Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021445.1 Corchorus olitorius cultivar O-4 contig21478, 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: 29566
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:556 original size:154 final size:153
Alignment explanation
Indices: 276--2557 Score: 3154
Period size: 154 Copynumber: 14.9 Consensus size: 153
266 ATTCGTATAA
* * *
276 TTTCCATTGTTTAGGGACTAACTATAATCATTTTGATAAGATTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* * ** * *
341 TAATTTGGAACACTTGTTATTTGGGGCCTATCGATGCCCATTAGTGACGTTTTGAATCGTCTTCT
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCGTTTTGAATCGTCTTCG
406 ATTTGGCAAACCTCAATGCTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
*
430 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* * *
495 TAATTTGGAACATTTGTTATTTGGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTC-GTTTTGAATCGTCTTCG
*
560 ATTTGGCAAACCTCAAAGCTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
* *
584 TTTCCATTTTTTATGGACTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* * **
649 TAATTTGGAACACTTGTTATTTGGGGCCTATCGATAGCCCATTAGTTCCGTTTTGAATCGTCTTT
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCG-GGGCCCATTAGTT-CGTTTTGAATCGTC-TT
* *
714 CGATTTGGCAACCCTCAATGCTTCTC
128 CGATTTGGCAAACCTCAATGCTTTTC
* * * * *
740 GTACCATTGTTTATGGCCTAACTATAATAATTTAGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* *
805 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCTATTAGTTCCGTTTTGAATCGTATTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT-CGTTTTGAATCGTCTTCG
*
870 ATTTGGCAAACCTCAAAGCTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
** * * * *
894 TTTAAATTGTTTATGGTCTAACTATAATCATTTTGATGAGATTATTCCACTATGAAG-TTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* *
958 TCATTTGGAACACTGGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCGTTTTGAATCGTCTTCG
1023 ATTTGGCAAACCTCAATGCTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
*
1047 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
**
1112 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCATATTAGTTCCGTTTTGAATCGTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT-CGTTTTGAATCGTCTTCG
1177 ATTTGGCAAACCTCAATGCTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
* *
1201 TTTCCATTGTTTATGGACTAACTATAATCATTTCGGTGAGATTAGTCCACTGTGAAGTTTTTAGA
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
** * *** *
1266 TTGTTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACAAATTGAATTGTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCGTTTTGAATCGTCTTCG
1331 ATTTGGCAAACCTCAATGCTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
* * *
1355 TTTCCACTGTTTATGGCCTAACTATAATTATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGT
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-
* ** * * *
1420 CTCATTTGGAACACTTCTTATTTTGGGCCTATCATGTCCCATTGGTGAC-TTATTGAATCGTCTT
65 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCGTT-TTGAATCGTCTT
* *
1484 CGATTTGCCAAACCTCCATGCTTTTC
128 CGATTTGGCAAACCTCAATGCTTTTC
** ** * *
1510 -TTAAATTGTTTATACACTAACTATAATCATTTTGGTGAGATTAGACCACTGTGAAGTTTTTACC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* *
1574 TCATTTGAAACACTTGTTATTTTAGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT-CGTTTTGAATCGTCTTCG
1639 ATTTGGCAAACCTCAATGCTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
* * *
1663 TTTCCATTGTTTAGGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* * * * * * * *
1728 TAATTTGGAACATTTGTTATTTGGGGCCTATCGAGGCCCATTTGTGACGTTTTGAATCATCTTCA
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCGTTTTGAATCGTCTTCG
*
1793 ATTTGGCAAATCTCTAATGCTTTTC
130 ATTTGGCAAACCTC-AATGCTTTTC
* *
1818 TTTCCATTGTTTATGGACTAACTATAATCATTTCGGTGAGATTAGTCCACTGTGAAGTTTTTAGA
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
** * *
1883 TTGTTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGACTTTG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT-CGTTTTGAATCGTCTTCG
* *
1948 ATTTGG-AAACCTCAAAGTTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
* * ** ** * * *
1971 TTT-AAGTTGTTTATGGCCTAGTTATAATCATTTTAATGAGATTAGTCTACTATGAAGTTCTTAG
1 TTTCCA-TTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
* * * * *
2035 CTCATTT-G----C---TTATTTCGCGCATATCGGGGCCCATTAGTTCCTTTTTGAATCGTCTTT
65 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT-CGTTTTGAATCGTCTTC
2092 GATTTGGCAAACCTCAATGCTTTTC
129 GATTTGGCAAACCTCAATGCTTTTC
* * *
2117 TTT-CATTGTTTAGGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* * * * *
2181 TCATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCCATTAGTGACATTTTGAATCATCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCGTTTTGAATCGTCTTCG
2246 ATTTGGCAAACCTCAATGCTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
2270 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
2335 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT-CGTTTTGAATCGTCTTCG
*
2400 ATTTGG-AAACCTCAATGTTTTTC
130 ATTTGGCAAACCTCAATGCTTTTC
*** * ** * * * * * *
2423 TTTAGGTTGTTTATGGCCTAGTTATAATCATCTTGATGAGATTAATCTACTATGAAGTTCTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
2488 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTT-CGTTTTGAATCGTCTTCG
2553 ATTTG
130 ATTTG
2558 TGATACGAAT
Statistics
Matches: 1890, Mismatches: 209, Indels: 59
0.88 0.10 0.03
Matches are distributed among these distances:
145 105 0.06
146 20 0.01
148 1 0.00
150 1 0.00
152 2 0.00
153 486 0.26
154 907 0.48
155 253 0.13
156 115 0.06
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (153 bp):
TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCGTTTTGAATCGTCTTCGA
TTTGGCAAACCTCAATGCTTTTC
Found at i:1814 original size:771 final size:767
Alignment explanation
Indices: 276--2557 Score: 3271
Period size: 771 Copynumber: 3.0 Consensus size: 767
266 ATTCGTATAA
* * *
276 TTTCCATTGTTTAGGGACTAACTATAATCATTTTGATAAGATTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* ** * *
341 TAATTTGGAACACTTGTTATTTGGGGCCTATCGATGCCCATTAGTGACGTTTTGAATCGTCTTCT
66 TAATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCG
406 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGA
131 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGA
* * *
471 TTAGTACACTGTGAAGTTTTTAGCTAATTTGGAACATTTGTTATTTGGGGCCTATCGGGGCCCAT
196 TTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTCGGGCCTATCGGGGCCCAT
* * * *
536 TAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTTTTTATGGA
261 TAGTAC-ATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGA
* *
601 CTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGT
325 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* ** * *
666 TATTTGGGGCCTATCGATAGCCCATTAGTTCCGTTTTGAATCGTCTTTCGATTTGGCAACCCTCA
390 TATTTTGGGCCTATC-AT-GCCCATTAGTGACATTTTGAATCGTC-TTCGATTTGGCAAACCTCA
* * * *
731 ATGCTTCTCGTACCATTGTTTATGGC-CTAACTATAATAATTTAGGTGAGATTAGTCCACTGTGA
452 ATGCTTTTCTTA-CATTGTTTAT-GCACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
*
795 AGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCTATTAGTTCCGTTTTGA
515 AGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGA
* * *
860 ATCGTATTCGATTTGGCAAACCTCAAAGCTTTTCTTTAAATTGTTTATGGTCTAACTATAATCAT
580 ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTAAATTGTTTATGGACTAACTATAATCAT
* *
925 TTTGATGAGATTATTCCACTATGAAG-TTTTAGCTCATTTGGAACACTGGTTATTTTGGGCCTAT
645 TTTGATGAGATTAATCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
989 CGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTC
710 CGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTC
*
1047 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* ** *
1112 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCATATTAGTTCCGTTTTGAATCGTCTTCG
66 TAATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCG
*
1177 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTCGGTGAGA
131 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGA
* ** *
1242 TTAGTCCACTGTGAAGTTTTTAGATTGTTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
196 TTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTCGGGCCTATCGGGGCCCAT
** * * *
1307 TAGTGACAAATTGAATTGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCACTGTTTATGGC
261 TAGT-ACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGA
* *
1372 CTAACTATAATTATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGTCTCATTTGGAACACTTC
325 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGGAACACTTG
* * *
1437 TTATTTTGGGCCTATCATGTCCCATTGGTGAC-TTATTGAATCGTCTTCGATTTGCCAAACCTCC
389 TTATTTTGGGCCTATCATG-CCCATTAGTGACATT-TTGAATCGTCTTCGATTTGGCAAACCTCA
* * *
1501 ATGCTTTTCTTAAATTGTTTATACACTAACTATAATCATTTTGGTGAGATTAGACCACTGTGAAG
452 ATGCTTTTCTTACATTGTTTATGCACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* * *
1566 TTTTTACCTCATTTGAAACACTTGTTATTTTAGGCCTATCGGGGCCCATTAGTTCCGTTTTGAAT
517 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAAT
** *
1631 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAGGGACTAACTATAATCATTT
582 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTAAATTGTTTATGGACTAACTATAATCATTT
* * * * * *
1696 TGATGAGATTAGTCCATTGTGAAGTTTTTAGCTAATTTGGAACATTTGTTATTTGGGGCCTATCG
647 TGATGAGATTAATCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
* * * * *
1761 AGGCCCATTTGTGACGTTTTGAATCATCTTCAATTTGGCAAATCTCTAATGCTTTTC
712 GGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AATGCTTTTC
* *
1818 TTTCCATTGTTTATGGACTAACTATAATCATTTCGGTGAGATTAGTCCACTGTGAAGTTTTTAGA
1 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
** * *
1883 TTGTTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGACTTTG
66 TAATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCG
* * * * ** **
1948 ATTTGG-AAACCTCAAAGTTTTTCTTT-AAGTTGTTTATGGCCTAGTTATAATCATTTTAATGAG
131 ATTTGGCAAACCTCAATGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAATCATTTTGGTGAG
* * * * * *
2011 ATTAGTCTACTATGAAGTTCTTAGCTCATTT-G----C---TTATTTCGCGCATATCGGGGCCCA
195 ATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTCGGGCCTATCGGGGCCCA
* * * *
2068 TTAGTTCCTTTTTGAATCGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTT-CATTGTTTAGGG
260 TTAG-TACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
* *
2132 ACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTG
324 ACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * ** *
2197 TTATTTTAGGCCTTTCGGGGCCCATTAGTGACATTTTGAATCATCTTCGATTTGGCAAACCTCAA
389 TTATTTTGGGCCTATC-ATGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAA
* *
2262 TGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
453 TGCTTTTC-TTACATTGTTTATGCACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
*
2327 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAAT
517 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAAT
* ** * ** *
2392 CGTCTTCGATTTGG-AAACCTCAATGTTTTTCTTTAGGTTGTTTATGGCCTAGTTATAATCATCT
582 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTAAATTGTTTATGGACTAACTATAATCATTT
* *
2456 TGATGAGATTAATCTACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
647 TGATGAGATTAATCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
**
2521 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
712 GGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
2558 TGATACGAAT
Statistics
Matches: 1349, Mismatches: 150, Indels: 35
0.88 0.10 0.02
Matches are distributed among these distances:
760 205 0.15
761 183 0.14
762 65 0.05
763 1 0.00
765 1 0.00
768 1 0.00
769 189 0.14
770 177 0.13
771 496 0.37
772 31 0.02
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (767 bp):
TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
TAATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCG
ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGA
TTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTCGGGCCTATCGGGGCCCAT
TAGTACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGAC
TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
ATTTTGGGCCTATCATGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
TTTTCTTACATTGTTTATGCACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
TTCGATTTGGCAAACCTCAATGCTTTTCTTTAAATTGTTTATGGACTAACTATAATCATTTTGAT
GAGATTAATCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGC
CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTC
Found at i:5352 original size:22 final size:22
Alignment explanation
Indices: 5312--5353 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5302 TTTCATAGGG
**
5312 AGGGAGGTTATTAAAATTTCCT
1 AGGGAGGTTAACAAAATTTCCT
*
5334 AGGGAGGTTAACAACATTTC
1 AGGGAGGTTAACAAAATTTC
5354 ATAGAATGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (22 bp):
AGGGAGGTTAACAAAATTTCCT
Found at i:5482 original size:21 final size:21
Alignment explanation
Indices: 5456--5505 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
5446 TGCGGTTACC
* * * *
5456 AAATTTATAGTGTGATTTTCA
1 AAATTTATAGGGAGAATATCA
5477 AAATTTCATAGGGAGAATATCA
1 AAATTT-ATAGGGAGAATATCA
5499 AAATTTA
1 AAATTTA
5506 ACAATGAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (21 bp):
AAATTTATAGGGAGAATATCA
Found at i:5569 original size:21 final size:22
Alignment explanation
Indices: 5515--5572 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
5505 AACAATGAGT
* *
5515 TTATCAAAATTTGATAGTCTGG
1 TTATCAAAATTTCACAGTCTGG
*
5537 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCACAGTCTGG
*
5559 TTATCAAATTTTCA
1 TTATCAAAATTTCA
5573 TAAGGAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCACAGTCTGG
Found at i:5620 original size:22 final size:21
Alignment explanation
Indices: 5558--5621 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 21
5548 TCACAGTGTG
*
5558 GTTATCAAATTTTCATAAGGAA
1 GTTATCAAATTTT-ATAATGAA
*
5580 GTTATCGAAATTTCATAATGAA
1 GTTATC-AAATTTTATAATGAA
*
5602 GTTATTAAATGTTTATAATG
1 GTTATCAAAT-TTTATAATG
5622 CGTTCCACCC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.11
22 26 0.72
23 6 0.17
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (21 bp):
GTTATCAAATTTTATAATGAA
Found at i:12235 original size:25 final size:25
Alignment explanation
Indices: 12190--12238 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
12180 TTTTAAACTC
*
12190 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
12215 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
12239 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:12238 original size:21 final size:21
Alignment explanation
Indices: 12158--12240 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
12148 CGTTTAGTAA
12158 TTAAATATATATTATTTATTTATT
1 TTAAA-ATATATTA-TTATTTA-T
* *
12182 TTAAACT-CATTATT-TATTAT
1 TTAAAATATATTATTAT-TTAT
12202 TTAAAATATATTTATTATTTAT
1 TTAAAATATA-TTATTATTTAT
12224 TTAATAATATA-TATTAT
1 TTAA-AATATATTATTAT
12241 ATCTAAGATA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
20 8 0.16
21 12 0.24
22 17 0.34
23 8 0.16
24 5 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAAAATATATTATTATTTAT
Found at i:12394 original size:11 final size:11
Alignment explanation
Indices: 12370--12399 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12360 TAAGTATACA
12370 GGCCGGGC-CG
1 GGCCGGGCTCG
12380 GGCCGGGCTCG
1 GGCCGGGCTCG
12391 GGCCGGGCT
1 GGCCGGGCT
12400 TTTATGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.00, C:0.37, G:0.57, T:0.07
Consensus pattern (11 bp):
GGCCGGGCTCG
Found at i:17711 original size:19 final size:19
Alignment explanation
Indices: 17687--17737 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
17677 TCAAATCAAG
17687 GAAACAATGCAAAAGAAGC
1 GAAACAATGCAAAAGAAGC
17706 GAAACAATGCAAAAGAAGC
1 GAAACAATGCAAAAGAAGC
* *
17725 AAAACAAAGCAAA
1 GAAACAATGCAAA
17738 GGAAAGCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.63, C:0.16, G:0.18, T:0.04
Consensus pattern (19 bp):
GAAACAATGCAAAAGAAGC
Found at i:24439 original size:24 final size:24
Alignment explanation
Indices: 24412--24458 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
24402 TCCAAACTGT
24412 AATTCCAAACTTTACCTGAGCAGC
1 AATTCCAAACTTTACCTGAGCAGC
**
24436 AATTTTAAACTTTACCTGAGCAG
1 AATTCCAAACTTTACCTGAGCAG
24459 GGACTCACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (24 bp):
AATTCCAAACTTTACCTGAGCAGC
Found at i:25976 original size:7 final size:7
Alignment explanation
Indices: 25964--26001 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
25954 TTACGGATCC
25964 TGCCATT
1 TGCCATT
25971 TGCCATT
1 TGCCATT
25978 TGCCATT
1 TGCCATT
25985 TGCCATT
1 TGCCATT
25992 TGCCATT
1 TGCCATT
25999 TGC
1 TGC
26002 TTCCCAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.13, C:0.29, G:0.16, T:0.42
Consensus pattern (7 bp):
TGCCATT
Found at i:27559 original size:14 final size:14
Alignment explanation
Indices: 27540--27568 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27530 AAACTTTTAT
27540 GATCTTTGTTTAAC
1 GATCTTTGTTTAAC
27554 GATCTTTGTTTAAC
1 GATCTTTGTTTAAC
27568 G
1 G
27569 TATGCTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (14 bp):
GATCTTTGTTTAAC
Done.