Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019396.1 Corchorus olitorius cultivar O-4 contig19429, 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: 79789
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3505 original size:27 final size:27
Alignment explanation
Indices: 3467--3550 Score: 141
Period size: 27 Copynumber: 3.1 Consensus size: 27
3457 TATTATAATT
3467 AATTTAAAAAAGTCTTTACCTCAAAAA
1 AATTTAAAAAAGTCTTTACCTCAAAAA
3494 AATTTAAAAAAGTCTTTACCTCAAAAA
1 AATTTAAAAAAGTCTTTACCTCAAAAA
* *
3521 AATTTTAAAAAGTCTTTCCCTCGAAAAA
1 AATTTAAAAAAGTCTTTACCTC-AAAAA
3549 AA
1 AA
3551 AAAATTTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
27 47 0.87
28 7 0.13
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (27 bp):
AATTTAAAAAAGTCTTTACCTCAAAAA
Found at i:3968 original size:11 final size:11
Alignment explanation
Indices: 3925--3962 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3915 TTTCTATATA
*
3925 AAATAAATTAT
1 AAATTAATTAT
3936 CAAA-TAATTAT
1 -AAATTAATTAT
3947 AAATTAATTAT
1 AAATTAATTAT
3958 AAATT
1 AAATT
3963 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:7719 original size:333 final size:330
Alignment explanation
Indices: 6947--8896 Score: 1801
Period size: 331 Copynumber: 5.9 Consensus size: 330
6937 GGTAAAAATA
* * * * *
6947 ACCCGAAATATTTTTCCTCAGTTTTTGGCAAAAATACTCATAAAATATATATAATTCAACGCCAA
1 ACCCGAAATATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTC-ACACCAA
* * * * * * *
7012 AAAGATAG-GAGGACTTTTCACGCTTTTAATATCGTTTTTCATATATTTTTTTTGAATTAATTTT
65 AAAGATTGAAAGG-CTTTTCACGCTTCTAATATCATTTTTC--CTATTTTTTTCGAATTAATTTC
* * * * * *
7076 TAATTAAATCGAAACAAAATTCAAATGCACGTAAAAACAAATCCTTAAATCCAATATGGTTGAAA
127 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * * * * * * * *
7141 TTTGATTAAATGAACAAAGATATTTTAAGGAGTATCGGCGCCAAAAATCATACAAAACAGAATCG
192 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCG
* * * * *
7206 TGGCCCCGGAACGTGTTTTTAGTCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTT
257 -GGCCTCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTTGGCTAAAATTTT
*
7271 GTAAAAATTG
321 GCAAAAATTG
* * * * * * *
7281 GCCCGAAAGATATTTCCTCAATTTTTTACTAAAATAC-CTACGAAAAAATATATAATTCGACATC
1 ACCCGAAATATTTTTCCTCAATTTTTTGCCAAAATACTC-A-TAAAAAATATATAATTC-ACACC
* * * *
7345 AAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTATTTTTCCTATTCTTTTCGAAATTAATTTC
63 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTTCG-AATTAATTTC
* * * * * ** *
7410 TAATGAAATCCAAACAAGATTGACATGGTCGTAAAAACAAATTGTTAAATCTAATGTGGCTGAGA
127 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * *
7475 TTTGGTTAGATAAATATAGATATTTCATGGAGTCTTGGCACCGAAAATCATTCAAAACTGAGTCG
192 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCG
* * * * *
7540 GGCCTTGGAACGCGTTTTTACCCGAAAACCGTGATGGTTAGTACACGATTTTAGCT-AAATTTTG
257 GGCCTCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTTGGCTAAAATTTTG
7604 CAAAAATTG
322 CAAAAATTG
* * *
7613 ACCCGAAAGATTTTTCCTCGATTTTTTGCGAAAATACTCATAAAAAATATATAATTCGACACCCA
1 ACCCGAAATATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTC-ACA-CCA
* * * *
7678 AAAAAACTGAAAGCCTTTTTCACGCTTCTAATATCATTTTTCCTATTTTATTTCCAAATTAATTT
64 AAAAGATTGAAAGGC-TTTTCACGCTTCTAATATCATTTTTCCTATTTT-TTT-CGAATTAATTT
* * * * ** * *
7743 TTCATTAAATTGAAACAAGATTTAGAAACTCGTAAAAA-AAATCCTTAAATACAATGTGGCTAAG
126 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
** *
7807 ATTTGGTTAGATGAATATAGATATATTTTTAGGAGTCTTGGCACC-AAAATCATGCAAAACTGAC
191 ATTTGGTTAGATGAATATAG--ATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAG
* * * * *** *****
7871 CCAGGGCCTCGGAACGCGTTTTAAGCAAAAAAAAAAAACCAACAGTACACGATTTCT-GCTAAAA
254 TC-GGGCCTCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTT-TGGCTAAAA
*
7935 TTATGCAAAAATTG
317 TTTTGCAAAAATTG
* * ** * *
7949 ACACAAAATATTTTT-CAAAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAACACCAA
1 ACCCGAAATATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTC-ACACCAA
* * * * *
8013 AAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTTCTATTTTTTTCAAATTAATTTCTAA
65 AAAGATTGAAAGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCTAA
* * * * * *
8078 TTAAATCGAGAA-ATGATTTAAATGCTCGTAAAAACAAATCCTTAAAGCCAATGTGGCTAAGCTT
130 TTAAATCGA-AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* * *
8142 TGGTTAGA-GAATATAGATATTTCAAGGAGTTTTGACACCAAAAATCATGCAAAACTGAGCCGGG
194 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTC-GG
* * * * * *
8206 GCC-CTGGAGCGCG-TTTTAGCTAAAAAACAGTAAT-G---GTACACGATTTCGACTATAATTTT
258 GCCTC-GGAACGCGTTTTTAGC-CAAAAACAGTGATGGTTAGTACACGATTTTGGCTAAAATTTT
8265 GCAAAAATTG
321 GCAAAAATTG
* * * * * * * *
8275 ACCTGAAATA-TTTTCCTCAATTTCTTGTCACAATACTCATAGAATATATATGATTAAACACCAA
1 ACCCGAAATATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATT-CACACCAA
* * * * * *
8339 AAAGATTGGAGAA--ATTTTCACGCTTTTAATATCGTTCTTCATATTTTTCT-GAATTAATTTCT
65 AAAGATT-GA-AAGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCT
* * *
8401 AATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAAAT
128 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * * * * * * * *
8466 TTGTTTCGATCAATATAGATATTTCAAGGAGTCTTTGCACAAAAAATCACGCAATATTCAGTCGG
193 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCGG
* * * * * *
8531 GACTCCAGAACGCCTTCTTAGCCAAAAACCGTGGTATGGTTAGTACACGATTTCGGCTAAAATTT
258 GCCT-CGGAACGCGTTTTTAGCCAAAAACAGT-G-ATGGTTAGTACACGATTTTGGCTAAAATTT
*
8596 TGCAAAAACTG
320 TGCAAAAATTG
* * * * *
8607 ACCTG-AATAATTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATATATAATTCAACGCCA
1 ACCCGAAAT-ATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTC-ACACCA
* * * * *
8671 AAAA-A-TGGAAGGGTATTTCACGCTTCTAATATCATTTTACC--TTTTTTCCGAATTTATTTCT
64 AAAAGATTGAAAGGCT-TTTCACGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCT
* * * * * *
8732 AATTAAATCGAAACAAGAATAAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTAGTTGGGAT
128 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * ** * *
8797 TTGATTTGATGAATATAGATATTTCAA-GAGGTCTTTACGCAAAAAATCATGCAAAACTGAGTCT
193 TTGGTTAGATGAATATAGATATTTCAAGGA-GTCTTGGCACCAAAAATCATGCAAAACTGAGTC-
** *
8861 GGG-CTCCGGAACATGTTTTTAGCCAAAAACCGTGAT
256 GGGCCT-CGGAACGCGTTTTTAGCCAAAAACAGTGAT
8897 CCCGAAAAAA
Statistics
Matches: 1321, Mismatches: 251, Indels: 93
0.79 0.15 0.06
Matches are distributed among these distances:
324 2 0.00
325 79 0.06
326 168 0.13
327 9 0.01
328 3 0.00
329 31 0.02
330 50 0.04
331 216 0.16
332 163 0.12
333 205 0.16
334 215 0.16
335 149 0.11
336 31 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (330 bp):
ACCCGAAATATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTCACACCAAA
AAGATTGAAAGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCTAAT
TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCGGGCC
TCGGAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAA
AATTG
Found at i:8814 original size:331 final size:327
Alignment explanation
Indices: 6947--8896 Score: 1768
Period size: 334 Copynumber: 5.9 Consensus size: 327
6937 GGTAAAAATA
* * * * *
6947 ACCCGAAATATTTTTCCTCAGTTTTTGGCAAAAATACTCATAAAATATATATAATTCAACGCCAA
1 ACCCGAAA-ATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTCAACACCAA
* * * ** *
7012 AAAGATAGG-AGGACTTTTCACGCTTTTAATATCGTTTTTCATATATTTTTTTTGAATTAATTTT
65 AAAGAT-GGAAGG-GTTTTCACGCTTCTAATATCATTTTTC----ATTTTTTCCGAATTAATTTC
* * * * *
7076 TAATTAAATCGAAACAAAATTCAA-ATGCACGTAAAAACAAATCCTTAAATCCAATATGGTTGAA
124 TAATTAAATCGAAACAAGATT-AAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * * * * * * * * *
7140 ATTTGATTAAATGAACAAAGATATTTTAAGGAGTATCGGCGCCAAAAATCATACAAAACAGAATC
188 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTC
* * * *
7205 GTGGCCCCGGAACGTGTTTTTAGTCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTT
253 G-GGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTT
*
7270 TGTAAAAATTG
317 TGCAAAAATTG
* * * * * * *
7281 GCCCGAAAGATATTTCCTCAATTTTTTACTAAAATAC-CTACGAAAAAATATATAATTCGACATC
1 ACCCGAAA-ATTTTTCCTCAATTTTTTGCCAAAATACTC-A-TAAAAAATATATAATTCAACACC
* * *
7345 AAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTATTTTTCCTATTCTTTT-CGAAATTAATTT
63 AAAAAGATGGAAGGG-TTTTCACGCTTCTAATATCATTTTT-C-ATT-TTTTCCG-AATTAATTT
* * * * * ** *
7409 CTAATGAAATCCAAACAAGATTGACATGGTCGTAAAAACAAATTGTTAAATCTAATGTGGCTGAG
123 CTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * *
7474 ATTTGGTTAGATAAATATAGATATTTCATGGAGTCTTGGCACCGAAAATCATTCAAAACTGAGTC
188 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTC
* * * **
7539 GGGC-CTTGGAACGCGTTTTTACCCGAAAACCGTGATGGTTAGTACACGATTTTAGCT-AAATTT
253 GGGCTC-CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTT
7602 TGCAAAAATTG
317 TGCAAAAATTG
* * *
7613 ACCCGAAAGATTTTTCCTCGATTTTTTGCGAAAATACTCATAAAAAATATATAATTCGACACCCA
1 ACCCGAAA-ATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTCAACA-CCA
* * ** *
7678 AAAAAACTGAAAGCCTTTTTCACGCTTCTAATATCATTTTTCCTATTTTATTTCCAAATTAATTT
64 AAAAGA-TGGAAG-GGTTTTCACGCTTCTAATATCATTTTT-C-A-TTT-TTTCCGAATTAATTT
* * * * ** * *
7743 TTCATTAAATTGAAACAAGATTTAGAAACTCGTAAAAA-AAATCCTTAAATACAATGTGGCTAAG
123 CTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
** *
7807 ATTTGGTTAGATGAATATAGATATATTTTTAGGAGTCTTGGCACC-AAAATCATGCAAAACTGAC
188 ATTTGGTTAGATGAATATAG--ATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAG
* * * ***** ***** *
7871 CCAGGGC-CTCGGAACGCGTTTTAAGCAAAAAAAAAAAACCAACAGTACACGATTTCTGCTAAAA
251 TC-GGGCTC-CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
*
7935 TTATGCAAAAATTG
314 TTTTGCAAAAATTG
* * ** * *
7949 ACAC-AAAATATTTTTCAAAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAACACCAA
1 ACCCGAAAAT-TTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTCAACACCAA
* * * * *
8013 AAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTTCTATTTTTTTCAAATTAATTTCTAA
65 AAAGATGGAAGGG-TTTTCACGCTTCTAATATC-ATTTTTC-ATTTTTTCCGAATTAATTTCTAA
* * * *
8078 TTAAATCGAGAA-ATGATTTAA-ATGCTCGTAAAAACAAATCCTTAAAGCCAATGTGGCTAAGCT
127 TTAAATCGA-AACAAGA-TTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * *
8141 TTGGTTAGA-GAATATAGATATTTCAAGGAGTTTTGACACCAAAAATCATGCAAAACTGAGCCGG
190 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTC-G
* * * * * *
8205 GGC-CCTGGAGCGCG-TTTTAGCTAAAAAACAGTAAT-G---GTACACGATTTCGACTATAATTT
254 GGCTCC-GGAACGCGTTTTTAGC-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTT
8264 TGCAAAAATTG
317 TGCAAAAATTG
* * * * * * * *
8275 ACCTG-AAATATTTTCCTCAATTTCTTGTCACAATACTCATAGAATATATATGATTAAACACCAA
1 ACCCGAAAAT-TTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTCAACACCAA
** * * * *
8339 AAAGATTGG-AGAAATTTTCACGCTTTTAATATCGTTCTTCATATTTTTCTGAATTAATTTCTAA
65 AAAGA-TGGAAG-GGTTTTCACGCTTCTAATATCATTTTTCAT-TTTTTCCGAATTAATTTCTAA
* * * *
8403 TTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAAATTT
127 TTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * * * * * *
8468 GTTTCGATCAATATAGATATTTCAAGGAGTCTTTGCACAAAAAATCACGCAATATTCAGTCGGGA
192 GGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCGGG-
* * *
8533 CTCCAGAACGCCTTCTTAGCCAAAAACCGTGGTATGGTTAGTACACGATTTCGGCTAAAATTTTG
256 CTCCGGAACGCGTTTTTAGCCAAAAACCGT-G-ATGGTTAGTACACGATTTCGGCTAAAATTTTG
*
8598 CAAAAACTG
319 CAAAAATTG
* * * * *
8607 ACCTGAATAATTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATATATAATTCAACGCCAA
1 ACCCGAA-AATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTCAACACCAA
* * *
8672 AAA-ATGGAAGGGTATTTCACGCTTCTAATATCATTTTACCTTTTTTCCGAATTTATTTCTAATT
65 AAAGATGGAAGGGT-TTTCACGCTTCTAATATCATTTTTCATTTTTTCCGAATTAATTTCTAATT
* * * * * *
8736 AAATCGAAACAAGAATAAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTAGTTGGGATTTGA
129 AAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG
* ** * *
8801 TTTGATGAATATAGATATTTCAA-GAGGTCTTTACGCAAAAAATCATGCAAAACTGAGTCTGGGC
194 TTAGATGAATATAGATATTTCAAGGA-GTCTTGGCACCAAAAATCATGCAAAACTGAGTC-GGGC
**
8865 TCCGGAACATGTTTTTAGCCAAAAACCGTGAT
257 TCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
8897 CCCGAAAAAA
Statistics
Matches: 1319, Mismatches: 246, Indels: 107
0.79 0.15 0.06
Matches are distributed among these distances:
324 7 0.01
325 81 0.06
326 162 0.12
327 10 0.01
328 2 0.00
329 29 0.02
330 44 0.03
331 220 0.17
332 163 0.12
333 200 0.15
334 225 0.17
335 156 0.12
336 20 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (327 bp):
ACCCGAAAATTTTTCCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTCAACACCAAA
AAGATGGAAGGGTTTTCACGCTTCTAATATCATTTTTCATTTTTTCCGAATTAATTTCTAATTAA
ATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT
AGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCGGGCTCCG
GAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAT
TG
Found at i:9164 original size:288 final size:289
Alignment explanation
Indices: 8618--9182 Score: 750
Period size: 288 Copynumber: 2.0 Consensus size: 289
8608 CCTGAATAAT
* *
8618 TTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATATATAATTCAACGCCAAAAAATGGAAGG
1 TTTTCCTCAATTTTTTGCCACAACACTAAGAAAAAATATATAATTCAACGCAAAAAAATGGAAGG
* * *
8683 GTATTTCACGCTTCTAATATCATTTTACCTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAA
66 ATATTTCACGCTTCTAATATCATTTTACCTTTTTTCCGAATTTATATCTAATGAAATCGAAACAA
* * * * ** *
8748 GAATAAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTAGTTGGGATTTGATTTGATGAATAT
131 GAATAAGATGCTCATAAAAACAAATCATTAAATCCAATATAGCCGAGATTTGATTTGATGAATAT
* * * *
8813 AGATATTTCAAGAGGTCTTTACGCAAAAAATCATGCAAAACTGAGTCTGGGCTCCGGAACATGTT
196 AGATATTTCAAGAGGTCTTTACGCAAAAAATCATGCAAAACTAAGTCCGGGCCCCGAAACATGTT
8878 TTTAGCCAAAAACCGTGATCCCGAAAAAA
261 TTTAGCCAAAAACCGTGATCCCGAAAAAA
* * *
8907 TTTTCCTTAA-TTTTTGCCACAACACTAAGAAAAAATATATAATTCAACATCAAAAAAATTGAAG
1 TTTTCCTCAATTTTTTGCCACAACACTAAGAAAAAATATATAATTCAAC-GCAAAAAAATGGAAG
* * *
8971 GAT-TTTCACGCTTCTAATATCGTTTTTCCATTTTTT-TGAATTTATATCTAATGAAATCGAAAC
65 GATATTTCACGCTTCTAATATCATTTTACC-TTTTTTCCGAATTTATATCTAATGAAATCGAAAC
* * *
9034 AAGATTCAGATGCTCATAAAAACAAATCATTAAATCCAATATTGCCGAGATTTCG-TTAT-ATGA
129 AAGAATAAGATGCTCATAAAAACAAATCATTAAATCCAATATAGCCGAGATTT-GATT-TGATGA
* * * *
9097 TTATAGGTATTTCAACGA-GTGTTT-CTGCCAAAAATCATGCAAAACTAAG-CCGGTGCCCCGAA
192 ATATAGATATTTCAA-GAGGTCTTTAC-GCAAAAAATCATGCAAAACTAAGTCCGG-GCCCCGAA
9159 ACATGTTTTTAGCCAAAAACCGTG
254 ACATGTTTTTAGCCAAAAACCGTG
9183 GTTAGTACAC
Statistics
Matches: 240, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
287 4 0.02
288 203 0.85
289 33 0.14
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.32
Consensus pattern (289 bp):
TTTTCCTCAATTTTTTGCCACAACACTAAGAAAAAATATATAATTCAACGCAAAAAAATGGAAGG
ATATTTCACGCTTCTAATATCATTTTACCTTTTTTCCGAATTTATATCTAATGAAATCGAAACAA
GAATAAGATGCTCATAAAAACAAATCATTAAATCCAATATAGCCGAGATTTGATTTGATGAATAT
AGATATTTCAAGAGGTCTTTACGCAAAAAATCATGCAAAACTAAGTCCGGGCCCCGAAACATGTT
TTTAGCCAAAAACCGTGATCCCGAAAAAA
Found at i:9486 original size:317 final size:316
Alignment explanation
Indices: 8897--9526 Score: 784
Period size: 317 Copynumber: 2.0 Consensus size: 316
8887 AAACCGTGAT
*
8897 CCCGAAAAAATTTTCCTTAATTTTTGCCACAACACTAAGAAAAAATATATAATTCAACATCAAAA
1 CCCGAAAAAATTTTCCTCAATTTTTGCCACAACACTAAGAAAAAATATATAATTCAACATCAAAA
* * *
8962 AAATTGAAGGATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTGAATTTATATCTAATGAAA
66 AAATTGAAGGATTTTCACGCTTATAATATCGTTTTCCCATTTTTTTGAATTAATATCTAATGAAA
* * * *
9027 TCGAAACAAGATTCAGATGCTCATAAAAACAAATCATTAAATCCAATATTGCCGAGATTTCGTTA
131 TCGAAAAAAGATTAAGATGCTCATAAAAACAAATCATTAAATCCAATATGGCCAAGATTTCGTTA
* * * * * *
9092 TATGATTATAGGTATTTCAACGAGTGTTTCTGCCAAAAATCATGCAAAACTAAGCCGGTGCCCCG
196 TATGAATATAGATATTTCAACGAGTCTTGCTGCCAAAAATCATGCAAAACTAAGCCGGGGCCACG
*
9157 AAACATGTTTTTAGCCAAAAACCGTG-GTTAGTACACGATTTCAGCTAAAAGCTGA
261 AAACACGTTTTTAGCCAAAAACCGTGAGTTAGTACACGATTTCAGCTAAAAGCTGA
** * * * *
9212 CCCGAAAATTTTTTTCTCAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGT-AAAA
1 CCCGAAAAAATTTTCCTCAATTTTTGCCACAACACTAAGAAAAAATATATAATTCAACATCAAAA
* * * * *
9276 AATATTGACGGGCTTTTCACGCTTATAATATTGTTTTCCCATTTTTTCTGAATTAATTTCTAATT
66 AA-ATTGA-AGGATTTTCACGCTTATAATATCGTTTTCCCATTTTTT-TGAATTAATATCTAATG
** * * *
9341 AAATCGAAAAAAGATTAAGATGCTTGTAAAAACAAATCGTTAAATCCAATGTGGTCAAGATTT-G
128 AAATCGAAAAAAGATTAAGATGCTCATAAAAACAAATCATTAAATCCAATATGGCCAAGATTTCG
* * * * * *
9405 TT-TCGATGAATATAGATATTTCAATGATTCTATGC-GCCTAAAATCATGGAAAATTTAGCCGGG
193 TTAT--ATGAATATAGATATTTCAACGAGTCT-TGCTGCCAAAAATCATGCAAAACTAAGCCGGG
* * * *
9468 GCTACGAAACGCGTTTTTAGCCAAAAACCGTGATAGTTAGTACATGATTTCGGCTAAAA
255 GCCACGAAACACGTTTTTAGCCAAAAACCGTG--AGTTAGTACACGATTTCAGCTAAAA
9527 TTTTGCTAAA
Statistics
Matches: 265, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
314 6 0.02
315 59 0.22
316 36 0.14
317 140 0.53
318 2 0.01
320 22 0.08
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (316 bp):
CCCGAAAAAATTTTCCTCAATTTTTGCCACAACACTAAGAAAAAATATATAATTCAACATCAAAA
AAATTGAAGGATTTTCACGCTTATAATATCGTTTTCCCATTTTTTTGAATTAATATCTAATGAAA
TCGAAAAAAGATTAAGATGCTCATAAAAACAAATCATTAAATCCAATATGGCCAAGATTTCGTTA
TATGAATATAGATATTTCAACGAGTCTTGCTGCCAAAAATCATGCAAAACTAAGCCGGGGCCACG
AAACACGTTTTTAGCCAAAAACCGTGAGTTAGTACACGATTTCAGCTAAAAGCTGA
Found at i:10032 original size:613 final size:603
Alignment explanation
Indices: 9026--10248 Score: 1573
Period size: 613 Copynumber: 2.0 Consensus size: 603
9016 ATCTAATGAA
* *
9026 ATCGAAACAAGATTCAGATGCTCATAAAAACAAATCATTAAATCCAATATTGCCGAGATTTCGTT
1 ATCGAAACAAGATTCAAATGCTCATAAAAAAAAATCATTAAATCCAATATTGCCGAGATTTCGTT
* * * * *
9091 ATATGATTATAGGTATTTCAACGAGTGTTTCTGCCAAAAATCATGCAAAACTAAGCCGGTGCCCC
66 AGATGAATATAGATATTTCAACGAGTCTTTCTGCAAAAAATCATGCAAAACTAAGCCGGTGCCCC
* * * * *
9156 GAAACATGTTTTTAGCCAAAAACCGTGGTTAGTACACGATTTCAGCTAAAAGCTGACCCGAAAAT
131 AAAACACGTTTTTAGCCAAAAACC--GGTAAGTACACGATTTCAGCTAAAAACTGACCCGAAAAC
9221 TTTTTTCTCAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGTAAAAAATATTGACG
194 TTTTTTCTCAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGTAAAAAATATTGACG
* ** ** *
9286 GGCTTTTCACGCTTATAATATTGTTTTCCCATTTTTTCTGAATTAATTTCTAATTAAATCGAAAA
259 CGCTTTTCACAATTATAATATCATTTTCCCATTTTTTCTGAATTAAGTTCTAATTAAATCGAAAA
* *
9351 AAGATTAAGATGCTTGTAAAAACAAATCGTTAAATCCAATGTGGTCAAGATTTGTTTCGATGAAT
324 AAGATTAAGATGCTCGTAAAAACAAATCGCTAAATCCAATGTGGTCAAGATTTGTTTCGATGAAT
* * * * *
9416 ATAGATATTTCAATGA-TTCTATGCGCCTAAAATCATGGAAAATTTAGCCGGGGCTACGA-AACG
389 ATAGATATTTCAAGGAGTT-TATGCGCCAAAAATCATGCAAAATTCAGCCGGGACT-CGAGAACG
* * *
9479 CGTTTTTAGCCAAAAACCGTGATA-GTTAGTACATGATTTCGGCTAAAATTTTGCTAAAACTGAC
452 CGTTTTTAGCCAAAAACCGTGATAGGCTAGTACACGATTTCGGCTAAAAATTTGC--AAACTG--
* * *
9543 CCAAAAAGTTTTTCCTCAATTCTTCGTCATAATACTAAGACAAAAAAAATTTAATTCAACGCC-A
513 ---AAAAGTTTTTCCTCAATTCTTCGCCACAATACTAAG--AAAAAAAATATAATTCAACGCCAA
*
9607 AAAAAATTAAAGGGT-TCTTCACGCTTCTAAT
573 AAAAAATTAAAGGGTAT-TTCACGCCTCTAAT
* * * * * * *
9638 ATCGAAACAAGATTCAAATGCTCGTAAAAAAAAATCCTTAAATCTATTGTTGCTGAGATTTTGTT
1 ATCGAAACAAGATTCAAATGCTCATAAAAAAAAATCATTAAATCCAATATTGCCGAGATTTCGTT
* * **
9703 AGATGAATATAGATATTTCAAGGAGTCTTTCTGTAAAAAATCATGCAAAACTAAGCCTGG-GCTT
66 AGATGAATATAGATATTTCAACGAGTCTTTCTGCAAAAAATCATGCAAAACTAAGCC-GGTGCCC
* * *
9767 CAAAACGCGTTTTTAGCCAACAACC-GTAACGTACACGATATT-GGCTAAAAACTGACCCGAAAA
130 CAAAACACGTTTTTAGCCAAAAACCGGTAA-GTACACGAT-TTCAGCTAAAAACTGACCCGAAAA
* * * *
9830 CTTTTTTCTTAATTTTTTGCCACAATACTCAGAAAAAATATTTCATTCAACGTCAAAAATATTGA
193 CTTTTTTCTCAA-TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGTAAAAAATATTGA
* * * *
9895 CGCGCTTTTCACAATTCTAATATCATTTTTCCATTTTTTTTTCGAATTAAGTTCTACTTAAATCG
257 CGCGCTTTTCACAATTATAATATCATTTTCCCA-TTTTTTCT-GAATTAAGTTCTAATTAAATCG
* * *
9960 AAACAAGATTCAGATGCTCGTAAAAACAAATCGCTAAATCCAATGTGG-CTGAGATTTGTTTCGA
320 AAAAAAGATTAAGATGCTCGTAAAAACAAATCGCTAAATCCAATGTGGTC-AAGATTTGTTTCGA
* * *
10024 TTAATATAGATATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTCAGCCGGGACTCTAGA
384 TGAATATAGATATTTCAAGGAGTTTATGCGCCAAAAATCATGCAAAATTCAGCCGGGACTCGAGA
*
10089 ACGCGTTTTTAGCCAAAAACCGTGATATGGCTAGTACACGATTTCGGCTAAAAATTTGCAACCTG
449 ACGCGTTTTTAGCCAAAAACCGTGATA-GGCTAGTACACGATTTCGGCTAAAAATTTGCAAACTG
* * * ** *
10154 AAAAGTTTTTCCTCAATTTTTTGCCACAATACTTAGAAAAATTATATAATTCATCGCCAAAAAAA
513 AAAAGTTTTTCCTCAATTCTTCGCCACAATACTAAGAAAAAAAATATAATTCAACGCCAAAAAAA
*
10219 ATTGAAGGGTATTTCACGCCTCTAAT
578 ATTAAAGGGTATTTCACGCCTCTAAT
10245 ATCG
1 ATCG
10249 TTTTTCCTAT
Statistics
Matches: 530, Mismatches: 68, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
606 18 0.03
607 32 0.06
608 32 0.06
609 3 0.01
610 38 0.07
611 77 0.15
612 139 0.26
613 162 0.31
614 2 0.00
615 27 0.05
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (603 bp):
ATCGAAACAAGATTCAAATGCTCATAAAAAAAAATCATTAAATCCAATATTGCCGAGATTTCGTT
AGATGAATATAGATATTTCAACGAGTCTTTCTGCAAAAAATCATGCAAAACTAAGCCGGTGCCCC
AAAACACGTTTTTAGCCAAAAACCGGTAAGTACACGATTTCAGCTAAAAACTGACCCGAAAACTT
TTTTCTCAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGTAAAAAATATTGACGCG
CTTTTCACAATTATAATATCATTTTCCCATTTTTTCTGAATTAAGTTCTAATTAAATCGAAAAAA
GATTAAGATGCTCGTAAAAACAAATCGCTAAATCCAATGTGGTCAAGATTTGTTTCGATGAATAT
AGATATTTCAAGGAGTTTATGCGCCAAAAATCATGCAAAATTCAGCCGGGACTCGAGAACGCGTT
TTTAGCCAAAAACCGTGATAGGCTAGTACACGATTTCGGCTAAAAATTTGCAAACTGAAAAGTTT
TTCCTCAATTCTTCGCCACAATACTAAGAAAAAAAATATAATTCAACGCCAAAAAAAATTAAAGG
GTATTTCACGCCTCTAAT
Found at i:10336 original size:329 final size:324
Alignment explanation
Indices: 9655--10770 Score: 1161
Period size: 329 Copynumber: 3.4 Consensus size: 324
9645 CAAGATTCAA
* * * *
9655 ATGCTCGTAAAAAAAAATCCTTAAATCTATTGTTGCTGAGATTT-TGTTAGATGAATATAGATAT
1 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGT-TTAGATGAATATAGATAT
** *
9719 TTCAAGGAGTCTTTCTGTAAAAAATCATGCAAAACTAAGCCTGGGCT-TCAAAACGCGTTTTTAG
65 TTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGCC-GGGCTCT-AGAACGCGTTTTTAG
* * *
9783 CCAACAACCGT-AA---C--GTACACGATATT-GGCTAAAAA-CTG--ACCCGAAAACTTTTTTC
128 CCAAAAACCGTGAATGGCTAGTACACGAT-TTCGGCTAAAAATTTGCAACCCGAAAAGTTTTTTC
* * * * * * * *
9838 TTAATTTTTTGCCACAATACTCAGAAAAAATATTTCATTCAACGTCAAAAATATTGACGCGCTTT
192 TCAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCATCGTCAAAAAAATTGAAG-GGTTT
** * * * * * *
9903 TCACAATTCTAATATCATTTTTCCATTTTTTTTTCGAATTAAGTTCTACTTAAATCGAAACAAGA
256 TCACGCTTCTAATATCGTTTTTCCA-TTTTTTTCCGAATTTATTTCTAATTAAAACGAAACAAGA
*
9968 TTCA-G
320 AT-ATG
* *
9973 ATGCTCGTAAAAACAAATCGC-TAAATCCAATGTGGCTGAGATTTGTTTCGATTAATATAGATAT
1 ATGCTCGTAAAAACAAATC-CTTAAATCCAATGTGGCTGAGATTTGTTTAGATGAATATAGATAT
* * *
10037 TTCAAGGAGTTTTTGC-GCCAAAAATCATGCAAAATTCAGCCGGGACTCTAGAACGCGTTTTTAG
65 TTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTAAGCCGGG-CTCTAGAACGCGTTTTTAG
* *
10101 CCAAAAACCGTGATATGGCTAGTACACGATTTCGGCTAAAAATTTGCAACCTGAAAAGTTTTTCC
128 CCAAAAACCGTGA-ATGGCTAGTACACGATTTCGGCTAAAAATTTGCAACCCGAAAAGTTTTTTC
* *
10166 TCAATTTTTTGCCACAATACTTAGAAAAATTATATAATTCATCGCCAAAAAAAATTGAAGGGTAT
192 TCAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCATCGTC-AAAAAAATTGAAGGGT-T
* *
10231 TTCACGCCTCTAATATCGTTTTTCCTATTTTTTTCCGAATTTATTTCTAATTAAACCGAAACAAG
255 TTCACGCTTCTAATATCGTTTTTCC-ATTTTTTTCCGAATTTATTTCTAATTAAAACGAAACAAG
10296 AATATG
319 AATATG
* ** *
10302 ATGCTCGTAAAAACCAATCCTTAAATTTAATGTGGCTGGGATTTGGTTT-GATGAATATAGATAT
1 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT-GTTTAGATGAATATAGATAT
* * * * ** *
10366 TTCAAGAAGTCTTTAC-ACCAAAAATCATGCAAAACTGAGTCGGGGC-CCGGAACGTGTTTTTAG
65 TTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTAAG-CCGGGCTCTAGAACGCGTTTTTAG
* * * * *
10429 ACAAAAATCGTG-ATGGTTAGTACACGATTTCGGTTAAAATTTTGCAAAAACTGACCCGAAAAGT
128 CCAAAAACCGTGAATGGCTAGTACACGATTTCGGCTAAAAATTTGC----A---ACCCGAAAAGT
* *
10493 TTTTTCTCAATTTTTTGCCACAATACTTACAAAAAATATATAATTCAAT-GTC-AAAAAATTGAT
186 TTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATATATAATTC-ATCGTCAAAAAAATTGAA
* *
10556 GGGTTTTTCATGCTTCTAATATCGTTTTTCCA--TTTTTCCAAATTTATTTCTAATTAAAACGAA
250 GGG-TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAAACGAA
*
10619 ACAAG-ATTTAG
314 ACAAGAATAT-G
* ** *
10630 ATGCTCGTAAAAA-AAATCCTT-AATACCAATGTTGCTGAGATGAGGTTAGATGAATATAGATAT
1 ATGCTCGTAAAAACAAATCCTTAAAT-CCAATGTGGCTGAGATTTGTTTAGATGAATATAGATAT
* * **
10693 TTCAAGGAGTCTTTCTGCCAAAAATCATGAAAAACTAAGTCGGTGC-CCCGAAACGCGTTTTTAG
65 TTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGCCGG-GCTCTAG-AACGCGTTTTTAG
10757 CCAAAAATCCGTGA
128 CCAAAAA-CCGTGA
10771 TGGTACACGA
Statistics
Matches: 672, Mismatches: 86, Indels: 68
0.81 0.10 0.08
Matches are distributed among these distances:
317 3 0.00
318 114 0.17
319 5 0.01
320 1 0.00
323 1 0.00
324 2 0.00
325 18 0.03
326 41 0.06
327 75 0.11
328 147 0.22
329 159 0.24
330 11 0.02
331 37 0.06
332 1 0.00
333 55 0.08
334 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (324 bp):
ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGTTTAGATGAATATAGATATT
TCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGCCGGGCTCTAGAACGCGTTTTTAGCCA
AAAACCGTGAATGGCTAGTACACGATTTCGGCTAAAAATTTGCAACCCGAAAAGTTTTTTCTCAA
TTTTTTGCCACAATACTTAGAAAAAATATATAATTCATCGTCAAAAAAATTGAAGGGTTTTCACG
CTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAAACGAAACAAGAATATG
Found at i:11114 original size:21 final size:21
Alignment explanation
Indices: 11089--11171 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
11079 TATCTTAGAT
11089 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
11110 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
11131 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
11153 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
11172 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:11122 original size:25 final size:25
Alignment explanation
Indices: 11091--11139 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
11081 TCTTAGATAT
*
11091 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
11116 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
11140 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:11967 original size:331 final size:329
Alignment explanation
Indices: 11365--11981 Score: 785
Period size: 331 Copynumber: 1.9 Consensus size: 329
11355 ACTTACTCAA
* * * *
11365 AAAATTTTTTCTCAATTTTTTGCCACAATACTAAAAAAATATATATTTCAACATAAAAAAGATTA
1 AAAATTTTTCCTCAATTCTTTGCCACAATACTAAAAAAATATATAATTCAACACAAAAAAGATTA
* *
11430 ACAGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTTTTTCCGAAATAATTACTAATCAAATCA
66 ACAGGCTTTTCACACTTCTAATATGGTTTTTCCATTTTTTTCCGAAATAATTACTAATCAAATCA
* * * *
11495 AAACAGGAATATTCAGATGCTCGTAAAAACAAATCGTTAAATTCAATCTGGCTAAAATTTGTTTC
131 AAAC--GAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATTCAATCTGGCTAAAATTTGGTTC
* * * * * * * * *
11560 AATCAATATCGATATTTCAAGGAGTCTTTTTGCTAAAAATCTTGGAAAATTGAGCCGGGGCTCTG
194 AATCAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGCCGGGACTCCG
11625 AAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTTGGCTAAAATTTGTCAAAACT
259 AAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTTGGCTAAAATTTGTCAAAACT
11690 GACCTG
324 GACCTG
* *
11696 AAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATTTAATTCAACGCCAAAAAA-A
1 AAAATTTTTCCTCAATTCTTTGCCACAATACT-A-AAAAAATATATAATTCAAC-ACAAAAAAGA
* * * * *
11760 TTAA-AGGGTTTTCACACTTCTAATATCGGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTA
63 TTAACAGGCTTTTCACACTTCTAATAT-GGTTTTTCCA-TTTTTTTCCGAAATAATTACTAATCA
* * * * *
11824 AGTCGAAAC-AAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATTCATTGTGGCTAAGATTTGG
126 AATCAAAACGAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATTCAATCTGGCTAAAATTTGG
* * * *
11888 TT-AGATGAGTATAGATATTTTAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGTCGGGAC
191 TTCA-ATCAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGCCGGGAC
* *
11952 -CGCGAAATGCGTTTTTAGCCAAAACCCGTG
255 TC-CGAAACGCGTTTTTAGCCAAAAACCGTG
11982 TATTAACCAA
Statistics
Matches: 242, Mismatches: 37, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
330 2 0.01
331 153 0.63
332 21 0.09
333 31 0.13
334 35 0.14
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (329 bp):
AAAATTTTTCCTCAATTCTTTGCCACAATACTAAAAAAATATATAATTCAACACAAAAAAGATTA
ACAGGCTTTTCACACTTCTAATATGGTTTTTCCATTTTTTTCCGAAATAATTACTAATCAAATCA
AAACGAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATTCAATCTGGCTAAAATTTGGTTCAA
TCAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGCCGGGACTCCGAA
ACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTTGGCTAAAATTTGTCAAAACTGA
CCTG
Found at i:20489 original size:2 final size:2
Alignment explanation
Indices: 20437--20476 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
20427 ATCATACAAT
20437 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
20477 GTATGGTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22340 original size:23 final size:22
Alignment explanation
Indices: 22295--22336 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
22285 TTTCATTGAA
22295 TTTTATGGAATAAAAACAAATT
1 TTTTATGGAATAAAAACAAATT
*
22317 TTTTATTGAATAAAAACAAA
1 TTTTATGGAATAAAAACAAA
22337 ATTTAACGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (22 bp):
TTTTATGGAATAAAAACAAATT
Found at i:23481 original size:48 final size:47
Alignment explanation
Indices: 23393--23537 Score: 163
Period size: 48 Copynumber: 3.0 Consensus size: 47
23383 GAGCGTGCCA
* * *
23393 ATCAATTTTGTCAAAAAAATTGATAAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTCATAAAAATTGAGAAAAAGTGC-AGGAAAATTAAAAG
* *
23441 ATCAATTTTGTCTTAAAAA-TGAGAAAAAGGTGCGAGGAAAAAT-AAAG
1 ATCAATTTTGTCATAAAAATTGAGAAAAA-GTGC-AGGAAAATTAAAAG
23488 ATTCAATTTTGT-AGTAAAAATTGAGAAAAAGTGCAGG-AAATGTAAAAG
1 A-TCAATTTTGTCA-TAAAAATTGAGAAAAAGTGCAGGAAAAT-TAAAAG
23536 AT
1 AT
23538 TGCTTTGAGT
Statistics
Matches: 83, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
46 3 0.04
47 18 0.22
48 53 0.64
49 9 0.11
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (47 bp):
ATCAATTTTGTCATAAAAATTGAGAAAAAGTGCAGGAAAATTAAAAG
Found at i:30253 original size:28 final size:27
Alignment explanation
Indices: 30217--30270 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
30207 TTGCAAGGGA
*
30217 TGGAGAAAGAATGTAAAAGGAAGGTAG
1 TGGAGAAAGAACGTAAAAGGAAGGTAG
**
30244 TGGAGAAAAGAACGTGGAAGGAAGGTA
1 TGGAG-AAAGAACGTAAAAGGAAGGTA
30271 ATTTTAGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.46, C:0.02, G:0.39, T:0.13
Consensus pattern (27 bp):
TGGAGAAAGAACGTAAAAGGAAGGTAG
Found at i:30398 original size:29 final size:30
Alignment explanation
Indices: 30366--30422 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
30356 ATACCATGAA
30366 TTGGGAAAT-AATTTTAAAAGTATAATAAT
1 TTGGGAAATAAATTTTAAAAGTATAATAAT
*
30395 TTGGGAAATAAATTTTCAAAGTATAATA
1 TTGGGAAATAAATTTTAAAAGTATAATA
30423 CATAGGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (30 bp):
TTGGGAAATAAATTTTAAAAGTATAATAAT
Found at i:33422 original size:11 final size:11
Alignment explanation
Indices: 33406--33436 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
33396 GTCGGTTAGG
33406 CGGTTTCGGGT
1 CGGTTTCGGGT
*
33417 CGGTTTCGAGT
1 CGGTTTCGGGT
33428 CGGTTTCGG
1 CGGTTTCGG
33437 TTTAGAACCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.03, C:0.19, G:0.42, T:0.35
Consensus pattern (11 bp):
CGGTTTCGGGT
Found at i:40929 original size:24 final size:23
Alignment explanation
Indices: 40902--40983 Score: 59
Period size: 20 Copynumber: 3.7 Consensus size: 23
40892 GACCGTTTAA
40902 TAATTTTATATATTATTATATAT
1 TAATTTTATATATTATTATATAT
40925 GTAA--TTATATA--ATCTA-ATAT
1 -TAATTTTATATATTAT-TATATAT
*
40945 T-ATTTTATATATGTAATATATATT
1 TAATTTTATATAT-TATTATATA-T
* *
40969 TAATTATAAATATTA
1 TAATTTTATATATTA
40984 CTAAACGGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 18
0.69 0.04 0.27
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 13 0.28
21 2 0.04
22 9 0.20
23 4 0.09
24 7 0.15
25 9 0.20
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (23 bp):
TAATTTTATATATTATTATATAT
Found at i:40952 original size:20 final size:20
Alignment explanation
Indices: 40904--40969 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
40894 CCGTTTAATA
*
40904 ATTTTATATAT-TATTATAT
1 ATTTTATATATCTAATATAT
40923 ATGTAATTATATAATCTAATAT-T
1 AT-T--TTATAT-ATCTAATATAT
*
40946 ATTTTATATATGTAATATAT
1 ATTTTATATATCTAATATAT
40966 ATTT
1 ATTT
40970 AATTATAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
19 10 0.26
20 12 0.31
22 7 0.18
23 5 0.13
24 5 0.13
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTATATATCTAATATAT
Found at i:50091 original size:13 final size:13
Alignment explanation
Indices: 50075--50100 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50065 ACCAACTAAT
50075 TATTGGATATAAA
1 TATTGGATATAAA
50088 TATTGGATATAAA
1 TATTGGATATAAA
50101 GTGCATCGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
TATTGGATATAAA
Found at i:52867 original size:29 final size:31
Alignment explanation
Indices: 52820--52896 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 31
52810 TGACACCAAA
*
52820 TTGTAAGTAGAGAGG-CCAAATTGA-CAGTTT
1 TTGTAAGTAGAG-GGACCAAATTGATCACTTT
* *
52850 TTGT-AGTAGGGGGACCAAATTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
52880 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
52897 TGTACGGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.05
29 15 0.38
30 12 0.30
31 11 0.28
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.30
Consensus pattern (31 bp):
TTGTAAGTAGAGGGACCAAATTGATCACTTT
Found at i:53599 original size:9 final size:9
Alignment explanation
Indices: 53587--53642 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
53577 AAGCCAAAGA
53587 AAAAAAAAC
1 AAAAAAAAC
53596 AAAAAAAAC
1 AAAAAAAAC
53605 AAAAACAAA-
1 AAAAA-AAAC
*
53614 AAGAACAAA-
1 AA-AAAAAAC
*
53623 AACAAAAAC
1 AAAAAAAAC
53632 AAAAAAAAC
1 AAAAAAAAC
53641 AA
1 AA
53643 CACACACACA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 4 0.10
9 31 0.77
10 5 0.12
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:53610 original size:15 final size:14
Alignment explanation
Indices: 53581--53642 Score: 79
Period size: 15 Copynumber: 4.2 Consensus size: 14
53571 CCAACAAAGC
*
53581 CAAAGAAAAAAAAA
1 CAAAAAAAAAAAAA
53595 CAAAAAAAACAAAAA
1 CAAAAAAAA-AAAAA
*
53610 CAAAAAGAACAAAAA
1 CAAAAA-AAAAAAAA
53625 CAAAAACAAAAAAAA
1 CAAAAA-AAAAAAAA
53640 CAA
1 CAA
53643 CACACACACA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
14 8 0.19
15 32 0.76
16 2 0.05
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAA
Found at i:53623 original size:21 final size:21
Alignment explanation
Indices: 53586--53642 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
53576 AAAGCCAAAG
*
53586 AAAAA-AAAACAAA-AAAAAC
1 AAAAACAAAAAAAACAAAAAC
*
53605 AAAAACAAAAAGAACAAAAAC
1 AAAAACAAAAAAAACAAAAAC
53626 AAAAACAAAAAAAACAA
1 AAAAACAAAAAAAACAA
53643 CACACACACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 5 0.15
20 6 0.18
21 22 0.67
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAACAAAAAAAACAAAAAC
Found at i:53647 original size:2 final size:2
Alignment explanation
Indices: 53642--53666 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53632 AAAAAAAACA
53642 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
53667 GAGTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:60435 original size:21 final size:21
Alignment explanation
Indices: 60409--60449 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
60399 ACCCTAGTTG
60409 GAAAATG-CAGAAATATATATC
1 GAAAATGACA-AAATATATATC
*
60430 GAAAATGACAAGATATATAT
1 GAAAATGACAAAATATATAT
60450 GTTCACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (21 bp):
GAAAATGACAAAATATATATC
Found at i:60511 original size:13 final size:14
Alignment explanation
Indices: 60493--60528 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
60483 ATTTACCGAC
60493 TTTCTTTTT-CTTT
1 TTTCTTTTTCCTTT
60506 TTTCTTTTTCCTTT
1 TTTCTTTTTCCTTT
*
60520 TTCCTTTTT
1 TTTCTTTTT
60529 TGGTATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTCCTTT
Found at i:76614 original size:60 final size:61
Alignment explanation
Indices: 76537--76661 Score: 189
Period size: 60 Copynumber: 2.1 Consensus size: 61
76527 GTATCGCCAT
* * * *
76537 GTGTACCAAAAATGACACATGGCATGCCATGTGTACA-AAAAATGACATGTGGCATACCAC
1 GTGTACCAAAAATGACACATGGCATGCCACGTGTACACAAAAATGACACGTGGCACACCAA
* *
76597 GTGTACCAAAAATGACACGTGGCATGCCGCGTGTACACAAAAATGACACGTGGCACACCAA
1 GTGTACCAAAAATGACACATGGCATGCCACGTGTACACAAAAATGACACGTGGCACACCAA
76658 GTGT
1 GTGT
76662 TACAAATTGC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 34 0.59
61 24 0.41
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.18
Consensus pattern (61 bp):
GTGTACCAAAAATGACACATGGCATGCCACGTGTACACAAAAATGACACGTGGCACACCAA
Found at i:76638 original size:31 final size:30
Alignment explanation
Indices: 76532--76651 Score: 168
Period size: 30 Copynumber: 4.0 Consensus size: 30
76522 CACATGTATC
* *
76532 GCCATGTGTACCAAAAATGACACATGGCAT
1 GCCACGTGTACCAAAAATGACACGTGGCAT
* * *
76562 GCCATGTGTACAAAAAATGACATGTGGCAT
1 GCCACGTGTACCAAAAATGACACGTGGCAT
*
76592 ACCACGTGTACCAAAAATGACACGTGGCAT
1 GCCACGTGTACCAAAAATGACACGTGGCAT
*
76622 GCCGCGTGTACACAAAAATGACACGTGGCA
1 GCCACGTGTAC-CAAAAATGACACGTGGCA
76652 CACCAAGTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 62 0.77
31 18 0.22
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (30 bp):
GCCACGTGTACCAAAAATGACACGTGGCAT
Found at i:77492 original size:2 final size:2
Alignment explanation
Indices: 77485--77513 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
77475 TTAAATACTT
77485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
77514 TAAGCTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.