC-ATCAATCAGTTATAACTTTGATTGGCAAAGTTAACTAATGACTAACTTGATTCATTTGTC
1 AATCAATCAATCAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAA-TGGATTCATTTATC
** * * *
20485 TATTTAGCATGTGCAAT-AATTAATTGTTTTGGTAACATAATCACTAATTGATTTATTTATTTAT
65 TAGCTAGCATGTGCAATCAATTAATTGTTTTGCTAACATAATCACTAATTGATTGATTGATTTAT
20549 GGTAA
130 GGTAA
20554 TTTTTTTGGT
Statistics
Matches: 115, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
141 86 0.75
142 29 0.25
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (142 bp):
AATCAATCAATCAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAATGGATTCATTTATCT
AGCTAGCATGTGCAATCAATTAATTGTTTTGCTAACATAATCACTAATTGATTGATTGATTTATG
GTAAAATTAAAT
Found at i:20755 original size:172 final size:168
Alignment explanation
Indices: 20401--20888 Score: 667
Period size: 172 Copynumber: 2.9 Consensus size: 168
20391 TTGATTGATT
* * *
20401 GATTTATGGTAAAATTAAATAATCATCAATCAGTTATAACTTTGATTGGCAAAGTTAACTAATGA
1 GATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGGCAAA-TTAACTAACGA
* * * * * *
20466 CTAACTTGATTCATTTGTCTATTTAGCATGTGCAATAATTAATTGTTTTGGTAACATAATCACTA
65 CTAACTTGATTCATTTATTTATTTAGCATGTTCAATAATTTATTTTTTTGGTAACATAATTACTA
*
20531 ATTG---ATTTATTTATTTATGGTAATTTTTTTGGTAGC
130 ATTGATTATTTATTTATTTATGATAATTTTTTTGGTAGC
* * *
20567 GATTTAAGGTAAAATTAAATAATTATCAATCAATTAAAACTTTGATTGACACAATTAACTAACGA
1 GATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGGCA-AATTAACTAACGA
* * *
20632 CTAACGTGGATTCATTTATTTATTTACCATGTTCAATAATTTATTTTTTTGGTGACATAATTACT
65 CTAAC-TTGATTCATTTATTTATTTAGCATGTTCAATAATTTATTTTTTTGGTAACATAATTACT
20697 AATTTGATTTATTTATTTATTTATGATAATTTTTTTGGTAGC
129 AA-TTGA-TTATTTATTTATTTATGATAATTTTTTTGGTAGC
* *
20739 GATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGGTTGGCAAAATTAACTAACGA
1 GATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGGC-AAATTAACTAACGA
* * * *
20804 CTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTATATTTTTGCTAACGTAACTAC
65 CTAACTTGATTCATTTATTTATTTAGCATGTTCAAT-AA-TTTATTTTTTTGGTAACATAATTAC
*
20869 TAATTGATTCGTTTATTTAT
128 TAATTGATT-ATTTATTTAT
20889 GGCAAAATTA
Statistics
Matches: 282, Mismatches: 29, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
166 61 0.22
167 54 0.19
168 3 0.01
171 31 0.11
172 109 0.39
173 24 0.09
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (168 bp):
GATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGGCAAATTAACTAACGAC
TAACTTGATTCATTTATTTATTTAGCATGTTCAATAATTTATTTTTTTGGTAACATAATTACTAA
TTGATTATTTATTTATTTATGATAATTTTTTTGGTAGC
Found at i:21064 original size:140 final size:140
Alignment explanation
Indices: 20905--21262 Score: 502
Period size: 141 Copynumber: 2.5 Consensus size: 140
20895 ATTATAGGAG
* *
20905 TAACTTTGATTGGCAAAGTTGACTTAGGACTAATTTGGTTCATTTATTTATTTAGCATGTTGAAT
1 TAACTTTGATTGGCAAAGTTGACTTAGGACTAATTTGATTCATTTATTTATTTAGCATGTTCAAT
* ** *
20970 CAATTTATTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGCAAAATTTAATAATCAT
66 CAATTTATTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGCAAAATCAAATAACCAT
* *
21035 CAATTAGTTA
131 CAATCAATTA
* * **
21045 TAACTTTGATTGGCAAAGTT-AATTAACGACTAATTTGATTCATTTATTTATTTATTATGTTCAA
1 TAACTTTGATTGGCAAAGTTGACTT-AGGACTAATTTGATTCATTTATTTATTTAGCATGTTCAA
* * *
21109 TCAATTTATTTTTTTCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATCACC
65 TCAATTTA-TTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGCAAAATCAAATAACC
21174 ATCAATCAATTA
129 ATCAATCAATTA
** * * *
21186 TAACTTTGATTAACAAAGTCGACTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
1 TAACTTTGATTGGCAAAGTTGACTTAGGACTAATTTGATTCATTTATTTATTTAGCATGTTCAAT
*
21251 CAAGTTATTTTT
66 CAATTTATTTTT
21263 TTTAGTGGCC
Statistics
Matches: 190, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
139 3 0.02
140 67 0.35
141 118 0.62
142 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.45
Consensus pattern (140 bp):
TAACTTTGATTGGCAAAGTTGACTTAGGACTAATTTGATTCATTTATTTATTTAGCATGTTCAAT
CAATTTATTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGCAAAATCAAATAACCAT
CAATCAATTA
Found at i:21419 original size:173 final size:172
Alignment explanation
Indices: 21107--21437 Score: 497
Period size: 173 Copynumber: 1.9 Consensus size: 172
21097 TATTATGTTC
*
21107 AATCAATTTATTTTTTTCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATCA
1 AATCAAGTTATTTTTTTCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATCA
* *
21172 CCATCAATCAATTATAACTTTGATTAACAAAGTCGACTAAGGACTAACTTGATTCATTTATTTAT
66 CCATCAATCAATTATAACTTTGATTAACAAAGTCAACTAACGACTAACTTGATTCATTTATTTAT
21237 TTAGCATGTTCAATCAAG-TTATTTTTTTTAGTGGCCAAAAAA
131 TTAGCATGTTCAATC-AGTTTATTTTTTTTAGTGGCCAAAAAA
* *
21279 AATCAAGTTATTTTTTTGAC-AACATAATTACTAATTGATT-TATTTATTTATGGCAAAATTAAA
1 AATCAAGTTATTTTTTT--CTAACATAATTACTAATTGATTCT-TTTATTTATAGCAAAATCAAA
* * * ** *
21342 TGATCATCCATCAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGATTCATTTATT
63 TCACCATCAATCAATTATAACTTTGATTAACAAAGTCAACTAACGACTAACTTGATTCATTTATT
*
21407 TATTTTGCATGTTCAATCAGTTTATTTTTTT
128 TATTTAGCATGTTCAATCAGTTTATTTTTTT
21438 CAACATAATA
Statistics
Matches: 143, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
172 19 0.13
173 123 0.86
174 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (172 bp):
AATCAAGTTATTTTTTTCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATCA
CCATCAATCAATTATAACTTTGATTAACAAAGTCAACTAACGACTAACTTGATTCATTTATTTAT
TTAGCATGTTCAATCAGTTTATTTTTTTTAGTGGCCAAAAAA
Found at i:28376 original size:21 final size:21
Alignment explanation
Indices: 28351--28433 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
28341 TATCTTAGAT
28351 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
28372 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
28393 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
28415 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
28434 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:28384 original size:25 final size:25
Alignment explanation
Indices: 28353--28401 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28343 TCTTAGATAT
*
28353 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
28378 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
28402 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:29493 original size:18 final size:19
Alignment explanation
Indices: 29472--29513 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
29462 AACTAGCTTT
29472 GAATGAAGA-ACTGACTTG
1 GAATGAAGAGACTGACTTG
* *
29490 GAATG-AGAGACTGGCTTT
1 GAATGAAGAGACTGACTTG
29508 GAATGA
1 GAATGA
29514 TCCTTAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.36, C:0.10, G:0.31, T:0.24
Consensus pattern (19 bp):
GAATGAAGAGACTGACTTG
Found at i:30807 original size:18 final size:18
Alignment explanation
Indices: 30784--30836 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
30774 CAATCCTAGG
30784 GAACTAGCTTTGAATGGA
1 GAACTAGCTTTGAATGGA
* *
30802 GAACTAACTTAGAAT-GA
1 GAACTAGCTTTGAATGGA
*
30819 GAGACTGGCTTTTGAATG
1 GA-ACTAGC-TTTGAATG
30837 ATCCTTAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 4 0.15
18 17 0.63
19 6 0.22
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (18 bp):
GAACTAGCTTTGAATGGA
Done.